{"quest":{"id":"1baa2fb6-21f","name":"Demo","description":"Demo showcase & end-to-end flows — polished demos exercising all five layers","layer":"Cross-cutting","priority":50,"status":"active","created_at":"2026-04-02T10:00:57.209491+00:00","updated_at":"2026-04-11T05:44:23.589823+00:00"},"tasks":[{"id":"89bb12c1-9fc9-4162-bd6d-c75a015f7b5d","title":"[Demo] CI: Verify all demo pages load correctly with rich content","description":"Curl the top 5 demo hypothesis pages, top 3 analyses, and /demo. Check for 200 status, >5KB content, no raw markdown. Report issues.","status":"open","priority":93,"task_type":"recurring","frequency":"every-12h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T16:22:59.459261+00:00","updated_at":"2026-04-17T16:22:59.459261+00:00","summary":"","completion_notes":"Auto-release: recurring task had no work this cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/89bb12c1-9fc_demo_ci_verify_all_demo_pages_load_corr_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 9}, \"auto_tagged_at\": \"2026-04-03T22:29:52.490153\", \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"any\", \"_stall_requeued_at\": \"2026-04-11 01:12:42\", \"completion_shas\": [\"53cca780bc5eb15075ea5def578bd9ec27d23411\", \"55b60fcc4e43c5d6d95049fd6c1dca5c988c13cc\"], \"completion_shas_checked_at\": \"2026-04-12T18:27:20.065075+00:00\", \"completion_shas_missing\": [\"8a773f861594aaf73f78e6e16cbc608320dd9006\", \"d22e1283e37b3f8406c256f5af258bd0638f9b54\", \"90be5add7a1de2e23a687219ff68e0d6c21c0f5c\", \"b1fb2e7c5063952504097b4e2fc053bfc24549fc\", \"f43a7955497fa82823a4d03da67eb1ca8006affa\", \"f188a7f4a90c9c30aa2caf096ffa42df66b245d2\", \"2bfa6ec5699b230953bca8eb4d65e257c05803dc\", \"ab8abc6075c770dbf7d2afee0a736ff8fb824dd8\", \"777ea6b624ff7c57fd9e8e9007a3086d4981563b\", \"856d040416db96268d449aec2af0c32ff831cad8\", \"f0cdae844c364e467bca365d6e2ec0e71c5776b2\", \"6156f647a2e44fd42b16eb9a723187eb573fa362\", \"f3a23a4501a6534b299c1421674942eb83aef112\", \"e19ba9f2e0645ab1ecaa745f1a683f5e92c21202\", \"9c1dfc4cef19d3e2a8d417253957132279ae9354\", \"7c7f9693a61d859cb3ae989a17bcf8cc22ed1a2f\", \"f0c1e14edd1f69e1dbfd6990d6df30b80a566460\", \"16bd7dfe54d450730960d66d6fa445b5d4a26338\", \"0c83fc87c0cb7ecd107297ee86859c7d97b8aca9\", \"bcf7b4bbc2cb5ad8cb1ae8d447741b7f8250f264\", \"9d05f7db6ef2a024254e18de60c66fef34b263f2\", \"bb3de901aa3715ce16e53e0933e8228ac95aebcb\", \"a0069a4436c62d121fb0321623bfc6c92caf0229\", \"99d38a23a727d5880c5f9643ff374f362c245ba3\", \"7c9eba0136e346987cd4bb93958ea4352bdb0ae7\", \"6e77b40ce282dfc252363cc67f413427e3dbda55\", \"018bf302d5de8c4d932f0d4d6891fa7466137186\", \"841b214231eb5b3dcb394b76e3a31091748132e3\", \"a3cbecbae335bd078abd61cd711406fe22299097\", \"d777ea32e329d783921392b7237e855843f40152\", \"26f25016b65c81244acae19811df582dc330ff99\", \"c88ab6c5869cbafe86f2439171503ba647a40550\", \"b1d8a02ce6318f5cfd82502b6b460fdd8af2d213\", \"d10c5c791004998ec89a8907f3b48464bc5c236d\", \"edcd3b2c8649bb76e240215bb09ec5f203852f94\", \"97b5754a39c5ca7ce8398a57f8c19edf74f6774b\", \"f1ef2ebf8c4c71398b7ae86f17f094b5d6a83f8c\", \"696c6215d705f8622e2c79ad9110500963b597eb\", \"fc14a137a7f7596cdc350c8f9f6965e820ca6761\", \"57aea26f144bccc723328c55884f9289306618dd\", \"2f3ce20bc162ad0a180bf7c67a44bead25bdf8e4\", \"40a65ebbba01fba288f044f638cc87176f406f6c\", \"79ffb1a23f2cac2b32df5f9465b8425ba8da6479\", \"b5fcc7d1bce217de92b6fc08510f34b50c53f9e9\", \"90aec62ba30ae6e03462aaad2e609365b1a2dc39\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"8c1ca59e-a8d6-49a3-8b20-f3b2893bf265","title":"[Quality] Review analysis showcase pages for presentation quality","description":"Visit /showcase and each walkthrough analysis. Check: debate transcript quality, hypothesis cards rendering, KG visualization, notebook links working, figure display. Fix rendering issues.","status":"open","priority":93,"task_type":"recurring","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:57:23.453063+00:00","updated_at":"2026-04-17T04:57:23.453063+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f4f66e36_agent_walkthrough_quality_audit_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 9}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"any\", \"_stall_requeued_at\": \"2026-04-11 01:12:55\", \"completion_shas\": [\"ead5ca7a0f8db5c3195c32727e6585bff719480f\", \"a0190cbf1ef9ad024391d79fd3dee2e68e6b6d55\"], \"completion_shas_checked_at\": \"2026-04-12T18:26:14.349901+00:00\", \"completion_shas_missing\": [\"fb72c00e72bdef4fd7b229596f3489a9753bb9e6\", \"71503aaf7d544482e46db675bac88943890db931\", \"f4b57839a58c8bbc98fb4c54e529f7b9b16687e9\", \"13f93e849f0670dd0a7764dab630c47696ce9a12\", \"af5d9648a371fd70c1fb2e6cbc7a900e62bcd734\", \"d74b879fd46224161691107b74a604792f200bf9\", \"c02ccdd1946124ea5ff62e0a9e8707cdee346f70\", \"34e62119852e425eda4be3b8e6f4cd069c4c7313\", \"85c3a91730aebe8c3bf5bff6ffb9dde78cea81cd\", \"e65cce175a07ad73b77e8a3a11a400b4a9aac1b2\", \"b1236f4581b6acd8bfe69d52da019bf44b74098c\", \"0ece77311bbd5abdffcd866bc40e6eaa0c5048e8\", \"3dd2b955e542af01c35508d100d9e2069871b803\", \"ae3494a0882af648fad2a2f1b56d4339f63e197e\", \"feca04f452f1404eca476fa666d5711b39b847e5\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"bcb62c5f-9d22-4677-a1f7-8b9a1ed27003","title":"[Demo] Audit ALL showcase navigation paths — every link from /showcase must lead to rich content","description":"Starting from /showcase, follow every link (walkthrough analyses, hypothesis cards, notebook links, challenge links). For each destination: verify content is substantial (not stubs), descriptions not truncated, figures render, notebooks have real output. Fix or remove broken links. De-prioritize protein 3D viewer (Mol*) in showcase cards — it is not core functionality.","status":"open","priority":93,"task_type":"recurring","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:17:28.233986+00:00","updated_at":"2026-04-17T04:17:28.233986+00:00","summary":"","completion_notes":"Auto-release: recurring task had no work this cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 6}, \"completion_shas\": [\"14df8cdf25bd9ddca1fa8bb8e6a280ce12bac98a\"], \"completion_shas_checked_at\": \"2026-04-12T23:48:16.208568+00:00\", \"completion_shas_missing\": [\"25de145fe80c0cf0ccb333fc3bdfe702af02abd1\", \"a58689a597001ecd099cde1bcc9389192dc44500\", \"0aaf36b5245936006d00f0d24501c2294d047be2\", \"98786ca8fcc887b9b5a18ba48197ed7427437a48\", \"d5ed15cc87352acfcfae7e1428642f779886ee9f\", \"c8dbedbf2985299218a1ceb4e0b6312c742bba5c\", \"f05334b1d23472b8aa157d7246f7bfdb50728fdd\", \"63b61a69734449551a8d8f9a3ad4102693e193c3\", \"476837a36592969d09609055174428b5fa998cef\", \"f1527d7b6e66c356430d71f69d8946eabcc7f4ca\"]}"},{"id":"4504fc8b-b50e-4df9-9333-88c8147cc1a6","title":"[Quality] Audit /forge/playground tools — verify all 12 tools return real data","description":"Visit each /forge/tool/{id} page. Click Run with default inputs. Verify non-null results, proper table rendering, external links working. Fix any broken tools.","status":"open","priority":93,"task_type":"recurring","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:06:06.547257+00:00","updated_at":"2026-04-17T04:06:06.547257+00:00","summary":"","completion_notes":"Auto-release: recurring task had no work this cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3df010f4_forge_ci_test_tools_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 6, \"reasoning\": 6, \"safety\": 7}, \"completion_shas\": [\"efe7975f8b2bfb4ffc3859fee07978fa7a30e9fd\", \"4018dad6e9fac6f9b5fb250085255a3c2417bbed\"], \"completion_shas_checked_at\": \"2026-04-12T18:17:58.871880+00:00\", \"completion_shas_missing\": [\"43f701b62170e48f14e52c98f82c896a4c97329f\", \"7dc5e42ac5ae254516de72c57549424e8247cd32\", \"7490ea5f55c18cde87c33e0498203bebbccdd4ca\", \"0a7353dbb89b76bf1d6eca26da4c1602ecb6ac99\", \"161489351f6713adaf4a872678b029ac382ae970\"]}"},{"id":"b40945ad-76af-4c77-89bc-cfc5cb0abe9d","title":"[Demo] D16.1: Enrich top 3 hypotheses to demo quality — deep descriptions, citations, pathway diagrams","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:14:37.629401+00:00","updated_at":"2026-04-16T17:14:37.629401+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b40945ad_76a_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [\"minimax\", \"codex\", \"max_outlook\"], \"_stall_requeued_by\": \"max_outlook\", \"_stall_requeued_at\": \"2026-04-15 22:28:48\", \"_stall_skip_at\": {\"codex\": \"2026-04-14T20:54:49.572049+00:00\", \"max_outlook\": \"2026-04-15T22:28:48.359877+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"0b351a3c-2657-4cdf-8cbe-29fe6bc66c75","title":"[Demo] Enrich top 3 hypotheses to demo quality","description":"Transform top 3 hypotheses (LRP1 Tau, Circadian Glymphatic, Acid Sphingomyelinase) into hero pages with 2000+ word descriptions, 10+ citations, evidence for/against, pathway diagrams, 3D protein viewers, and clinical trial links.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:14:35.419994+00:00","updated_at":"2026-04-16T10:14:35.419994+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16_1_enrich_top_hypotheses_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [\"minimax\", \"codex\", \"max_outlook\"], \"_stall_requeued_by\": \"max_outlook\", \"_stall_requeued_at\": \"2026-04-15 22:22:11\", \"_stall_skip_at\": {\"codex\": \"2026-04-14T20:54:50.116383+00:00\", \"max_outlook\": \"2026-04-15T22:22:11.798833+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"427dbb2b-9c28-497a-ab5e-f1e813a3dd62","title":"[Demo] Enrich top 3 hypotheses to demo quality with deep descriptions and pathway diagrams","description":"D16.1: Enrich top 3 hypotheses (LRP1 Tau Uptake, Circadian Glymphatic, Acid Sphingomyelinase) with 2000+ word descriptions, 10+ PubMed citations, evidence for/against, pathway diagrams (mermaid), and mechanism details. These become hero pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T19:55:41.901878+00:00","updated_at":"2026-04-14T19:55:41.901878+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/427dbb2b_9c2_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"160ca4c149c8845c63a5651a0f3d1ecd27f76840\", \"0bc9c347b9aabebe0ce505bbe9b5a49cc4306c91\", \"1666024a853709bc31f37195ac998c373aef971b\"], \"completion_shas_checked_at\": \"2026-04-14T19:55:41.883261+00:00\"}"},{"id":"12a5f20a-15c6-44f9-8e8e-5560657943fc","title":"[Demo] Enrich top 3 hypotheses to demo quality","description":"Transform top 3 hypotheses (LRP1 Tau uptake, Circadian glymphatic, Acid sphingomyelinase) into hero pages with 2000+ word descriptions, 10+ citations, pathway diagrams, evidence for/against, linked proteins, clinical trials. See docs/planning/specs/d16_1_enrich_top_hypotheses_spec.md\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T16:19:40.676683+00:00","updated_at":"2026-04-14T16:19:40.676683+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16_1_enrich_top_hypotheses_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"6a2208d2af821bab9598e4531535ee9301a76d4b\"], \"completion_shas_checked_at\": \"2026-04-13T19:37:45.936311+00:00\", \"completion_shas_missing\": [\"d0ba016dddf4542deb4ee59ba5b271a920f9d9ad\"]}"},{"id":"5974d1e5-6cc3-4625-8429-f9b5e5aba25e","title":"[Demo] Enrich top hypothesis: Microbial Inflammasome Priming Prevention — from 313 chars to 2000+ with full evidence","description":"Score 0.9 but only 313 chars description. This is the top-scoring hypothesis — make it the hero page. Add: detailed mechanism, PubMed citations, pathway diagram, evidence for/against, related proteins.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T10:58:32.091615+00:00","updated_at":"2026-04-14T10:58:32.091615+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"codex\", \"_stall_requeued_at\": \"2026-04-14 03:06:44\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"b5c0a73a7e2cf7e8a6fac5d878810991a46d049f\"], \"completion_shas_checked_at\": \"2026-04-14T10:58:32.073195+00:00\"}"},{"id":"e90797ac-25a5-4bdb-b4ca-5bfe8f9c04aa","title":"[Demo] Recurring: Read all quest/task specs, identify demo-ready features, create integration tasks","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:54:56.339794+00:00","updated_at":"2026-04-13T19:54:56.339794+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"reasoning\": 7}, \"completion_shas\": [\"f2db2dc35f10d56dd8084323f13ddc88ac5ce405\"], \"completion_shas_checked_at\": \"2026-04-13T19:54:56.319257+00:00\", \"completion_shas_missing\": [\"6514fe212b9fba159b8246921a3876748f7ff6d3\", \"b89cd60736aa49b866144738ceac0fd93785459e\", \"56814865edb1b31bcbb9f3f32061e5186f49a0a5\"]}"},{"id":"e38a9454-1652-46a5-a9c5-1b5200b5c79d","title":"[Demo] Enrich top 3 hypotheses with deep descriptions and evidence chains","description":"D16.1: Enrich top 3 hypotheses (LRP1 Tau Uptake, Circadian Glymphatic, Acid Sphingomyelinase) with 2000+ word descriptions, mechanism details, PubMed citations, evidence_for/evidence_against, and pathway diagrams. These become hero pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:35:40.618537+00:00","updated_at":"2026-04-13T19:35:40.618537+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e38a9454_165_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"673335833d0905831e7757fb9897a6972a978b6e\", \"03a798fd0edd82cce3f0da5284a2293819ae7676\"], \"completion_shas_checked_at\": \"2026-04-13T19:35:40.598658+00:00\", \"completion_shas_missing\": [\"a6c77aef519837d42887ebdbe6cf0f329c9431ff\", \"ca45cd3cc5adf1461ffdb9079c9b642709f32af6\"]}"},{"id":"d16-01-63128A4A","title":"[Demo] Enrich top 3 hypotheses to demo quality","description":"Deep-enrich LRP1 Tau Uptake (h-4dd0d19b), Circadian Glymphatic (h-9e9fee95), Acid Sphingomyelinase (h-de0d4364). Each needs: 2000+ word description with mechanism details, 10+ PubMed citations with abstracts, evidence_for/evidence_against with strength ratings, mermaid pathway diagram, related clinical trials, gene expression context. These become hero pages.","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:52:17","updated_at":"2026-04-02 09:42:41","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"2009b5b0-3934-470e-aed8-944c54f27a48","title":"[Demo] SEA-AD Single-Cell Analysis (Allen Institute)","description":"Run agentic analysis on Seattle Alzheimer's Disease Brain Cell Atlas data. Produce hypotheses about cell-type vulnerability with differential expression analysis. Generate Jupyter notebook with heatmaps, volcano plots, and pathway enrichment.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":98,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:16:03.296809+00:00","updated_at":"2026-04-16T17:16:03.296809+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16_2_sea_ad_analysis_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 11:22:37\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"09b35b05-e29f-44c2-99aa-8b064b942cc2","title":"[Demo] SEA-AD Single-Cell Analysis (Allen Institute)","description":"Analyze Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) data using Allen Brain Cell API. Query gene expression data across cell types, produce hypotheses about cell-type vulnerability in AD, generate Jupyter notebook with heatmaps and differential expression analysis. Link to TREM2/APOE hypotheses. See docs/planning/specs/d16_2_sea_ad_analysis_spec.md\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":98,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:06:20.639036+00:00","updated_at":"2026-04-13T20:06:20.639036+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16_2_sea_ad_analysis_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"ecabefaffdb4ad5cd49226ea2c92c57ade720025\"], \"completion_shas_checked_at\": \"2026-04-13T20:06:20.619113+00:00\"}"},{"id":"e995e7bc-3582-4090-a50e-a6709bd81575","title":"[Demo] Enrich top hypotheses with PubMed papers and evidence ratings","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":98,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:04:03.418438+00:00","updated_at":"2026-04-13T20:04:03.418438+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e995e7bc_358_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"d528035f72915a012a22f31150ff8384ec7b2226\", \"5cad5294c31bb1cf00c5f34c852923989f1a1c42\", \"7dc71021ecc1db22b859f0a77ed3da4d471cc7e0\"], \"completion_shas_checked_at\": \"2026-04-13T20:04:03.399439+00:00\", \"completion_shas_missing\": [\"f4aef1bcf5b77b4b1691ca41e73cdc5d253934ea\"]}"},{"id":"d16-02-EB0C0B9E","title":"[Demo] SEA-AD Allen Brain Cell Atlas analysis with Jupyter notebook","description":"Run agentic analysis on Seattle Alzheimer Disease Brain Cell Atlas (SEA-AD) data. Use Allen Brain Map API to fetch cell-type specific gene expression. Create Jupyter notebook with: differential expression analysis across cell types, heatmaps of AD-associated genes (TREM2, APOE, APP, MAPT), statistical tests, pathway enrichment. Produce 3-5 hypotheses about cell-type vulnerability. Link to wiki pages for cell types and genes.","status":"done","priority":98,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:46:46","updated_at":"2026-04-02 09:42:41","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"829ae22b-3dee-4875-85c5-119c0eca824b","title":"[Demo] Enrich 4 Featured Discovery hypotheses — fix diagrams, expand descriptions, wire debates","description":"Homepage showcase audit found: (1) h-b2aeabb1 CRITICAL: pathway_diagram shows generic BBB dysfunction instead of PEA-PPARA mechanism — swap with the correct embedded mermaid from description body. (2) SDA-e5bf6e0d: description only 10.8K chars with 0 inline PMIDs — expand to 20K with SIRT1/NAD+/PGC-1alpha/NAMPT detail + 15-node diagram. (3) h-b2aeabb1: expand description to 18K with PEA pharmacology, PPARA biology, microglial polarization. (4) All 4: debate_count claims debates but 0 linked debate_sessions — wire up real debate records. (5) h-11ba42d0: link to analysis. Use parallel agents (2 hypotheses each). Priority: h-b2aeabb1 diagram fix FIRST since it's visually broken on homepage.","status":"archived","priority":97,"task_type":"one_shot","frequency":"","assigned_slot":"62","started_at":"2026-04-17T08:20:43.848300+00:00","completed_at":"2026-04-17T02:24:36.925187+00:00","updated_at":"2026-04-17T08:42:47.838186+00:00","summary":"","completion_notes":"","last_error":"Watchdog bulk: 7 abandonments, queued for repair","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"_watchdog_repair_task_id\": \"76621989-e2cc-42be-817f-6ecc35b8258d\", \"_watchdog_repair_created_at\": \"2026-04-17T08:26:37.695477+00:00\"}"},{"id":"c75f4947-a18f-48d9-b46f-d15438b02b1c","title":"[Demo] Enrich top hypothesis: Circadian Glymphatic Entrainment — add pathway diagrams, protein viewers, evidence matrix","description":"The Circadian Glymphatic hypothesis (score 0.8) already has 9939 chars of description. Add: mermaid pathway diagram of orexin->glymphatic->clearance cascade, evidence_for/evidence_against sections with PubMed citations, related clinical trials, and link to relevant wiki pages.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":97,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:30:54.488118+00:00","updated_at":"2026-04-16T22:30:54.488118+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 11:39:43\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"d16-03-EB857966","title":"[Demo] Aging Mouse Brain Atlas cross-age gene expression analysis","description":"Analyze Allen Mouse Brain Aging Atlas data. Compare gene expression across age groups (young/middle/old) in hippocampus, cortex, cerebellum. Jupyter notebook with volcano plots, trajectory analysis. Hypotheses about aging-neurodegeneration overlap. Cross-reference with human SEA-AD data.","status":"done","priority":97,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:57:18","updated_at":"2026-04-02 09:42:41","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"987ffe4a-21be-4d45-bd1e-14b81a4b62b4","title":"[Demo] Add Mol* 3D protein structure viewer to top hypothesis pages","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"0","started_at":"2026-04-17T08:24:48.429738+00:00","completed_at":"2026-04-17T08:24:47.809925+00:00","updated_at":"2026-04-17T09:11:51.980092+00:00","summary":"","completion_notes":"","last_error":"Watchdog bulk: 12 abandonments, queued for repair","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/987ffe4a_21b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:24:55\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"6f1a33bb-b5a6-4fa3-9047-deede2fee0bb\", \"_watchdog_repair_created_at\": \"2026-04-17T09:07:07.061583+00:00\"}"},{"id":"b2223c3b-ac37-407e-9e15-05c8518a834b","title":"[Demo] Embed Mol* 3D protein viewer on hypothesis pages for target proteins","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T08:50:57.388870+00:00","updated_at":"2026-04-17T08:50:57.388870+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b2223c3b_ac3_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 11:51:00\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"fc23ff2c-ee37-4b3a-b3fa-823be789ad5a\", \"_watchdog_repair_created_at\": \"2026-04-17T08:26:38.362045+00:00\"}"},{"id":"e1e01fc0-069f-4740-b337-06499becb19d","title":"[Demo] Add Mol* 3D protein structure viewer to hypothesis pages","description":"Embed the Mol* (molstar) 3D protein structure viewer on hypothesis detail pages for target proteins. Load PDB structures via RCSB PDB API. Show the structure in a collapsible panel. Map target_gene to PDB IDs for top hypotheses.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T08:19:35.761002+00:00","updated_at":"2026-04-17T08:36:32.431806+00:00","summary":"","completion_notes":"","last_error":"Paused after 33 exit-0 runs with no commits on branch=(none)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e1e01fc0_069_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:30:46\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"df9bced1-2383-4ee4-ad39-69e8588dc0f4\", \"_watchdog_repair_created_at\": \"2026-04-17T08:26:33.195588+00:00\"}"},{"id":"dcd7455c-ee46-4f31-ab44-8a9eaf97360d","title":"[Demo] Add Mol* 3D protein structure viewer to target detail pages","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"72","started_at":"2026-04-17T08:19:07.487136+00:00","completed_at":"2026-04-17T00:31:55.750140+00:00","updated_at":"2026-04-17T08:35:45.024176+00:00","summary":"","completion_notes":"","last_error":"Watchdog bulk: 12 abandonments, queued for repair","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/dcd7455c_ee4_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:19:22\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"3f85dca2-58d2-419f-9912-ff3f96430ed9\", \"_watchdog_repair_created_at\": \"2026-04-17T08:26:35.303391+00:00\"}"},{"id":"08d275f8-3285-4b9d-8144-c1eae7e70610","title":"[Demo] Add Mol* 3D protein viewer to hypothesis detail pages","description":"D16.4: Embed Mol* 3D protein structure viewer on hypothesis detail pages for target proteins. Use AlphaFold structures via Mol* (https://molstar.org/). Show interactive 3D view of target protein next to hypothesis description. Priority targets: TREM2, APOE, LRP1, SMPD1, MTOR.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"2","started_at":"2026-04-17T08:24:59.827007+00:00","completed_at":"2026-04-17T08:24:59.631566+00:00","updated_at":"2026-04-17T08:34:11.306704+00:00","summary":"","completion_notes":"","last_error":"Watchdog bulk: 29 abandonments, queued for repair","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/08d275f8_328_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:38:23\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"04427714-477a-4c4e-9118-8613c3a37a83\", \"_watchdog_repair_created_at\": \"2026-04-17T08:26:33.497348+00:00\"}"},{"id":"6e631ed4-baca-4501-bab5-b1f6a3ed1c9f","title":"[Demo] Add Mol* 3D protein viewer to hypothesis pages","description":"Embed Mol* (molstar) 3D protein structure viewer on hypothesis detail pages that have target proteins. Map target gene names to UniProt IDs and PDB structures. Show interactive 3D viewer inline.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:49:40.926598+00:00","updated_at":"2026-04-16T23:49:40.926598+00:00","summary":"","completion_notes":"Bash tool completely non-functional in this environment (ENOENT session-env error on every invocation). Code verified present in api.py at lines 31700-32150 (hypothesis pages) and 34600-35099 (target pages). Spec updated to done. Cannot commit/push without working shell access.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6e631ed4_bac_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:17:27\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"2ccc4582-8661-4eb1-92cf-a6ad65dc2b47","title":"[Demo] Enrich top hypothesis pages with deep descriptions and evidence chains","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:08:34.972559+00:00","updated_at":"2026-04-16T11:08:34.972559+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/2ccc4582_866_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:07:44\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"5cd00627-941f-4e59-870a-4b550144e093","title":"[Demo] D16.9: Guided demo walkthrough page spanning all five layers","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:33:15.086894+00:00","updated_at":"2026-04-16T10:33:15.086894+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5cd00627_941_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:37:05\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"b689b545-1288-4c19-bbb2-e487583744ed","title":"[Demo] Add mermaid pathway diagrams to top 5 hypotheses","description":"None of the top 15 hypotheses have mermaid pathway diagrams. Per Quest 16 D16.1, hero hypotheses need mechanism pathway diagrams. Add mermaid flowcharts showing the molecular mechanism cascade for the top 5 by confidence score: Microbial Inflammasome Priming (0.90), Membrane Cholesterol Gradient (0.85), CYP46A1 Gene Therapy (0.85), Nutrient-Sensing Epigenetic (0.85), Gamma Entrainment (0.82).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T19:50:29.569350+00:00","updated_at":"2026-04-14T19:50:29.569350+00:00","summary":"","completion_notes":"All 5 top hypotheses have pathway diagrams. Top 5: h-11ba42d0 (0.845, 788 chars), h-var-6612521a02 (0.709, 1504 chars), h-58e4635a (0.703, 2016 chars), hyp-SDA-2026-04-12-20260411-082446-2c1c9e2d-1 (0.7, 833 chars), h-var-3b982ec3d2 (0.697, 1504 chars). All validated. Task was already complete.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b689b545_128_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"4c44cf99-89d4-461e-bcb1-6cdbf9201235","title":"[Demo] Add Mol* 3D protein structure viewer to hypothesis pages (D16.4)","description":"Embed Mol* (molstar) 3D protein structure viewers on hypothesis detail pages for target proteins. Map hypotheses to their key proteins, look up PDB IDs, and render interactive 3D views. Start with top hypotheses (LRP1 Tau Uptake, Circadian Glymphatic, Acid Sphingomyelinase). This is Quest 16 task D16.4 at P96.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T12:54:53.824304+00:00","updated_at":"2026-04-14T12:54:53.824304+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4c44cf99_89d_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 20:56:10\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"293a643913f7e85a964d53cdc8df5ca15d5a5df7\"], \"completion_shas_checked_at\": \"2026-04-14T12:54:53.810667+00:00\"}"},{"id":"561f5481-8a14-46a5-a429-b139d7e55cd4","title":"[Demo][Artifacts] Artifact-aware demo page verifier","description":"Expand verify_main_pages.py to assert rich content markers for demo-critical pages and add tests to prevent regressions.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T21:34:14.779563+00:00","updated_at":"2026-04-13T21:34:14.779563+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/561f5481_8a1_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"a36cc75738a07d63af56dca88eb8ef0d45537fbe\"], \"completion_shas_checked_at\": \"2026-04-13T21:34:14.760822+00:00\", \"completion_shas_missing\": [\"14546aeabe91a1ace8e40fa2db1b852b46d48dbc\"]}"},{"id":"0b66d649-f22e-4eb0-a40c-515ef47cd6e4","title":"[Demo] Make link checker complete within 5-minute CI timeout","description":"Optimize link_checker.py crawl/validation flow so timeout 300 python3 link_checker.py reliably completes and reports actionable failures; tolerate transient localhost:8000 restarts without false negatives.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T21:17:31.654193+00:00","updated_at":"2026-04-13T21:17:31.654193+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0b66d649_f22_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"completion_shas\": [\"2a566190894886984585f3d49de379f73d42e195\", \"7592cc9a4d829e4a91535c1e8a47bddb8992ebe7\", \"275dd3729e2f5d63e0f3951ebca624e5bdd7d575\"], \"completion_shas_checked_at\": \"2026-04-13T21:17:31.636276+00:00\"}"},{"id":"cb52ff0c-084b-4242-bd52-46ec57a18f0a","title":"[Demo] Fix demo route regressions for walkthrough and demo page","description":"Smoke check currently fails for /walkthrough.html (404) and /demo.html demo-content expectation. Add robust route handling/content to restore demo flow reliability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T21:04:00.840494+00:00","updated_at":"2026-04-13T21:04:00.840494+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/cb52ff0c_084_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"62b7e43c9ff6ee03b0ad35c6cbfd1a880c88553a\"], \"completion_shas_checked_at\": \"2026-04-13T21:04:00.823330+00:00\"}"},{"id":"1b0e2554-a272-4078-8072-5344ab7a7577","title":"[Demo] Add Mol* 3D protein structure viewer to hypothesis detail pages (D16.4)","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:57:09.598032+00:00","updated_at":"2026-04-13T20:57:09.598032+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1b0e2554_a27_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"completion_shas\": [\"cf4dc96b8a18cff78aadca9800f649de13c8dc8b\"], \"completion_shas_checked_at\": \"2026-04-13T20:57:09.580921+00:00\"}"},{"id":"8462bd42-d018-4bda-a1bb-c5e03bd21048","title":"[Demo] Fix /notebooks 500 error and ensure notebook viewer works","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:48:35.133223+00:00","updated_at":"2026-04-13T20:48:35.133223+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8462bd42_d01_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"2ea4c9b7df26c4c609b1d6359333e7cc69b3d462\"], \"completion_shas_checked_at\": \"2026-04-13T20:48:35.093654+00:00\", \"completion_shas_missing\": [\"16152601970c5f3546284e0ea13be401876feb0c\"]}"},{"id":"feb1601e-061e-46f4-8da6-1316475b3318","title":"[Demo] Enrich top 5 hypothesis evidence chains with PubMed citations","description":"Enrich evidence_for and evidence_against fields for top 5 hypotheses by clinical_relevance_score. Add structured PubMed-backed citations with PMIDs, brief abstracts, and relevance explanations. Target 3KB+ for each evidence field. This directly supports D16.1 demo quality.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:39:08.903381+00:00","updated_at":"2026-04-13T20:39:08.903381+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/feb1601e_061_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"98f84f9dd99af19137baa087725df5bcd7a8caaa\"], \"completion_shas_checked_at\": \"2026-04-13T20:39:08.877032+00:00\"}"},{"id":"52028fdd-f198-4191-9c5a-05ca69579844","title":"[Demo] Add target pages for top hypotheses missing targets (ACSL4, GFAP, SIRT3)","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:37:50.469107+00:00","updated_at":"2026-04-13T20:37:50.469107+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/52028fdd_f19_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"0079977b560183235fcbcdb1a3d63555c39c957b\", \"0eb3c6adfb773d0c0f1fa44cf7e09d997a2d499f\"], \"completion_shas_checked_at\": \"2026-04-13T20:37:50.452750+00:00\"}"},{"id":"339e93e6-8155-4228-8d1f-434e41cc2609","title":"[Demo] Build /showcase page with top hypothesis hero cards and walkthrough","description":"Create /showcase page (D16.9) as the guided demo entry point. Shows top 5 hypotheses with rich cards (description preview, scores, protein viewer thumbnail, evidence count). Links to /walkthrough for end-to-end demo flow. Currently 404ing with 7+ hits in last 30 min.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:37:13.048227+00:00","updated_at":"2026-04-13T20:37:13.048227+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/339e93e6_815_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"01711dfe7ba1dd05725fb0e951b73c63c8311554\", \"fb90e472d169a93c2253ba1e91112b272d86534f\"], \"completion_shas_checked_at\": \"2026-04-13T20:37:13.031317+00:00\"}"},{"id":"e1f13048-7096-4ca0-953b-d00660b4e291","title":"[Demo] Enrich top hypotheses missing pathway diagrams and clinical trials","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:31:23.719132+00:00","updated_at":"2026-04-13T20:31:23.719132+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e1f13048_709_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"cbfdfe372937a2b8f65adbe0a80af83a95867092\", \"ce43551acb7a4beef25a87fe32776cd134d17cac\"], \"completion_shas_checked_at\": \"2026-04-13T20:31:23.702200+00:00\"}"},{"id":"634d0abd-b3e6-450e-86be-7899edfe6f20","title":"[Demo] Enrich top hypothesis: Acid Sphingomyelinase Modulation — add pathway diagrams, citations, evidence matrix","description":"The Acid Sphingomyelinase hypothesis (score 0.8) has 12178 chars. Add: mermaid pathway diagram, structured evidence matrix, Mol* protein viewer for ASM structure, and cross-links to related hypotheses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:04:49.261293+00:00","updated_at":"2026-04-13T19:04:49.261293+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"1832de1153c1cfd820a75f0227a2e4bc3e491e2d\", \"9ba783a129a9b6f6a63992c1f61f1a6edb8e8a28\"], \"completion_shas_checked_at\": \"2026-04-13T19:04:49.243301+00:00\", \"completion_shas_missing\": [\"f005731ac48ec663beb305f3ba4dda6d8492581c\"]}"},{"id":"d16-04-BC3E8EEA","title":"[Demo] Add Mol* 3D protein viewer to hypothesis detail pages","description":"Embed Mol* (molstar) 3D protein structure viewer on hypothesis pages for target proteins. Load PDB structures: LRP1 (2FCW), TREM2 (6YXY), APOE (2L7B), CYP46A1 (2Q9F), SMPD1 (5I73). Add viewer below hypothesis description. Use Mol* lite CDN. Show binding sites, mutation sites relevant to hypothesis.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.","status":"archived","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:54:00","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"0d1af4f7-0084-4c5e-88df-5fc472934fe0","title":"[Demo] Add mermaid pathway diagrams to hypothesis detail pages","description":"Add interactive mermaid.js pathway diagrams showing disease mechanism cascades on hypothesis detail pages. Each hypothesis with a target_pathway or target_gene should display a relevant pathway diagram. This is D-PRIORITY for Quest 16 (Demo Showcase) and Quest 2 (Exchange).","status":"archived","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"21","started_at":null,"completed_at":"2026-04-02 17:29:53","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0d1af4f7_008_spec.md","provider":"any","payload_json":"{}"},{"id":"17b1ccf9-12e2-4821-9edd-3af9ed3a3fe1","title":"[Demo] Add Mol* 3D protein viewer to hypothesis detail pages","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.","status":"archived","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"21","started_at":null,"completed_at":"2026-04-02 21:44:18","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/17b1ccf9_12e_spec.md","provider":"any","payload_json":"{}"},{"id":"42996801-3fe7-4e29-8c6f-c78875edb978","title":"[Demo] Add Mol* 3D protein viewer to hypothesis detail pages","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.","status":"archived","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:04:46","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/42996801_3fe_spec.md","provider":"any","payload_json":"{}"},{"id":"b278d4d3-7b17-4069-b2a1-320a0247e3f4","title":"[Quality] Remove or de-prioritize Mol*/protein viewer in showcase hypothesis cards","description":"The 3D protein structure viewer (Mol*) is prominently shown on showcase hypothesis cards but is not core SciDEX functionality. It is a distraction for first-time visitors. Either: remove it from showcase cards, or move it below the fold. Keep it on individual hypothesis detail pages where it adds value.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":null,"started_at":null,"completed_at":"2026-04-09 01:00:31","updated_at":null,"summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8}}"},{"id":"347c79aa-962b-47a2-a83a-fec2222a2525","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:24:52.757350+00:00","updated_at":"2026-04-17T04:24:52.757350+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{}"},{"id":"1d42f6e5-f7fa-4c1a-a254-735a1db29826","title":"[Demo] Run debates for 10 undebated analyses","description":"IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists.\n\n10 analyses have no debates. Run 4-persona debates for: Investigate prion-like spreading of tau , epigenetic reprogramming aging neurons, APOE4-driven lipid metabolism dysregulat. Use Forge tools for PubMed evidence.","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T06:33:41.518925+00:00","updated_at":"2026-04-16T06:33:41.518925+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8, \"safety\": 9}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 02:09:24\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"d16d62d0-36bd-4a34-8f83-53b9d78464ba","title":"[Demo] Fix /compare 500 errors and add /showcase+/gaps page caching","description":"Fixed /compare endpoint 500 errors (evidence items as strings instead of dicts). Fixed target pages 500 errors (clinical_phase as string in arithmetic). Added page caching to /showcase (was 3-13s, now <100ms) and /gaps (was 13s, now <5ms). All demo-critical pages now load under 60ms.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T04:22:56.037218+00:00","updated_at":"2026-04-16T04:22:56.037218+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16d62d0_36b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 9}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:03:24\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"32e2d8cabe469284b7b18ba4bafaa4785c792650\", \"83bd0083ff2fef076f8cf2a331b27fc2127e10eb\", \"0495b57abea9f1eea9ca9e0f2ce6dee22c10d170\"], \"completion_shas_checked_at\": \"2026-04-16T04:22:56.018778+00:00\"}"},{"id":"2f2ca080-0527-4485-9211-eadf045bf3d1","title":"[Demo] Run debates for 10 undebated analyses","description":"IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists.\n\n10 analyses have no debates. Run 4-persona debates for: Astrocyte Reactivity Subtypes in Neurode, GBA-Synuclein Loop: Therapeutic Strategi, TREM2 Therapeutic Strategy Post-INVOKE-2. Use Forge tools for PubMed evidence.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T01:27:54.047384+00:00","updated_at":"2026-04-16T01:27:54.047384+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 02:03:14\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"c04447e4e1577ce26a68a795165a6d03cd787f32\", \"d3e12f0102efc5fbe76ab193472f7004c5b0066f\", \"f671f2a1eea5e2e62a230012b6d841dbce5ab92f\", \"824fd505caa840c0e8803a8efb8c3e8d527e5d01\", \"4766fb65040cabf5ae1600938fd27bf962dda84e\", \"202f1124349b9228a04877ef4d6d8838c0b79de0\"], \"completion_shas_checked_at\": \"2026-04-16T01:27:54.026175+00:00\"}"},{"id":"115fcd6b-5c92-4f60-a47d-db6454a40b06","title":"[Demo] Fix hypothesis detail page crash - missing edit_history table","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:14:12.056799+00:00","updated_at":"2026-04-16T00:14:12.056799+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/115fcd6b_5c9_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 00:54:21\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"7b3c834ec9445162f072926dfffa497544d76c75\", \"8a6def16068977437e4f7479a177837a18902b89\", \"86e1e4c6fb10c04b802efb79ca07f9137e9605d3\", \"5dbb08666aa473044511ead867ad4a64648179d5\", \"157670d2526151ad63a7e5590c887a1b41755747\", \"fe876813431e5b9d14048a60e1c21738f8e5e25f\", \"9fe869a7a861673dfdbd0cd00618aa350b1b11a6\"], \"completion_shas_checked_at\": \"2026-04-16T00:14:11.953464+00:00\"}"},{"id":"b73ca71c-c7bc-4755-82a5-cdb5a1b557cb","title":"[Demo] Run debates for 10 undebated analyses","description":"IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists.\n\n10 analyses have no debates. Run 4-persona debates for: TREM2 Therapeutic Strategy Post-INVOKE-2, GBA-Synuclein Loop Therapeutics for PD, Gut-Brain Axis Therapeutics for AD. Use Forge tools for PubMed evidence.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:10:00.076549+00:00","updated_at":"2026-04-16T00:10:00.076549+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:28:43\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"cb1611342b9741703f0ef12c8c67483296b578b3\", \"b1d91da429a33164f884787fa128e1e148d7af73\"], \"completion_shas_checked_at\": \"2026-04-16T00:10:00.058443+00:00\"}"},{"id":"5948c249-1462-4324-b54b-99424222e606","title":"[Demo] Enrich top 5 no-evidence hypotheses with descriptions and PubMed citations","description":"5 high-scoring hypotheses (score > 0.5) have both thin descriptions (<200 chars) and no PubMed evidence (evidence_for=[]). These include the #1 ranked hypothesis (h-e5f1182b, score 0.74). Enrich all 5 with: (1) expanded descriptions 1000+ words, (2) 3-5 PubMed citations supporting the hypothesis, (3) 1-2 citations against/caveats. Hypothesis IDs: h-e5f1182b, h-494861d2, h-d4ff5555, h-cc1076c1, h-48775971. This is Quest 16 D16.1 work.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:57:16.164023+00:00","updated_at":"2026-04-15T23:57:16.164023+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5948c249_146_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:18:11\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"d1103ffdd4c6a285625e7df0aedeafe998d3497c\", \"edba28c0d9bd620daf08070ebeb536a74c8b7439\"], \"completion_shas_checked_at\": \"2026-04-15T23:57:16.146841+00:00\"}"},{"id":"0a9c3b2a-bf65-488e-9cf3-4f764daec03d","title":"[Demo] Update showcase: add microglial analysis to walkthrough and five-layer demo narrative","description":"Add SDA-2026-04-04-gap-20260404-microglial-priming-early-ad to WALKTHROUGH_IDS alongside the existing three analyses. This analysis has 7 rich hypotheses (including Epigenetic Reprogramming h-e5f1182b with composite_score=0.74), evidence citations, 1 debate, 16 KG edges - making it an excellent demo analysis. Also verify the showcase page correctly displays all layers (Agora debates, Exchange pricing, Forge tools, Atlas KG, Senate governance) for each walkthrough analysis.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:45:17.685187+00:00","updated_at":"2026-04-15T23:45:17.685187+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0a9c3b2a_bf6_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:07:54\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"9bcf93b73ab6f25efd823e7673f32a23da343dd4\", \"04d9bbf9c51bca38c88f3438ab6a8d2a864e1c1d\", \"24201391c79f1d4035efef284496dd67f92e38d5\", \"bb75518a6352a855114dd568020842a6d5392c58\", \"3ae9436eaae9d5b99e787a4912e17ccb6f2c74e4\", \"dc17ff6a1bd466a7787c21a541ba05dfa92b6d6f\"], \"completion_shas_checked_at\": \"2026-04-15T23:45:17.667522+00:00\"}"},{"id":"64047bf2-805c-43ee-aecd-0cef37726e11","title":"[Demo] Fix /challenges page - missing current_bounty_usd column","description":"The /challenges page returns 500 due to sqlite3.OperationalError: no such column: current_bounty_usd. Need to either add the column migration or fix the query to use an existing column. Line ~34061 in api.py.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:40:24.162150+00:00","updated_at":"2026-04-15T23:40:24.162150+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/64047bf2_805_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 00:54:04\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"2a7fd49c165887359395d53a08376a270e59ec9d\", \"65ef7a12aa5bf542262abfcdf7a1bfe0105ead06\", \"9a8520e16ecceabd7091d053a04ee6a455b75d9b\", \"da98691791cf0fd9aaef257d1cbe4e8a8220622f\"], \"completion_shas_checked_at\": \"2026-04-15T23:40:24.134783+00:00\"}"},{"id":"6bb6ec05-3376-4c7e-9594-73c7326b16b0","title":"[Demo] Run new analysis: Neuroinflammation and microglial priming in early AD","description":"Run a full 4-persona debate analysis on the topic of neuroinflammation and microglial priming in early Alzheimer's Disease. Generate hypotheses, score them, extract KG edges, and produce a polished HTML report. This directly advances Quest 16 (Demo Showcase) by adding compelling, rich scientific content to the platform.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:37:48.978308+00:00","updated_at":"2026-04-15T23:37:48.978308+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6bb6ec05_337_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:09:47\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"5dfa31894ae24eb006e40ecc29ffd0581ae83f4b\", \"6932b6a7b283d29236a61c1a3b4271dd2cd245fd\", \"2e0c1ad638e0bf5954c5ef5240acc00695747661\", \"8ffb054430dec7179ddd9119567bf3bf2ae52a69\", \"969e40bfe5d3a841d2105c79d42730a3f166f0c2\"], \"completion_shas_checked_at\": \"2026-04-15T23:37:48.960418+00:00\"}"},{"id":"3b282ccb-e655-4d19-982f-1be786910343","title":"[Demo] Restore /leaderboard route lost in merge","description":"The /leaderboard route was added in commit 95e181b8 but was lost when commit 4fe7bcb1 merged a branch that overwrote api.py with an older version. The route needs to be restored.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:19:19.137673+00:00","updated_at":"2026-04-15T23:19:19.137673+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3b282ccb_e65_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 00:50:19\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"89405c5248d7b11c1b73e1c9873797d5dedca1be\"], \"completion_shas_checked_at\": \"2026-04-15T23:19:19.122090+00:00\"}"},{"id":"2dc94a3b-bc7b-4af0-a5fb-7861fd6a133d","title":"[Demo] Create demo Jupyter notebooks with real data analysis","description":"Create 2-3 exemplar Jupyter notebooks with Allen Institute data analysis. Include SEA-AD gene expression analysis, pathway enrichment, and visualizations (heatmaps, volcano plots). Add /notebooks viewer page. Link notebooks from hypothesis pages. See docs/planning/specs/d16_5_demo_jupyter_notebooks_spec.md\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:10:31.473018+00:00","updated_at":"2026-04-15T23:10:31.473018+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16_5_demo_jupyter_notebooks_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:27:15\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"448b4f1c-3703-4f1d-94b3-b694ea965554","title":"[Demo] Run debates for 3 undebated analyses","description":"3 analyses have no debates. Run 4-persona debates for: How do astrocyte-neuron metabolic intera, How do neurodegeneration gene expression, Which metabolic biomarkers can distingui. Use Forge tools for PubMed evidence.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:03:32.560154+00:00","updated_at":"2026-04-15T23:03:32.560154+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/448b4f1c_3703_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 00:49:21\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"bf44ca60-0945-46a7-85f4-0f6a587b56de","title":"[Demo] Add /demo/showcase route with polished overview of all demo flows","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T21:40:22.066030+00:00","updated_at":"2026-04-15T21:40:22.066030+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/bf44ca60_094_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 23:45:26\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"d354e238-f228-4664-93f6-dafe93c70b19","title":"[Demo] Add figure gallery to analysis detail pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T19:33:29.625551+00:00","updated_at":"2026-04-15T19:33:29.625551+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d354e238_f22_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 23:14:39\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"774ee90f-3706-446a-843c-6a8c9b2a8247","title":"[Demo] Fix malformed placeholder links in demo/showcase pages","description":"Demo/showcase currently emit literal /${r.link} hrefs that 404 due to unrendered placeholder syntax. Fix rendering to output valid internal links and verify /demo and /showcase no longer expose malformed placeholders.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T01:55:01.320293+00:00","updated_at":"2026-04-14T01:55:01.320293+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/774ee90f_370_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"5e271fd6edd8564e9e5c94679db7b6a488b62ca2\"], \"completion_shas_checked_at\": \"2026-04-14T01:55:01.301272+00:00\"}"},{"id":"536778a9-c91b-4a18-943e-51b740e444f8","title":"[Demo] Rebuild showcase notebooks with real Forge-powered analysis","description":"Replace 4 showcase analysis stubs with real notebooks using Forge tools (PubMed, STRING, Reactome, Gene Info, etc.), live DB queries, and executed analysis. See spec for full template and acceptance criteria.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T01:36:36.517120+00:00","updated_at":"2026-04-14T01:36:36.517120+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/showcase_notebook_rebuild_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"analysis\": 7}, \"completion_shas\": [\"f05f592fbc6d34194a56b647584434638bce7b2c\", \"e753280d8e9650092455a6555f67178669535f41\"], \"completion_shas_checked_at\": \"2026-04-14T01:36:36.499940+00:00\", \"completion_shas_missing\": [\"443abe3a9a7e7070501c10771b36dd594ed3e7cf\"]}"},{"id":"605ce1e1-a6cf-46eb-95c9-08c45a8a321c","title":"[Demo] Fix hypothesis detail page - missing price_history table","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T01:04:52.221666+00:00","updated_at":"2026-04-14T01:04:52.221666+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/605ce1e1_a6c_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"d864b8a8c4cda294a70203bae71f85456358d0a6\"], \"completion_shas_checked_at\": \"2026-04-14T01:04:52.202544+00:00\", \"completion_shas_missing\": [\"018c6f227a564e7009380c4778ee54e1dd97933a\", \"439440eff618f2b33ab28f026bda09908811e462\", \"bd3b12e8a2312e3d6e03d976b65a29e7828f680c\"]}"},{"id":"3d740e07-0d3f-4a59-a021-064a528b9218","title":"[Demo] Make biophysical demo route resilient when HTML artifact missing","description":"Ensure /demo/biophysical-model never returns 404 by serving a graceful fallback page and validating demo routes.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T00:30:08.489597+00:00","updated_at":"2026-04-14T00:30:08.489597+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3d740e07_0d3_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"466af089985a9a6ae47d55ab10a99b77b20aac98\"], \"completion_shas_checked_at\": \"2026-04-14T00:30:08.472976+00:00\"}"},{"id":"33e99cfc-4243-4191-81d4-a64c2614e482","title":"[Demo] Create /showcase page — unified gallery of all rich artifacts","description":"Build /showcase page displaying protein designs (21), models (5), datasets (6), dashboards (5), and featured notebooks. Include filters, search, and links to detail pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T00:29:28.890546+00:00","updated_at":"2026-04-14T00:29:28.890546+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/33e99cfc_424_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"90502cfa4d8e0027186452968bb4095b6a5e93ff\"], \"completion_shas_checked_at\": \"2026-04-14T00:29:28.870728+00:00\"}"},{"id":"def680a4-95f1-4a0f-b848-45f870d4d8e5","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T00:03:42.456820+00:00","updated_at":"2026-04-14T00:03:42.456820+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/def680a4-95f_demo_create_polished_analysis_walkthrou_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"4b9ccb59d93f3971f04b88dacde4d190c55b574b\"], \"completion_shas_checked_at\": \"2026-04-14T00:03:42.438772+00:00\"}"},{"id":"7a15efc1-8438-4815-b531-0c567dd0f4b0","title":"[Demo] Add SEA-AD analysis to walkthrough showcase as Demo Flow 1","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:55:19.505218+00:00","updated_at":"2026-04-13T23:55:19.505218+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7a15efc1_843_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"9528c90ead54df9f18d3cc7d8fc523866bd91d12\"], \"completion_shas_checked_at\": \"2026-04-13T23:55:19.486872+00:00\"}"},{"id":"360add5f-0d75-4808-9c08-d20283f60004","title":"[Demo] Generate HTML report for SEA-AD Gene Expression analysis","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:27:41.938104+00:00","updated_at":"2026-04-13T23:27:41.938104+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/360add5f_0d7_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"cdecf898d2ed9c95077fac000fce1a2288696c21\", \"eb7ff1ae83449b79a8df52f4e4dd7629734442e5\"], \"completion_shas_checked_at\": \"2026-04-13T23:27:41.921964+00:00\"}"},{"id":"fd1197a5-19b7-4f3c-b5dc-1fced03eabaa","title":"[Demo] Add Mol* 3D protein viewer to hypothesis pages for target proteins","description":"Embed RCSB PDB Mol* viewer on hypothesis detail pages that have a target_gene with known protein structures. Maps gene names to PDB IDs, loads the 3D structure viewer inline. Quest 17 task A17.1.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:25:37.631160+00:00","updated_at":"2026-04-13T23:25:37.631160+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/fd1197a5_19b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"completion_shas\": [\"8d7c79d5a7ef31d89a458a37d88a3b07760c547d\"], \"completion_shas_checked_at\": \"2026-04-13T23:25:37.613890+00:00\"}"},{"id":"b6ee8d4e-54f0-4e86-a2bf-59780e156df5","title":"[Demo] Add interactive Mol* 3D protein viewer to top hypothesis pages","description":"Quest 17 task A17.1: Embed Mol* 3D protein viewer on the top 3 hypothesis detail pages (LRP1, TREM2, PARP1). Load PDB structures for target proteins. This is a high-priority demo artifact that makes hypothesis pages visually compelling.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:17:53.576298+00:00","updated_at":"2026-04-13T23:17:53.576298+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b6ee8d4e_54f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"completion_shas\": [\"a8d3dcdc4c4252861407eb2c1e213829150d0301\"], \"completion_shas_checked_at\": \"2026-04-13T23:17:53.558942+00:00\"}"},{"id":"7d07b3f5-513c-4c9f-9a89-c5fe732c292b","title":"[Demo] Add debate detail page at /debate/{id}","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:16:23.079755+00:00","updated_at":"2026-04-13T23:16:23.079755+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7d07b3f5_513_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"9598c2f9203acfcf3bed3ab7bc6325afe5693bca\", \"b4ea09d2076a8d9b8092b49533c6b6d1d2930669\"], \"completion_shas_checked_at\": \"2026-04-13T23:16:23.062670+00:00\"}"},{"id":"7f3fe7b0-1b85-4d05-9499-525fccbfd4f4","title":"[Demo] Create guided demo walkthrough page at /demo","description":"Create a /demo page that serves as a guided walkthrough of all SciDEX features. Should link to showcase hypotheses, analyses, wiki pages, and artifacts. Shows the five-layer architecture in action.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:01:08.032322+00:00","updated_at":"2026-04-13T23:01:08.032322+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7f3fe7b0_1b8_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"a3592486567ddbec749e4a0dd2aeebc0b834e8d9\", \"ea8e59ee3c28311e3b8db3af684b57a70703d051\"], \"completion_shas_checked_at\": \"2026-04-13T23:01:08.014892+00:00\"}"},{"id":"6df0750b-ee33-4dc2-b344-8d8e0675abba","title":"[Demo] Include /demo and /artifacts in automated page-health checks","description":"Ensure recurring site/page validation explicitly covers demo showcase and artifacts routes to preserve end-to-end demoability.","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 13:23:07","updated_at":"2026-04-04T13:12:51.323870+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6df0750b_ee3_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"d01caac3-02aa-4091-8913-c8e3dede5023","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. 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These are hero content.","status":"archived","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 10:00:02","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"cdcb3856-505d-44b9-bc1d-41c2f2f9bb29","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 10:04:51","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"6a14cfb2-4763-481a-aff4-15894217a19f","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:38:14","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"5810fbef-2526-43d7-a14c-6e5d19b1dcca","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"d16-05-7CF9AEE5","title":"[Demo] Create Jupyter notebook viewer and demo notebooks","description":"Build /notebook/{id} page that renders .ipynb files with code cells, outputs, plots, and markdown. Create 2-3 demo notebooks: (1) Gene expression analysis of TREM2 in AD, (2) Allen Brain Atlas cell type query, (3) Pathway enrichment for top hypothesis targets. Store in notebooks/ directory, register in DB.","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:54:05","updated_at":"2026-04-02 09:42:41","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"d16-06-3DD3879C","title":"[Demo] Immune atlas neuroinflammation analysis","description":"Analyze immune cell subtypes in neurodegeneration context. Focus on microglia subtypes (DAM, homeostatic, inflammatory), astrocyte reactivity states, T-cell infiltration. Use existing TREM2 and complement cascade hypotheses as anchors. Produce inflammatory pathway mermaid diagrams. 3-5 new hypotheses connecting immune findings to disease mechanisms.","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 10:00:17","updated_at":"2026-04-02 09:42:41","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"3506b244-904a-4f8c-9c70-546b9e5463e0","title":"[Demo] Add live statistics and hypothesis preview cards to demo walkthrough page","description":"The /demo walkthrough page should show real-time statistics from the database (hypothesis count, debate count, analysis count, wiki pages, KG edges) and include preview cards for the top 3 hypotheses with their scores, target genes, and pathway diagrams. This makes the demo page feel alive and connected to real data rather than static.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:41:45.103990+00:00","updated_at":"2026-04-16T00:41:45.103990+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3506b244_904_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 02:20:17\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"d0a83f6a-7855-421e-ae9d-fba85d67e3c8","title":"[Demo] Rebuild notebook: Gut-brain axis Parkinson","description":"Rebuild notebook for analysis SDA-2026-04-01-gap-20260401-225149 (Gut-brain axis Parkinson). Current notebook is a stub with hardcoded data. Replace with real Forge-tool-powered analysis: 20 hyps, 494 edges, PubMed + STRING + Reactome + Allen Brain. Query DB for hypotheses/edges/debate, run real analysis, produce genuine plots. See showcase_notebook_rebuild_spec.md.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:30:35.615342+00:00","updated_at":"2026-04-16T00:30:35.615342+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d0a83f6a_785_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"analysis\": 7}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 02:46:32\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"fe87ae66033eb46785549eb420be3ad9f6988aa0\", \"e753280d8e9650092455a6555f67178669535f41\"], \"completion_shas_checked_at\": \"2026-04-16T00:30:35.602056+00:00\"}"},{"id":"65e3ca0a-9c58-45e7-ad55-6af6ffee2744","title":"[Demo] Fix broken walkthrough links on demo page — conditional link for non-hero analyses","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:16:18.682180+00:00","updated_at":"2026-04-16T00:16:18.682180+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/65e3ca0a_9c5_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 02:35:06\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"02b646d8-96f4-48aa-acf7-a13e19d8effa","title":"[Demo] Rebuild notebook: Microglial priming early AD","description":"Rebuild notebook for analysis SDA-2026-04-04-gap-20260404-microglial-priming-early-ad (Microglial priming early AD). Current notebook is a stub with hardcoded data. Replace with real Forge-tool-powered analysis: 14 hyps, 106 edges, PubMed + STRING + Reactome + UniProt. Query DB for hypotheses/edges/debate, run real analysis, produce genuine plots. See showcase_notebook_rebuild_spec.md.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:38:32.295515+00:00","updated_at":"2026-04-14T03:38:32.295515+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/02b646d8_96f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"analysis\": 7}, \"completion_shas\": [\"a67ee42420d175afa012e143c14046351b536634\", \"9ab35758fe5df9def57c54e250bac949b73f7441\", \"e753280d8e9650092455a6555f67178669535f41\"], \"completion_shas_checked_at\": \"2026-04-14T03:38:32.276786+00:00\", \"completion_shas_missing\": [\"1fb21b59ba6a9db700221f56447df781687d1ac5\"]}"},{"id":"4d2d2963-364e-4b5c-be35-d6be6e38932b","title":"[Demo] Rebuild notebook: Aging mouse brain","description":"Rebuild notebook for analysis SDA-2026-04-03-gap-aging-mouse-brain-v3-20260402 (Aging mouse brain). Current notebook is a stub with hardcoded data. Replace with real Forge-tool-powered analysis: 28 hyps, 216 edges, PubMed + Allen Brain + STRING + Open Targets. Query DB for hypotheses/edges/debate, run real analysis, produce genuine plots. See showcase_notebook_rebuild_spec.md.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:53:19.483516+00:00","updated_at":"2026-04-14T02:53:19.483516+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4d2d2963_364_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"analysis\": 7}, \"completion_shas\": [\"f1d97efea301f73d8989b90c2c0e60b35e3de6d2\", \"e753280d8e9650092455a6555f67178669535f41\"], \"completion_shas_checked_at\": \"2026-04-14T02:53:19.463978+00:00\", \"completion_shas_missing\": [\"2470a0ba4e39a95ba087d00060028df82f9e264c\"]}"},{"id":"d8c5165c-ea11-47c2-a972-9ce4c3ab8fad","title":"[Demo] Rebuild notebook: CRISPR neurodegeneration","description":"Rebuild notebook for analysis SDA-2026-04-03-gap-crispr-neurodegeneration-20260402 (CRISPR neurodegeneration). Current notebook is a stub with hardcoded data. Replace with real Forge-tool-powered analysis: 14 hyps, 432 edges, PubMed + Gene Info + ClinVar + Clinical Trials. Query DB for hypotheses/edges/debate, run real analysis, produce genuine plots. See showcase_notebook_rebuild_spec.md.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:49:51.457034+00:00","updated_at":"2026-04-14T02:49:51.457034+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d8c5165c_ea1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"analysis\": 7}, \"completion_shas\": [\"5cd47dbf2618f971ec7b44529a1614aeba7fd726\", \"e753280d8e9650092455a6555f67178669535f41\"], \"completion_shas_checked_at\": \"2026-04-14T02:49:51.436877+00:00\", \"completion_shas_missing\": [\"f1ecdf4c2ac908c9eaa4dcdf7a567f42e04bfdb0\"]}"},{"id":"9f68c05c-cc98-4773-9b06-0e88439c9b94","title":"[Demo] Enrich showcase analyses with top hypothesis evidence summaries","description":"For each of the 4 WALKTHROUGH_IDS analyses, generate/verify evidence summaries for the top hypothesis showing evidence_for/against counts, citations, and key findings. Update the /showcase page to show richer hypothesis metadata cards with evidence balance scores.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:32:23.729002+00:00","updated_at":"2026-04-14T02:32:23.729002+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9f68c05c_cc9_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"d9fc81385837db2b39692942f425f8150469c524\", \"d088949382669657616da75265fa53dbbe0bf354\", \"9c5b88722acbfa7e958de54017363e01f728a075\"], \"completion_shas_checked_at\": \"2026-04-14T02:32:23.709752+00:00\"}"},{"id":"7e3a6790-cff0-42ab-8125-a585b51d62eb","title":"[Demo] Link notebooks from analysis detail pages","description":"Modify analysis detail page template to display associated notebooks (via analysis_id foreign key). Show notebook title, preview, and link to /notebook/{id}.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:29:58.139962+00:00","updated_at":"2026-04-14T02:29:58.139962+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7e3a6790_cff_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"ccfc2a576f68b96effd6b6da27f36f1a682bc64f\", \"9d8d55a8ecab110a2f8fc9477e075a3019e660f7\"], \"completion_shas_checked_at\": \"2026-04-14T02:29:58.123148+00:00\"}"},{"id":"bbb6f3eb-4398-407d-931a-24d60c5ea70e","title":"[Demo] Harden smoke check with localhost fallback","description":"Improve smoke_check.py so demo route verification works in environments where localhost:8000 is not reachable by adding robust base URL fallback and clearer diagnostics.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:27:09.286853+00:00","updated_at":"2026-04-14T02:27:09.286853+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/bbb6f3eb_439_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"7c1a61d0956e9075a0b8315ee71390028eec7777\"], \"completion_shas_checked_at\": \"2026-04-14T02:27:09.269807+00:00\"}"},{"id":"8e866f0a-91f6-4186-829c-392de6a7c67c","title":"[Demo] Add mermaid pathway diagrams to hypothesis detail pages","description":"A17/D16.4: Add inline mermaid pathway diagrams to hypothesis detail pages showing the mechanism cascade for the hypothesis target gene. Query knowledge_edges for the target gene and render as mermaid flowchart.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:23:30.980558+00:00","updated_at":"2026-04-14T02:23:30.980558+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8e866f0a_91f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"fbc35c3de6b9a4fd5052e792f4515b5939bba11e\"], \"completion_shas_checked_at\": \"2026-04-14T02:23:30.961669+00:00\"}"},{"id":"a750a1fa-9137-4a0b-a406-f430fbb046de","title":"[Demo] Fix broken walkthrough links on demo page — only link walkthroughs that exist","description":"Demo page generates walkthrough links for all showcase analyses, but only 3 are in WALKTHROUGH_IDS. Analyses not in the list return 404. Only show walkthrough link if the analysis has a walkthrough.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:13:31.580134+00:00","updated_at":"2026-04-14T02:13:31.580134+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a750a1fa_913_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"471e21f65d987f92b45c27246f593f4b759dc583\"], \"completion_shas_checked_at\": \"2026-04-14T02:13:31.561456+00:00\"}"},{"id":"a17ab8d1-1e45-4dde-b3f7-da28c3daae37","title":"[Demo] Add mermaid pathway diagrams to top hypothesis pages","description":"Add rendered mermaid.js pathway diagrams to the top hypothesis detail pages showing mechanism cascades. E.g., for APOE4 hypothesis: APOE4 -> hypolipidation -> reduced Abeta clearance -> plaque formation. Use mermaid CDN, render inline on hypothesis pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:08:12.729729+00:00","updated_at":"2026-04-14T02:08:12.729729+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17ab8d1_1e4_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"75591735a0f6b3bda768355cd5cc41a64fd6e9fb\"], \"completion_shas_checked_at\": \"2026-04-14T02:08:12.709836+00:00\"}"},{"id":"4940371b-9637-43ba-ba4b-34b47a87e938","title":"[Demo] Add PubMed citation references to top 10 hypothesis descriptions","description":"148/149 hypotheses lack PubMed references. Per Quest 16 D16.1, hero hypotheses need 10+ PubMed citations. Use PubMed API to find relevant papers for top 10 hypotheses by score, add PMID references with titles and key findings to each description.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:05:14.813075+00:00","updated_at":"2026-04-14T02:05:14.813075+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4940371b_963_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"bb98544330e5f051ede0b6f7cbcc393c2e0cac29\"], \"completion_shas_checked_at\": \"2026-04-14T02:05:14.798628+00:00\", \"completion_shas_missing\": [\"82e2b65f863e6366235e5c84b3a18196f93f9280\"]}"},{"id":"d16-07-E4F36058","title":"[Demo] Neural dynamics circuit analysis with Allen OpenScope","description":"Use Allen Institute Neural Dynamics papers to analyze circuit-level changes in neurodegeneration. Focus on hippocampal circuit disruption, cortical dynamics, sensory processing changes. Connect to existing KG entities. Produce 2-3 hypotheses about circuit-based therapeutic targets.","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:54:06","updated_at":"2026-04-02 09:42:41","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"b1c46945-4466-4a28-84f9-5e4cef3dce87","title":"[Demo] Harden demo smoke checks with internal CTA link validation","description":"Quest 16/17 reliability: extend scripts/demo_smoke_check.py to validate key internal links discovered on /demo and /showcase (status, latency, size), add explicit reporting, and verify script passes on localhost.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:51:13.150958+00:00","updated_at":"2026-04-17T04:51:13.150958+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b1c46945_446_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"5722c169-9e5f-42f9-9f3d-4f96d64f1ba6","title":"[Demo] Enrich 10 thin hypothesis descriptions to 1000+ words","description":"IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists.\n\n29 hypotheses have <500 char descriptions. Expand with mechanisms, evidence, clinical relevance.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:41:11.321902+00:00","updated_at":"2026-04-17T04:41:11.321902+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"cafef3bf-932b-4bcf-9bda-6946de13a573","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:37:10.588005+00:00","updated_at":"2026-04-17T04:37:10.588005+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{}"},{"id":"4ac1f8b5-dd8b-4822-a1a4-4fd3a8c8b48c","title":"[Demo] Repair missing top-nav links for demo surfaces","description":"Audit top navigation links on core demo pages and fix broken/incorrect href targets to improve end-to-end demoability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:30:27.874655+00:00","updated_at":"2026-04-17T04:30:27.874655+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4ac1f8b5_dd8_spec.md","provider":"any","payload_json":"{}"},{"id":"12bd92f9-109b-4727-a558-d56762df7f8f","title":"[Demo] Fix /demo.html smoke-check content assertion","description":"Resolve smoke_check failure for /demo.html missing expected demo marker while preserving page behavior.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:29:46.785684+00:00","updated_at":"2026-04-17T04:29:46.785684+00:00","summary":"","completion_notes":"Verification confirms task is already done on origin/main (commit 03b2dc687, the latest main HEAD). The fix was previously applied by commit 42761e189 and is now part of the main branch. The /demo page correctly generates 5 hypothesis snippets matching the HYPOTHESIS_SNIPPET_PATTERN, with no raw markdown artifacts.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/12bd92f9_109_spec.md","provider":"any","payload_json":"{}"},{"id":"8ee4c367-46a4-4dd9-a242-27b3c0ff5637","title":"[Demo] Create /forge page showing tool registry and usage","description":"Build /forge page displaying all 48 registered tools from skills table. Show tool name, type, times_used, and examples of analyses using each tool.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:23:58.270574+00:00","updated_at":"2026-04-17T04:23:58.270574+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8ee4c367_46a_spec.md","provider":"any","payload_json":"{}"},{"id":"a0102e96-cdf6-4f11-ae1f-07d26eeb7008","title":"[Demo] Add evidence matrix table to hypothesis pages with citation quality scoring","description":"Quest 17 A17.6: Add a structured evidence matrix table to hypothesis detail pages showing all citations with quality x relevance scoring. Display evidence_for and evidence_against items in a tabular format with strength ratings, source journals, year, and PMID links. Replaces plain bullet list with a rich, sortable evidence matrix.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:23:38.956848+00:00","updated_at":"2026-04-17T04:23:38.956848+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a0102e96_cdf_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"87cc5967-a187-4e03-ad40-5f1de4981034","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:21:55.955578+00:00","updated_at":"2026-04-17T04:21:55.955578+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/87cc5967-a18_demo_generate_figures_for_all_analyses_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 5}}"},{"id":"217b0e36-849a-4eed-bbcb-a6a1c7baf80a","title":"[Demo] Add guided five-layer quickstart rail on demo page","description":"Improve /demo with an explicit start-here quickstart rail linking the five layers and primary walkthrough entry points for end-to-end demoability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:19:31.003402+00:00","updated_at":"2026-04-17T04:19:31.003402+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/217b0e36_849_spec.md","provider":"any","payload_json":"{}"},{"id":"0628f2ea-1b8e-42c8-97f8-b199b3a766fa","title":"[Demo] Harden link checker timeout handling to always emit partial report","description":"Ensure link_checker writes logs/link-check-latest.json and exits cleanly when close to runtime deadline by skipping expensive LLM analysis/task creation under low remaining budget.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:16:45.512815+00:00","updated_at":"2026-04-17T04:16:45.512815+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0628f2ea_1b8_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"06d4e19e-1782-4768-b233-864dfc787fe9","title":"[Demo] Add structured evidence matrix with citation quality scores to hypothesis pages","description":"Quest 17 task A17.6: Build a structured evidence matrix component on hypothesis detail pages. Show citations in a table with columns: citation title, PMID link, relevance score, quality score, evidence type (supporting/opposing). Replace the current plain-text evidence lists with a rich, sortable table. This makes hypothesis pages much more compelling for demos.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:59:41.306805+00:00","updated_at":"2026-04-16T00:59:41.306805+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/06d4e19e_178_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 03:25:48\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"89c6c50ca6b7a22226c395012f6f9fbb489d77bd\"], \"completion_shas_checked_at\": \"2026-04-16T00:59:41.284620+00:00\"}"},{"id":"68ae1f33-6182-43f5-9b40-ab7cd333faec","title":"[Demo] Expand Mol* 3D protein viewer PDB mappings for top 20 hypothesis targets","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:53:56.010477+00:00","updated_at":"2026-04-16T00:53:56.010477+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/68ae1f33_618_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 03:24:12\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"727de71f8e353a593a35cc83d1fdf33f8bc2ccc2\"], \"completion_shas_checked_at\": \"2026-04-16T00:53:55.989948+00:00\"}"},{"id":"0e962abd-b625-43d5-8515-20631cf736e9","title":"[Demo] Build analysis walkthrough page at /walkthrough/{id}","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:45:59.966196+00:00","updated_at":"2026-04-16T00:45:59.966196+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0e962abd_b62_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 03:56:31\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"788144ddf07b4b022f3cbccbca698931449be190\", \"2b1ffee5583d8a3a4f611a6f7514001572bc065e\"], \"completion_shas_checked_at\": \"2026-04-16T00:45:59.947039+00:00\"}"},{"id":"90ca80d5-bc47-4ab9-9d8c-fd81b4cc3c10","title":"[Demo] Generate figures for top 20 analyses to populate artifact gallery","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T05:15:19.824434+00:00","updated_at":"2026-04-14T05:15:19.824434+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/90ca80d5_bc4_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"b2dc83e44d7b023058ac2e754e7fb415daed3799\"], \"completion_shas_checked_at\": \"2026-04-14T05:15:19.807225+00:00\", \"completion_shas_missing\": [\"349e8dd8e83856c20787a25725be7d3c5d27e50a\"]}"},{"id":"89109399-28f5-4815-9b25-40c88874900f","title":"[Demo] Protein design gallery with 3D viewer integration","description":"Create /protein-designs page showing all 21 designs. Integrate TREM2 3D viewer for designs with PDB structures. Display sequences, mutations, stability scores, binding affinities.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T04:48:25.154195+00:00","updated_at":"2026-04-14T04:48:25.154195+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/89109399_28f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"completion_shas\": [\"5e3a118b5f8fc6ae5bc2f91cdfce8e197d4e5803\"], \"completion_shas_checked_at\": \"2026-04-14T04:48:25.137137+00:00\", \"completion_shas_missing\": [\"13c4ea62eac64e7d63f219fed36644a493aee0ff\"]}"},{"id":"6d25ffd0-fb79-451a-b3cd-ddb1baff286c","title":"[Demo] Expand walkthroughs to 5 hero analyses — add sleep disruption, digital biomarkers","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T04:19:14.921071+00:00","updated_at":"2026-04-14T04:19:14.921071+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6d25ffd0_fb7_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"1093901bfee47ef2326b517abe69f7d49596d2b4\", \"59566c540ebfdc5ad429ffd56b1dac02dcde6ca2\", \"242b5b9a8829072ec776c18e12968ee67fea1702\"], \"completion_shas_checked_at\": \"2026-04-14T04:19:14.901735+00:00\"}"},{"id":"a4dfe11e-dd75-43d8-aeac-5456932ce199","title":"[Demo] Build guided demo walkthrough page at /demo","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:40:27.716133+00:00","updated_at":"2026-04-14T03:40:27.716133+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a4dfe11e_dd7_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"0752e93c5a15eceb4945a4fc322edf84caebe75b\"], \"completion_shas_checked_at\": \"2026-04-14T03:40:27.698061+00:00\"}"},{"id":"e6265b0c-1c60-42f9-8550-06fd21b68f48","title":"[Demo] Add featured discoveries carousel to home page","description":"Add a 'Featured Discoveries' section to the home page showing top 3 hypotheses with scores, pathway diagrams, and linked analyses. This gives visitors an immediate sense of the platform's scientific depth.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:36:09.148697+00:00","updated_at":"2026-04-14T03:36:09.148697+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e6265b0c_1c6_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"cc0451cd3d6c5fbd3241628cd91185aa0f566c68\"], \"completion_shas_checked_at\": \"2026-04-14T03:36:09.129708+00:00\"}"},{"id":"5c2c16ad-76c1-4fd3-a75d-b9a721a0196e","title":"[Demo] Generate HTML renderings for all 39 analysis notebooks","description":"Convert all .ipynb notebooks in site/notebooks/ to HTML for web viewing. Many notebooks exist but lack HTML counterparts. Run jupyter nbconvert for all missing HTML files.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:28:04.887060+00:00","updated_at":"2026-04-14T03:28:04.887060+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5c2c16ad_76c_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"4a2d232eb8c7a876523fa313d5f7830e67856212\", \"be3c6a25051dfaea94b822f819187619ecb755f3\", \"b84035ff3a5a1b6f31324c9c1c9ce7e7258d02a3\"], \"completion_shas_checked_at\": \"2026-04-14T03:28:04.870717+00:00\"}"},{"id":"0a9b1fd7-3ea6-431e-8944-d671068548c9","title":"[Demo] Create /walkthrough demo tour page linking all five layers","description":"D16.9: Build an end-to-end demo walkthrough page at /walkthrough that guides visitors through SciDEX's five layers with showcase content. Links to best hypotheses, debates, tools, KG, and governance.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:23:15.043759+00:00","updated_at":"2026-04-14T03:23:15.043759+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0a9b1fd7_3ea_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"0147141b5d95fcee96825099bba7d0c2bb362122\", \"a253cbb2779dcc8620bf6a886aa6fac4f3f56af6\"], \"completion_shas_checked_at\": \"2026-04-14T03:23:15.025482+00:00\"}"},{"id":"d16-26-DDSH0001","title":"[Demo] Create live dashboard: Knowledge Growth Monitor","description":"Build a dashboard artifact that shows real-time SciDEX knowledge growth: paper count, KG edge count, hypothesis count, and trend sparklines. Data sources: sql_query against scidex.db metrics tables. Dashboard auto-refreshes every 5 minutes. Embed it in the demo authored paper to show a living document. Demonstrates: dashboard creation, data source binding, auto-refresh, embedding in papers. Depends on: a17-28-DASH0001, a17-30-DREF0001.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:14:28.857683+00:00","updated_at":"2026-04-14T03:14:28.857683+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-26-DDSH0001_dashboard_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"completion_shas\": [\"2aaccb2fa74cb2ff59459bcb80cb813a525bcd00\", \"8b9af1467b299dcf82c365d8fd95cded16d468d7\", \"47f7bb0ed24fca6b9646a07efa2652326896161c\", \"3c6b6be639cd27545e8b3991aa170f209cff19bd\"], \"completion_shas_checked_at\": \"2026-04-14T03:14:28.838018+00:00\"}"},{"id":"d16-20-AVER0001","title":"[Demo] Versioned artifact demo: create protein design with 3 iterations","description":"Register a protein design artifact (e.g. an engineered TREM2 variant for AD) with 3 successive versions showing iterative refinement: v1 (initial design from AlphaFold prediction), v2 (stability-optimized via mutations), v3 (binding-affinity tuned). Each version has different metadata (mutations, predicted_stability, binding_affinity). Show version timeline and diff on the artifact page. Exercises: artifact versioning, protein_design type, version browser UI. Depends on: a17-18-VERS0001, a17-19-TYPE0001, a17-20-VAPI0001.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:09:42.731411+00:00","updated_at":"2026-04-14T03:09:42.731411+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-20-AVER0001_versioned_protein_design_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"completion_shas\": [\"b05ae0e344158622934e32dec372b9f6a94e7597\", \"8dc7cfd7fa9e3913a219208b9a8f6a7267687518\", \"3ed28a8ea3eed4800e33c0749bd2398b315c2aa3\", \"e9e0997c789d373ea5b286e8ceb127bf75619aec\"], \"completion_shas_checked_at\": \"2026-04-14T03:09:42.712185+00:00\"}"},{"id":"d16-24-PROV0001","title":"[Demo] End-to-end provenance demo: trace reasoning chain from paper to model","description":"Create a showcase provenance walkthrough: Paper (PubMed) -> KG edges (extracted) -> Hypothesis (generated) -> Dataset (referenced) -> Analysis (executed) -> Model (built) -> Figure (produced). Display the full DAG with artifact versions pinned at each step. Demonstrate verify_reproducibility() showing all inputs are intact. This is the capstone demo for the artifact versioning system. Depends on: a17-24-REPR0001, d16-23-BMOD0001.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:55:24.707966+00:00","updated_at":"2026-04-14T02:55:24.707966+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-24-PROV0001_end_to_end_provenance_demo_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"524da90d0754a2e8bb249a8d935807f866cb43f6\", \"a418f9b55766709979138f5972b2574b9e500049\", \"c8c5b62caf3ee43be0f122c7aef0f630b2807664\"], \"completion_shas_checked_at\": \"2026-04-14T02:55:24.689630+00:00\"}"},{"id":"4cdb9f30-7c4a-40bd-8183-1a95e2afde37","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03T05:59:37.793810","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"7d7ff29c-11aa-4e89-9772-1a245a3c0fb7","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03T05:27:21.713051","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"8afebaa6-1823-40a5-a85d-7291dd419b96","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 13:39:59","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"2996c642-29aa-4ab1-9f52-6ce47419f6b1","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 13:59:32","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"e8d6786c-52f1-4238-8877-0ecc9d7faf92","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:54:46","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"8261beb1-a260-4a1b-95fc-ab7b9624a2da","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:15:07","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"53762ad0-f9a4-4ba3-befb-5f5cebad768b","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. 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Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:58:04","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"aa5102eb-5b1a-4b16-b612-c1de8bef85e1","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:37:26","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"b6a8a881-55b8-4139-aea8-14778f6823d9","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:44:56","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"ce2ea11b-c4c7-46b9-a65a-758bc4bd9fa2","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:51:32","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"8f20855c-2c56-49a9-a482-ebd967d6ca88","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:59:42","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"fc4fd5c3-c5cf-431c-bc94-8cae8add4603","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:58:09","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"b2e872c8-a897-4641-b89a-8e9850804722","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 10:05:51","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"f55201b3-7387-4019-8e00-a0eac54db601","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:39:17","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"e9bcbacd-cc96-413f-9604-0d6f4ef3f560","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"d16-08-7273E0A5","title":"[Demo] Enrich top 20 wiki pages with mermaid diagrams and cross-links","description":"Add pathway diagrams (mermaid), infoboxes, cross-links to hypotheses/analyses for: TREM2, APOE, tau-propagation, neuroinflammation, microglia, autophagy, AD-cascade, alpha-synuclein, BBB, glymphatic, mitochondria, PARP1, LRP1, SMPD1, CYP46A1, complement-system, senescence, epigenetic-clocks, GBA, TDP43. Each should have at least one mermaid diagram and links to relevant hypotheses.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:48:45","updated_at":"2026-04-02 09:42:41","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}}"},{"id":"8aba1c2f-6223-4836-bbd8-e0c02e958a44","title":"[Demo] Add Mol* 3D protein viewers to walkthrough pages","description":"The walkthrough pages (our primary demo pages) don't have inline Mol* 3D protein structure viewers. The challenge detail pages already have this. We need to add inline Mol* viewers for key target genes in the walkthrough protein section, using the existing PDB mapping in api.py. This will significantly improve the demo quality for Quest 16.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:02:40.572198+00:00","updated_at":"2026-04-16T10:02:40.572198+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8aba1c2f_622_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"completion_shas\": [\"0235fc86ff953a59eecc61f0907d2ecef4f37723\", \"1650d2174064e836a7a3232d04ce447284749de2\", \"3c90807e76c2375592959842f830baef0aa09ab0\", \"afebddfeca53bdebe896a36fd63d532b3d2559fa\"], \"completion_shas_checked_at\": \"2026-04-16T10:02:40.553931+00:00\"}"},{"id":"b0e67854-a3ef-4c1e-ae00-970b9d5d7e10","title":"[Demo] Add multi-hypothesis radar chart to analysis detail pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:46:14.376347+00:00","updated_at":"2026-04-16T09:46:14.376347+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b0e67854_a3e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"d9ad02ce-6e8f-45ae-ba0e-94924a0bceaf","title":"[Demo] Add /search and /pitch to demo smoke coverage","description":"Expand scripts/demo_smoke_check.py route coverage to include /search and /pitch; validate command output and keep timeout-safe usage.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:36:30.870754+00:00","updated_at":"2026-04-16T09:36:30.870754+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d9ad02ce_6e8_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"0ef6d46de\"], \"completion_shas_checked_at\": \"2026-04-16T09:36:30.852017+00:00\"}"},{"id":"896b24fa-9055-4834-8b6e-c4374165f200","title":"[Demo] Audit and repair demo page route regressions","description":"Slot 3 batch task: run targeted demo page health checks, fix any route/template regressions, and verify core demo pages return healthy status codes.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:27:05.583533+00:00","updated_at":"2026-04-16T09:27:05.583533+00:00","summary":"","completion_notes":"Verified 18 demo routes (/, /exchange, /gaps, /graph, /analyses/, /atlas.html, /how.html, /demo, /demo/walkthrough, /demo/showcase, /entity/TREM2, /hypothesis, /forge, /senate, /market, /api/health, /api/status, /atlas). All returned acceptable HTTP codes. Task content (spec file) is on origin/main at docs/planning/specs/896b24fa_905_spec.md. Individual task commits (ca4377558, 0f51a649c) exist in refs/check/fd26f10d0ea6 — not as direct main-branch commits due to squash merge path, but the work is verified on main.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/896b24fa_905_spec.md","provider":"any","payload_json":"{}"},{"id":"73f5ece2-7342-463e-b45c-b716b9599287","title":"[Demo] Validate key demo routes and fix render/content regressions","description":"Check /demo, top hypothesis pages, and top analyses for status/content quality; fix any regressions in routing or rendering and document results.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:21:29.866519+00:00","updated_at":"2026-04-16T09:21:29.866519+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/73f5ece2_734_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"bb26a052-4f82-4156-bebc-133afaeb9e9f","title":"[Demo] Versioned artifact demo: create protein design with 3 iterations","description":"Create a showcase protein design artifact (TREM2 variant) with 3 successive versions demonstrating iterative refinement and the version browser UI.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:15:53.524146+00:00","updated_at":"2026-04-16T09:15:53.524146+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-20-AVER0001_versioned_protein_design_demo_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"74864dee1\"], \"completion_shas_checked_at\": \"2026-04-16T09:15:53.507047+00:00\"}"},{"id":"5d834fd8-c5f0-4e2e-9fd5-686c6f76ae44","title":"[Demo] Add supporting evidence panel to hypothesis pages","description":"The evidence_for/evidence_against columns store JSON arrays with pmid, claim, source, year, strength. Add a 'Supporting Evidence' section to /hypothesis/{id} pages showing top 5 evidence_for papers and top 3 evidence_against papers with their claims and journal/year. This makes hypothesis quality visible to demo viewers.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:13:52.607987+00:00","updated_at":"2026-04-16T09:13:52.607987+00:00","summary":"","completion_notes":"Verified feature already present on main at origin/main (commit 9a3b0cb53). No new commits needed. The work was done previously and is live.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5d834fd8_c5f_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"9a3b0cb53\"], \"completion_shas_checked_at\": \"2026-04-16T09:13:52.587815+00:00\"}"},{"id":"65eb10aa-aef7-4d0e-84b4-77a6dae0af1a","title":"[Demo] Exclude non-HTML CTA assets from demo smoke quality checks","description":"scripts/demo_smoke_check.py should not fail on .ipynb/.json/static asset links extracted from /demo and /showcase CTAs; validate only page-like internal routes for content-size/latency checks.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:11:32.107715+00:00","updated_at":"2026-04-16T09:11:32.107715+00:00","summary":"","completion_notes":"Verified: commit ecba66083 IS on main (merge-base --is-ancestor returns true). The file was later archived from scripts/demo_smoke_check.py → scripts/archive/oneoff_scripts/demo_smoke_check.py at commit 1178a0c46. The NON_PAGE_SUFFIXES and is_page_like_path filtering logic is present in the archived file on main. Audit ORPHAN_BRANCH flag appears to be a false positive — the implementation landed on main correctly.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/65eb10aa_aef_spec.md","provider":"any","payload_json":"{}"},{"id":"ef614bb0-06d7-43f1-bae5-4a900eca8d7b","title":"[Demo] Fix broken internal links on showcase and dashboard pages","description":"Targeted demo-link quality pass: replace stale senate.html/hypothesis links that 404 with live routes or remove dead CTAs; verify affected pages return 200/3xx.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:09:34.397913+00:00","updated_at":"2026-04-16T09:09:34.397913+00:00","summary":"","completion_notes":"Task was already complete. All ef614bb0 commits (17c11d39f, 7e21443f2, f451f8025, 5cd677a2a) are in origin/main. The audit's NO_COMMITS flag was a false positive — the work landed correctly on main before this branch was created. smoke_check.py 20/20 pass, no broken links remain. Branch already pushed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ef614bb0_06d_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"6e95afff-d644-4e03-93f8-0c6591bd0ae0","title":"[Demo] Repair demo page readiness issues discovered by CI sweep","description":"Quest 16 batch: run targeted demo page verification, fix concrete rendering/content/link defects, validate health checks, and document completion.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:05:55.624356+00:00","updated_at":"2026-04-16T09:05:55.624356+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6e95afff_d64_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"9a3b0cb53e6e880f24abdb50031e32dd3858020c\"], \"completion_shas_checked_at\": \"2026-04-16T09:05:55.607745+00:00\"}"},{"id":"068b7689-7035-4c49-9e5c-402c17d6ab5b","title":"[Demo] Fix walkthrough route 500 for hero analyses","description":"walkthrough_detail has mis-indented analysis lookup causing UnboundLocalError for hero walkthrough IDs; patch route and verify /demo linked walkthrough pages return 200\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:04:36.353893+00:00","updated_at":"2026-04-16T09:04:36.353893+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/068b7689_703_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"9aa0e113-0dc6-4e3a-ad2a-4261b7b42093","title":"[Demo] Add deterministic demo route smoke check script","description":"Build a bounded-time smoke-check script for demo-critical routes with status code, latency, and key content assertions to improve end-to-end demo reliability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:49:26.734143+00:00","updated_at":"2026-04-16T08:49:26.734143+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9aa0e113_0dc_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"7410645d23e86c7b756826c5e1bdd9f12ddda677\", \"ea4405dd868ef331ea9c4d2e4de16383b2914864\", \"3e0845faa7cc2fee2f7af0f19479fc1a5caddc4c\"], \"completion_shas_checked_at\": \"2026-04-16T08:49:26.582292+00:00\"}"},{"id":"a3909fdc-d626-4d68-91b4-15442f1dc1c7","title":"[Demo] Fix /agora /agents /missions /experiments 500 errors: create missing DB tables","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:43:25.243937+00:00","updated_at":"2026-04-16T08:43:25.243937+00:00","summary":"","completion_notes":"Verified all 4 pages return 200. The fix (commit fc79f50fa) landed on main via squash merge from this branch — audit incorrectly flagged as ORPHAN_BRANCH. The tables `agent_personas`, `missions`, `experiments` exist in scidex.db and the pages work.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a3909fdc_d62_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"91ebb28f-f2af-4453-86f3-38f130fa9c4d","title":"[Demo] Harden scidex status when scidex.db is malformed","description":"Make scidex CLI status resilient to sqlite DatabaseError so service health checks still work during DB corruption incidents; add clear warning and continue reporting service status.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:42:57.269638+00:00","updated_at":"2026-04-16T08:42:57.269638+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/91ebb28f_f2a_spec.md","provider":"any","payload_json":"{}"},{"id":"be2ac004-f698-490b-ac2d-b223d13dab90","title":"[Demo] Fix broken internal links on hero showcase pages","description":"Run targeted link audit for top demo routes, repair broken internal links in generated/hand-authored pages, and verify key routes return 200.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:42:26.455468+00:00","updated_at":"2026-04-16T08:42:26.455468+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/be2ac004_f69_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"14d91db42a576c98da76af475318d11fce6fbdde\"], \"completion_shas_checked_at\": \"2026-04-16T08:42:26.434617+00:00\"}"},{"id":"8b5bbc06-590a-4cde-abf4-c80484380bbb","title":"[Demo] One-shot: verify demo pages and repair regressions","description":"Run immediate demo page health checks for /demo plus top hypotheses/analyses pages, fix concrete regressions, and document verification results.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:41:19.524652+00:00","updated_at":"2026-04-16T08:41:19.524652+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8b5bbc06_590_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"b6f8c69c-cda3-4e92-8154-5736c86a3f6e","title":"[Demo] Restore missing QUESTS.md roadmap document","description":"Create and commit QUESTS.md roadmap index so autonomous agents can prioritize Quest 16/17 when no tasks are eligible.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:32:39.971399+00:00","updated_at":"2026-04-16T08:32:39.971399+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b6f8c69c_cda_spec.md","provider":"any","payload_json":"{}"},{"id":"d704027d-ddd8-41c9-8871-344d769f7618","title":"[Demo] Add missing QUESTS.md roadmap source-of-truth","description":"Create canonical QUESTS.md defining all 17 SciDEX quests and current priorities (Quest 16 Demo Showcase, Quest 17 Rich Artifacts), since self-improve workflow references it but file is missing.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:30:58.217682+00:00","updated_at":"2026-04-16T08:30:58.217682+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d704027d_ddd_spec.md","provider":"any","payload_json":"{}"},{"id":"d2687802-e7d9-487b-ba9d-0dd83f5de578","title":"[Demo] Create deep hypothesis showcase with rich evidence","description":"Build /demo page with 3-5 exemplar hypotheses showing: multi-round debates, rich evidence arrays (10+ papers per hypothesis), price history charts, threaded discussions (when WS1 delivers), linked analyses. Goal: demonstrate full SciDEX capability to visitors. Supports Quest 16 (Demo Showcase).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:26:40.876492+00:00","updated_at":"2026-04-16T08:26:40.876492+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d2687802_e7d_spec.md","provider":"any","payload_json":"{}"},{"id":"4d604c9d-daf7-4508-b54b-9ba741a6219b","title":"[Demo] Render 4 unrendered Jupyter notebooks to HTML","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:01:32.996600+00:00","updated_at":"2026-04-16T08:01:32.996600+00:00","summary":"","completion_notes":"Work already landed on origin/main in squash merges ec79ae4ab (3 notebooks) and 43ab73f67 (spec update). Verified: origin/main has 830 notebooks, worktree has 818. No SHA check needed — work confirmed on main.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4d604c9d_daf_spec.md","provider":"any","payload_json":"{}"},{"id":"e439a9e3-5c45-4484-887c-63565849eae5","title":"[Demo] Create end-to-end demo walkthrough page at /demo/walkthrough","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T06:44:57.254048+00:00","updated_at":"2026-04-16T06:44:57.254048+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e439a9e3_5c4_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"e28b00dc14b187700aabd945594235cf4d6d2651\"], \"completion_shas_checked_at\": \"2026-04-16T06:44:57.232009+00:00\"}"},{"id":"09e54732-0825-4969-8b78-d8e726a7ea0e","title":"[Demo] Add evidence strength badges and structured display on hypothesis pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T06:42:36.333582+00:00","updated_at":"2026-04-16T06:42:36.333582+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/09e54732_082_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"5de825ad2378a26fd68d493843e0cc111ab25b24\"], \"completion_shas_checked_at\": \"2026-04-16T06:42:36.316005+00:00\"}"},{"id":"6f2c4d26-b2c3-44bf-b59d-b74d1bcd3d08","title":"[Demo] Build demo walkthrough page — guided tour of all 5 layers","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T06:25:45.142653+00:00","updated_at":"2026-04-16T06:25:45.142653+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6f2c4d26_b2c_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"158e4032b706bdd1c236666aaa4164372affcd47\", \"f7992f71458b343ebef4f3a5b7a3c9171a8410ba\"], \"completion_shas_checked_at\": \"2026-04-16T06:25:45.121964+00:00\"}"},{"id":"3ea6ec71-baa7-4e53-a14d-461e754ee78c","title":"[Demo] Enhance demo walkthrough with live data links and five-layer tour","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T06:02:48.392301+00:00","updated_at":"2026-04-16T06:02:48.392301+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3ea6ec71_baa_spec.md","provider":"any","payload_json":"{}"},{"id":"4e2211c5-77bb-4260-9ec6-d49a07f75086","title":"[Demo] Add 3D protein structure viewers (Mol*) to hypothesis detail pages","description":"Embed Mol* (molstar) 3D protein viewers on hypothesis pages for target proteins. Use PDB IDs mapped to target genes. Show the actual protein structures that hypotheses discuss, making the science tangible and visual. Ref: QUESTS D16.4.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T05:43:38.747549+00:00","updated_at":"2026-04-16T05:43:38.747549+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4e2211c5_77b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}}"},{"id":"8124130e-1e43-47e7-b1f9-d4d9c8d28bb2","title":"[Demo] Expand walkthrough whitelist with richest new analyses (CRISPR, SEA-AD, BBB)","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T05:31:47.102975+00:00","updated_at":"2026-04-16T05:31:47.102975+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8124130e_1e4_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"782273432d87f90d791fea8e5d90e5d1b337a6c8\"], \"completion_shas_checked_at\": \"2026-04-16T05:31:47.066419+00:00\"}"},{"id":"b6fcaf88-1609-49a2-9602-def144d9a422","title":"[Demo] End-to-end demo walkthrough page — guided tour linking all features","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T05:05:27.287578+00:00","updated_at":"2026-04-16T05:05:27.287578+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b6fcaf88_160_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"e0e83d83981bd54e2db2c636e8277df4b12b93dc\"], \"completion_shas_checked_at\": \"2026-04-16T05:05:27.255067+00:00\"}"},{"id":"0b543336-d96a-4c4d-a4cf-fbd48ffc57ca","title":"[Demo] D16.9: Create end-to-end demo walkthrough page — guided tour linking all features","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T05:01:09.909179+00:00","updated_at":"2026-04-16T05:01:09.909179+00:00","summary":"Duplicate - walkthrough pages already exist for top 3 analyses","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0b543336_d96_spec.md","provider":"any","payload_json":"{}"},{"id":"670a14f8-347a-4f23-ac41-63c2d4a1e272","title":"[Demo] End-to-end discovery walkthrough page with guided tour","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16 04:32:13","updated_at":"2026-04-16T04:27:17.428099+00:00","summary":"","completion_notes":"Add LIMIT 1000 (or similar conservative cap) back to knowledge_edges query: 'SELECT * FROM knowledge_edges WHERE analysis_id=? LIMIT 1000'\nAdd LIMIT 5000 back to price_history query, or add application-level pagination if full history is needed\n\nChanged files:\n- .orchestra-slot.json\n- api.py\n- docs/planning/specs/0f2c20d4_e85_spec.md\n- docs/planning/specs/10b008c7-874_broken_links_in_entity_http_400_1_links_spec.md\n- docs/planning/specs/1bb03794_fba_spec.md\n- docs/planning/specs/29a9f423-8aa5-489b-8e6b-b3bbbd9be52b_spec.md\n- docs/planning/specs/29cf4473_c50_spec.md\n- docs/planning/specs/46597930_d55_spec.md\n- docs/planning/specs/5cd5ad2a_3e6_spec.md\n- docs/planning/specs/670a14f8_347_spec.md\n- docs/planning/specs/6d789cd7_082_spec.md\n- docs/planning/specs/7fc7b480_095_spec.md\n- docs/planning/specs/a7934e54_4aa_spec.md\n- docs/planning/specs/bb296f89_43d_spec.md\n- docs/planning/specs/facbd5d5_d55_spec.md\n- enrich_next20_hypotheses.py\n- enrichment/enrich_thin_evidence_batch.py\n- site/demo.html\n\nDiff stat:\n.orchestra-slot.json | 2 +-\n api.py | 93 ++-\n docs/planning/specs/0f2c20d4_e85_spec.md | 30 +-\n ...broken_links_in_entity_http_400_1_links_spec.md | 11 +-\n docs/planning/specs/1bb03794_fba_spec.md | 22 +-\n .../29a9f423-8aa5-489b-8e6b-b3bbbd9be52b_spec.md | 18 +-\n docs/planning/specs/29cf4473_c50_spec.md | 26 +-\n docs/planning/specs/46597930_d55_spec.md | 12 +-\n docs/planning/specs/5cd5ad2a_3e6_spec.md | 13 -\n docs/planning/specs/670a14f8_347_spec.md | 41 +-\n docs/planning/specs/6d789cd7_082_spec.md | 20 +-\n docs/planning/specs/7fc7b480_095_spec.md | 22 +-\n docs/planning/specs/a7934e54_4aa_spec.md | 15 +-\n docs/planning/specs/bb296f89_43d_spec.md | 27 +-\n docs/planning/specs/facbd5d5_d55_spec.md | 8 -\n enrich_next20_hypotheses.py | 236 -------\n enrichment/enrich_thin_evidence_batch.py | 302 ---------\n site/demo.html | 743 +++++++--------------\n 18 files changed, 344 insertions(+), 1297 deletions(-)","last_error":"Review gate REVISE attempt 2/10: Unbounded queries in hypothesis_detail endpoint: knowledge_edges LIMIT 200 and price_history LIMIT 500 were removed without replacement pagination cap, risking memory exhaustion on data-rich hypotheses/analyses","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/670a14f8_347_spec.md","provider":"any","payload_json":"{\"_gate_retry_count\": 2, \"_gate_last_decision\": \"REVISE\", \"_gate_last_reason\": \"Unbounded queries in hypothesis_detail endpoint: knowledge_edges LIMIT 200 and price_history LIMIT 500 were removed without replacement pagination cap, risking memory exhaustion on data-rich hypotheses/analyses\", \"_gate_last_instructions\": \"Add LIMIT 1000 (or similar conservative cap) back to knowledge_edges query: 'SELECT * FROM knowledge_edges WHERE analysis_id=? LIMIT 1000'\\nAdd LIMIT 5000 back to price_history query, or add application-level pagination if full history is needed\", \"_gate_branch\": \"orchestra/task/670a14f8-end-to-end-discovery-walkthrough-page-wi\", \"_gate_changed_files\": [\".orchestra-slot.json\", \"api.py\", \"docs/planning/specs/0f2c20d4_e85_spec.md\", \"docs/planning/specs/10b008c7-874_broken_links_in_entity_http_400_1_links_spec.md\", \"docs/planning/specs/1bb03794_fba_spec.md\", \"docs/planning/specs/29a9f423-8aa5-489b-8e6b-b3bbbd9be52b_spec.md\", \"docs/planning/specs/29cf4473_c50_spec.md\", \"docs/planning/specs/46597930_d55_spec.md\", \"docs/planning/specs/5cd5ad2a_3e6_spec.md\", \"docs/planning/specs/670a14f8_347_spec.md\", \"docs/planning/specs/6d789cd7_082_spec.md\", \"docs/planning/specs/7fc7b480_095_spec.md\", \"docs/planning/specs/a7934e54_4aa_spec.md\", \"docs/planning/specs/bb296f89_43d_spec.md\", \"docs/planning/specs/facbd5d5_d55_spec.md\", \"enrich_next20_hypotheses.py\", \"enrichment/enrich_thin_evidence_batch.py\", \"site/demo.html\"], \"_gate_diff_stat\": \".orchestra-slot.json | 2 +-\\n api.py | 93 ++-\\n docs/planning/specs/0f2c20d4_e85_spec.md | 30 +-\\n ...broken_links_in_entity_http_400_1_links_spec.md | 11 +-\\n docs/planning/specs/1bb03794_fba_spec.md | 22 +-\\n .../29a9f423-8aa5-489b-8e6b-b3bbbd9be52b_spec.md | 18 +-\\n docs/planning/specs/29cf4473_c50_spec.md | 26 +-\\n docs/planning/specs/46597930_d55_spec.md | 12 +-\\n docs/planning/specs/5cd5ad2a_3e6_spec.md | 13 -\\n docs/planning/specs/670a14f8_347_spec.md | 41 +-\\n docs/planning/specs/6d789cd7_082_spec.md | 20 +-\\n docs/planning/specs/7fc7b480_095_spec.md | 22 +-\\n docs/planning/specs/a7934e54_4aa_spec.md | 15 +-\\n docs/planning/specs/bb296f89_43d_spec.md | 27 +-\\n docs/planning/specs/facbd5d5_d55_spec.md | 8 -\\n enrich_next20_hypotheses.py | 236 -------\\n enrichment/enrich_thin_evidence_batch.py | 302 ---------\\n site/demo.html | 743 +++++++--------------\\n 18 files changed, 344 insertions(+), 1297 deletions(-)\", \"_gate_history\": [{\"ts\": \"2026-04-16 04:23:09\", \"decision\": \"REVISE\", \"reason\": \"Auto-deploy blocked: Merge failed (conflicts?):\", \"instructions\": \"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\", \"judge_used\": \"\", \"actor\": \"minimax:55\", \"retry_count\": 1}, {\"ts\": \"2026-04-16 04:26:19\", \"decision\": \"REVISE\", \"reason\": \"Unbounded queries in hypothesis_detail endpoint: knowledge_edges LIMIT 200 and price_history LIMIT 500 were removed without replacement pagination cap, risking memory exhaustion on data-rich hypotheses/analyses\", \"instructions\": \"Add LIMIT 1000 (or similar conservative cap) back to knowledge_edges query: 'SELECT * FROM knowledge_edges WHERE analysis_id=? LIMIT 1000'\\nAdd LIMIT 5000 back to price_history query, or add application-level pagination if full history is needed\", \"judge_used\": \"minimax:MiniMax-M2.7\", \"actor\": \"minimax:55\", \"retry_count\": 2}], \"_gate_judge_used\": \"minimax:MiniMax-M2.7\"}"},{"id":"1bb03794-fbab-4637-bde4-b0dd09090666","title":"[Demo] Build end-to-end demo walkthrough page at /demo","description":"Create a guided tour page at /demo that walks visitors through all 5 SciDEX layers with links to the best content. Show: hero hypotheses with rich evidence -> debates that produced them -> tools that gathered data -> KG connections -> governance tracking. D16.9 from QUESTS.md.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T04:01:02.807767+00:00","updated_at":"2026-04-16T04:01:02.807767+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1bb03794_fba_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"84e35e6807583844b1329239ab4b2f90e96b87ed\"], \"completion_shas_checked_at\": \"2026-04-16T04:01:02.788346+00:00\"}"},{"id":"29cf4473-c50f-4d6a-a6f9-c480d9d875c7","title":"[Demo] End-to-end demo walkthrough page — guided tour linking all five layers","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T03:26:55.200581+00:00","updated_at":"2026-04-16T03:26:55.200581+00:00","summary":"","completion_notes":"VERIFIED ALREADY DONE. Work merged to main in commit 67f0cfc75 and squash-merged in 04e1d688d. site/demo.html (125KB) serves HTTP 200 with all required elements. Audit was false-positive: NO_COMMITS search matched zero commits because task ID search was against partial hash.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/29cf4473_c50_spec.md","provider":"any","payload_json":"{}"},{"id":"de4c85a0-f841-4b71-80e7-97513a4ce3b0","title":"[Demo] Enrich demo walkthrough page with rich embedded content and guided tour","description":"D16.9: Transform minimal demo.html into a polished guided tour with embedded hero hypothesis cards, live stats, figure gallery, and notebook links. Show all 5 layers with real data snippets.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T03:04:26.737465+00:00","updated_at":"2026-04-16T03:04:26.737465+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/de4c85a0_f84_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"0dcd7be1447e236ae6b11f258f0d7651c2fa41c6\", \"a6d9ab65d5bc97a70dddce7e41de143faa01a387\", \"1ddf2d98779c7a0e50011cff4355ec70ae25badb\"], \"completion_shas_checked_at\": \"2026-04-16T03:04:26.716908+00:00\"}"},{"id":"91161be1-97c2-4cc1-a2d1-2c8cce0625ba","title":"[Demo] Add hypothesis detail page — deep dive view with evidence, pathway diagrams, and debate links","description":"Create /hypothesis/{id} detail page that renders the full hypothesis with: description, evidence_for/against with citations, linked experiments, debate sessions, pathway diagrams. This is the hero page that demo visitors click into from /exchange.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T02:36:46.908630+00:00","updated_at":"2026-04-16T02:36:46.908630+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/91161be1_97c_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"292ab415-360f-4243-8672-0bbc163f9f5c","title":"[Demo] Build end-to-end demo walkthrough page (D16.9)","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T02:31:12.780167+00:00","updated_at":"2026-04-16T02:31:12.780167+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/292ab415_360_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"e6b40dbdd88492343b8abd99ac2939eaac59df25\"], \"completion_shas_checked_at\": \"2026-04-16T02:31:12.759655+00:00\"}"},{"id":"0e838b9d-3237-4c95-9c55-6c7bd318d30a","title":"[Demo] End-to-end demo walkthrough page — guided tour of all five layers","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T02:30:59.209473+00:00","updated_at":"2026-04-16T02:30:59.209473+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0e838b9d_323_spec.md","provider":"any","payload_json":"{}"},{"id":"52dd0d6b-23a5-461e-b769-3fde52a2d777","title":"[Demo] End-to-end demo walkthrough page — guided tour of all 5 layers","description":"Create /demo page: a guided walkthrough tour linking all 5 SciDEX layers (Agora, Exchange, Forge, Atlas, Senate). Shows the platform's capabilities with links to best content in each layer. Quest D16.9.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T02:26:19.253652+00:00","updated_at":"2026-04-16T02:26:19.253652+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/52dd0d6b_23a_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"c668b285b7b47d64246559c0450f0274566500be\"], \"completion_shas_checked_at\": \"2026-04-16T02:26:19.232556+00:00\"}"},{"id":"d16-23-BMOD0001","title":"[Demo] Build simple biophysical model from KG-derived parameters","description":"Build a demo biophysical model: a minimal ODE model of microglial activation in AD (e.g. Ab accumulation -> microglial response -> cytokine release). Derive initial rate constants from KG edge weights and literature values. Run parameter fitting against the demo tabular dataset. Register as versioned model artifact linked to source hypothesis, dataset, and analysis. Show model outputs (time-course plots) as figure artifacts. Exercises: model building, biophysical template, artifact versioning, provenance chains. Depends on: frg-mb-02-BIOP, d16-22-TABD0001.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T10:43:55.460681+00:00","updated_at":"2026-04-14T10:43:55.460681+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-23-BMOD0001_biophysical_model_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"completion_shas\": [\"028007a8f87fff63e5801b95c850a86bb8ac07f6\"], \"completion_shas_checked_at\": \"2026-04-14T10:43:55.440037+00:00\"}"},{"id":"200534d6-ef24-4358-b7bb-6b8017abd45e","title":"[Demo] Add Mol* 3D protein structure viewer to top hypothesis pages","description":"Add interactive 3D molecular structure viewer (Mol* / PDBe Molstar) to hypothesis detail pages for target proteins. Query RCSB PDB for structures by gene name, embed viewer via PDBe Molstar web component. Priority: top 10 hypotheses by composite_score. This is D16.4 from Quest 16.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.","status":"archived","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":"2026-04-02T19:49:58.746951+00:00","completed_at":"","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/200534d6_ef2_spec.md","provider":"any","payload_json":"{}"},{"id":"620f67ae-3e36-4fbf-a687-979a6931d2d3","title":"[Demo] End-to-end demo walkthrough page — guided tour linking all features","description":"","status":"archived","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 18:06:31","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/620f67ae_3e3_spec.md","provider":"any","payload_json":"{}"},{"id":"ea332662-aabf-41e2-b750-1c3329e10615","title":"[Demo] Build guided demo walkthrough page at /demo","description":"Create a polished /demo page that guides visitors through all 5 SciDEX layers with curated links to the best content. Show: top hypothesis with 3D viewer -> debate that produced it -> Forge tools used -> KG connections -> Senate quality tracking. Include stats, screenshots-like sections, and a compelling narrative about how multi-agent AI accelerates scientific discovery. This is D16.9 from QUESTS.md.","status":"archived","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 19:24:40","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ea332662_aab_spec.md","provider":"any","payload_json":"{}"},{"id":"d16-09-7924D488","title":"[Demo] End-to-end demo walkthrough page","description":"Create /demo or /tour page that guides visitors through: (1) Start at a hypothesis, (2) See the debate that produced it, (3) Explore the evidence and tools used, (4) Navigate the knowledge graph, (5) Check governance/quality metrics. Interactive guided tour with highlights and arrows. This is the entry point for new visitors.","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:55:45","updated_at":"2026-04-02 09:42:41","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"822b6a6a-187f-45ea-9180-d79a2c40cb86","title":"[Demo] Harden link checker against transient localhost timeout storms","description":"Make link_checker resilient when localhost:8000 intermittently times out by adding per-URL circuit-breaking/fallback so CI demo verification can complete within timeout 300.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:28:09.611256+00:00","updated_at":"2026-04-16T11:28:09.611256+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/822b6a6a_187_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"8dc2011f-aeb6-4863-a752-778d779a4833","title":"[Demo] Register Allen Brain Cell Atlas as external dataset artifact","description":"Register the Allen Brain Cell Atlas SEA-AD dataset as an external dataset artifact in SciDEX. Creates a traceable reference that analyses can link to.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:05:23.753279+00:00","updated_at":"2026-04-16T11:05:23.753279+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-21-DSET0001_allen_brain_external_dataset_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"a07bd425-88a8-4e0d-a299-928cd04a1797","title":"[Demo][UI] Add /demos alias redirect to /demo","description":"Create a compatibility route so /demos redirects to /demo, preventing 404s in demo links and improving end-to-end demoability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:00:15.048357+00:00","updated_at":"2026-04-16T11:00:15.048357+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a07bd425_88a_spec.md","provider":"any","payload_json":"{}"},{"id":"29acf921-068b-4ec3-bded-73eb128356b7","title":"[Demo] Fix broken walkthrough links on demo landing page","description":"Audit /demo internal links for 404s and patch route/data selection so all showcased walkthrough CTAs resolve.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:58:35.419041+00:00","updated_at":"2026-04-16T10:58:35.419041+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/29acf921_068_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"39fdaefa-c95b-441a-8f22-14cc243d5df0","title":"[Demo] Harden key page links and rendering checks","description":"Run bounded render/link verification on core demo pages, fix any discovered broken internal links or template regressions, and verify service health.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:56:05.360627+00:00","updated_at":"2026-04-16T10:56:05.360627+00:00","summary":"","completion_notes":"Verified: prior commits 2cf4dd491 (api.py fix) and f1439b5d6 (spec) are on auth/main/direct-origin/main branches and incorporated into current HEAD=cbdf735d7 which matches origin/main. Fixes are live in api.py lines 30578-30765 (analysis_id gating for empty /analyses/ links). All core routes healthy (200/302/307). Only uncommitted change is .orchestra-slot.json (slot breadcrumb, not task-related).","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/39fdaefa_c95_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"d98b5ffb-2c11-4c15-bf73-aff5b7d2a5fb","title":"[Demo] Add remaining 8 analysis notebooks to complete full coverage","description":"8 analyses still lack notebooks. Create .ipynb + .html for: gut-brain axis PD, mitochondrial transfer v2, protein cross-seeding v2, sleep-neurodegeneration x2, aging mouse brain v1-v4, SEA-AD v1-v2. Use hypothesis data from related analyses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:55:44.243275+00:00","updated_at":"2026-04-16T10:55:44.243275+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d98b5ffb_2c1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"d2b6209f-bde5-404e-8cd1-c8208d8594a2","title":"[Demo] Add structured evidence matrix table to hypothesis detail pages","description":"Replace simple evidence bullet lists with structured evidence matrix tables showing: claim, source journal, year, PMID link, strength badge (high/medium/low with color coding), and evidence type (for/against). Sortable columns. This is A17.6 from Quest 17 (Rich Artifacts).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:26:40.439195+00:00","updated_at":"2026-04-16T10:26:40.439195+00:00","summary":"","completion_notes":"Task already implemented on main via task 634d0abd ([Exchange] Add structured evidence matrix table). Evidence matrix at api.py:28612-28776 renders on hypothesis pages with claim, source, year, PMID link, strength badge (high/medium/low), evidence type (for/against), quality score, and expandable abstracts. Sortable columns via JavaScript. Confirmed working via curl. Closing as duplicate.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d2b6209f_bde_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"61c555a10\"], \"completion_shas_checked_at\": \"2026-04-16T10:26:40.401125+00:00\"}"},{"id":"d16-21-DSET0001","title":"[Demo] Register Allen Brain Cell Atlas as external dataset artifact","description":"Register the SEA-AD Allen Brain Cell Atlas as an external dataset artifact with full metadata: source=allen_brain, URL, description, schema summary (cell types, gene expression columns, donor metadata). Link it to existing SEA-AD hypotheses and analyses via artifact_links. Show that browsing the dataset surfaces related KG entities and hypotheses. Exercises: external dataset references, artifact linking. Depends on: a17-21-EXTD0001.","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 10:55:44","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-21-DSET0001_allen_brain_external_dataset_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"c1284dcd-a41c-4993-83ab-b1cf4843448a","title":"[Demo] Seed 7 rich TREM2 hypotheses for DAM microglia analysis","description":"Seed 7 curated, LLM-enriched hypotheses for analysis SDA-2026-04-01-gap-001 (TREM2 agonism vs antagonism in DAM microglia). Each hypothesis gets a 1200-1600 word scientific description, evidence for/against citations, and a Mermaid pathway diagram. Advances Quest 16 D16.1: Deep enrichment of top demo hypotheses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:12:36.835796+00:00","updated_at":"2026-04-16T16:12:36.835796+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c1284dcd_a41_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"54d41c1a-ba60-4a14-90dc-7694c802d937","title":"[Demo] Enrich top 5 demo hypotheses with PubMed citations and mechanism details","description":"Find the top 5 hypotheses by composite score, fetch additional PubMed citations for each using the tools.py search functions, update their citations_count and evidence_for fields, and verify hypothesis pages render correctly with rich evidence.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:07:35.492289+00:00","updated_at":"2026-04-16T16:07:35.492289+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/54d41c1a_ba6_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"4732ae38-3b59-4a79-95e3-07bca1eeb8be","title":"[Demo] Add guided walkthrough page linking all five layers","description":"Create a polished /demo walkthrough page with explicit five-layer flow and add clear entry links from existing navigation surfaces for end-to-end demoability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:45:24.565672+00:00","updated_at":"2026-04-16T15:45:24.565672+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4732ae38_3b5_spec.md","provider":"any","payload_json":"{}"},{"id":"686511ea-8998-4843-ab91-ac1a9972e94e","title":"[Demo] Strengthen demo smoke check API readiness assertions","description":"Extend scripts/demo_smoke_check.py to validate key API endpoints and include clearer failure diagnostics for demo readiness.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:44:21.404880+00:00","updated_at":"2026-04-16T15:44:21.404880+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/686511ea_899_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"a635337ac\"], \"completion_shas_checked_at\": \"2026-04-16T15:38:33.199953+00:00\"}"},{"id":"e625ca06-3329-4549-acfb-0d9d34099d40","title":"[Demo] Verify end-to-end demo pages and repair any render blockers","description":"Run demo-critical page checks (home, analyses, exchange, atlas, graph, gaps, how), fix any render/link blockers found, and record results.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:44:00.540025+00:00","updated_at":"2026-04-16T15:44:00.540025+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e625ca06_332_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"7f3e9aaf-cd7a-4c70-a3eb-bc224938d08a","title":"[Demo] Tighten local demo smoke validation for notebook artifact links","description":"Improve demo smoke validation to catch broken notebook artifact links in local runs and keep Quest 16/17 demo surfaces stable.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:42:49.534886+00:00","updated_at":"2026-04-16T15:42:49.534886+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7f3e9aaf_cd7_spec.md","provider":"any","payload_json":"{}"},{"id":"0b58e9eb-493c-4abc-bd92-b4d86e0c00de","title":"[Demo] Harden link checker readiness for demo/showcase routes","description":"Add explicit readiness probes for /demo and /showcase in link_checker.py so demo-critical route outages are detected before crawl, with clear logging for transient restart diagnosis.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:42:46.273550+00:00","updated_at":"2026-04-16T15:42:46.273550+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0b58e9eb_493_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"c442133c-b269-4ecd-9c97-81fc1a49b857","title":"[Demo] CI: Add /forge and /notebooks to demo smoke-check route list","description":"The demo smoke check (scripts/demo_smoke_check.py) verifies that key routes load correctly. The /forge and /notebooks pages were recently fixed to use disk-backed caching (fixing 18-21s load times). The smoke check already checks /notebooks (under Artifacts), but the latency threshold check could be tightened. Task: Review the smoke check's route list and required_tokens, verify all 5 layers have health checks, and ensure the disk cache warm-up after restart is fast enough to pass 2s latency budget consistently.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:37:38.543506+00:00","updated_at":"2026-04-16T15:37:38.543506+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c442133c_b26_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"2e0e2408-151e-4b19-8276-2955a87f2adf","title":"[Demo] Improve transient outage diagnostics in link checker","description":"When link_checker detects restart cascades, report concise actionable diagnostics and persist summary fields in JSON without counting transient retries as opaque failures.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:36:44.799422+00:00","updated_at":"2026-04-16T15:36:44.799422+00:00","summary":"","completion_notes":"Task completed - transient diagnostics implemented on origin/main (dee11bae2 merged via 74942f128). Current HEAD (8883118bc) already includes the feature. No code changes needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/2e0e2408_151_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"de03c8da-9a93-47f7-b9d5-5da9fddc4236","title":"[Demo] Seed challenges table from knowledge gaps for /challenges page","description":"The /challenges page exists and was recently fixed (DB migrations added) but the challenges table is empty. Seed it with 10-15 high-quality scientific challenges derived from knowledge_gaps, hypotheses, and analyses. Each challenge should have a title, question, description, domain, bounty, scores, and linked analysis/hypothesis IDs. This makes /challenges demoable as part of Quest 16 (Demo Showcase).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:36:09.500449+00:00","updated_at":"2026-04-16T15:36:09.500449+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/de03c8da_9a9_spec.md","provider":"any","payload_json":"{}"},{"id":"f2165a12-fb1b-4340-8fc0-12b1e143d2ca","title":"[Demo] CI: Validate core demo routes and fix first failing endpoint","description":"Run demo route checks on port 8000, identify the first failing endpoint in the core demo flow, implement a fix, and verify all critical pages return 200/3xx.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:31:07.806484+00:00","updated_at":"2026-04-16T15:31:07.806484+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f2165a12_fb1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"ec5b21dc-88de-41b5-b619-99cc2ca51d61","title":"[Demo] Add guided five-layer walkthrough page and homepage entrypoint","description":"Implement a polished demo walkthrough page spanning Agora, Exchange, Forge, Atlas, Senate with direct links and verification checks for end-to-end demoability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:27:03.379016+00:00","updated_at":"2026-04-16T15:27:03.379016+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ec5b21dc_88d_spec.md","provider":"any","payload_json":"{}"},{"id":"4e386ba7-cecc-48fa-b746-68e5d056fd34","title":"[Demo] Stabilize link checker API readiness probe","description":"Fix false-negative API readiness timeouts in link_checker.py so CI checks run reliably for demo validation.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:14:28.371098+00:00","updated_at":"2026-04-16T15:14:28.371098+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4e386ba7_cec_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"63263427-d9ea-4f0d-a25b-b8e3120c8109","title":"[Demo] Add Mol* protein viewer + score radar chart to challenge detail pages","description":"Challenge detail pages (/challenge/{id}) lack visual richness. Add: (1) auto-link challenges to relevant targets by parsing gene symbols from title/description, (2) embed Mol* 3D protein viewer for linked targets with known PDB IDs, (3) show a visual score radar chart for the 5 scoring dimensions (gap_importance, therapeutic_potential, existing_investment, urgency, landscape). This directly advances Quest 16 (Demo Showcase) by proving the Atlas+Exchange layers in a single compelling view.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:13:20.570717+00:00","updated_at":"2026-04-16T15:13:20.570717+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/63263427_d9e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}}"},{"id":"8ac5df2e-b561-4661-814d-a6b5b94d95b1","title":"[Demo] Populate /targets with drug target data from hypotheses — page shows 0 targets","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:11:21.170953+00:00","updated_at":"2026-04-16T15:11:21.170953+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8ac5df2e_b56_spec.md","provider":"any","payload_json":"{}"},{"id":"6b8e7ec5-4806-4c72-9a0d-94341117bef4","title":"[Demo] Verify and polish demo walkthrough pages (/demo, /showcase, /origins)","description":"Ensure all demo routes render correctly with rich content. Fix any 404s/500s. Add missing content cards.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:05:21.970218+00:00","updated_at":"2026-04-16T15:05:21.970218+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6b8e7ec5_demo_walkthrough_spec.md","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"e14242a4-9256-4b3d-9c3b-b02d3d6960ba","title":"[Demo] Add Allen Institute data analysis examples","description":"Create 2-3 analysis pages using Allen Institute datasets (Brain Atlas, single-cell RNA-seq, etc.). Show tool usage, KG integration, debate-driven insights. Link from /demo. Demonstrates Forge layer capabilities. Supports Quest 16.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:03:05.979355+00:00","updated_at":"2026-04-16T15:03:05.979355+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e14242a4_925_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"09052e66-1f0b-48e8-9a6f-ce9843edb414","title":"[Demo] Tabular dataset demo: gene expression matrix linked to KG entities","description":"Create a demo showing tabular gene expression matrix from Allen data linked to KG entities (genes, brain regions). Demonstrates the tabular dataset artifact type.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:01:12.739563+00:00","updated_at":"2026-04-16T15:01:12.739563+00:00","summary":"","completion_notes":"Fixed critical bug: html.escape(None) crash in artifact_detail() for tabular datasets. All 4 tabular dataset artifact pages now return HTTP 200. Task marked as done.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-22-TABD0001_tabular_gene_expression_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 6}, \"completion_shas\": [\"2f55baa1a\", \"66a0801ba\", \"c09f7c483\"], \"completion_shas_checked_at\": \"2026-04-16T15:01:12.723574+00:00\"}"},{"id":"19e6d400-1bda-4bf7-81b7-2362d8c212b9","title":"[Demo] Provenance visualization UI for artifacts","description":"Build interactive provenance graph visualization using /api/artifacts/{id}/provenance-graph. Show parent artifacts, processing steps, and derivation chains. Use D3.js or similar.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T14:47:51.160520+00:00","updated_at":"2026-04-16T14:47:51.160520+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/19e6d400_1bd_spec.md","provider":"any","payload_json":"{}"},{"id":"74c44af2-13fc-4728-a8b1-04773fb19185","title":"[Demo] Generate HTML reports for 5 recent completed analyses missing reports","description":"5 recent completed analyses (epigenetic reprogramming, SEA-AD v3/v4, senescent clearance, EV biomarkers) have debate JSON but no HTML reports. Run post_process.py report generation for each.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T13:50:15.204098+00:00","updated_at":"2026-04-16T13:50:15.204098+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/74c44af2_13f_spec.md","provider":"any","payload_json":"{}"},{"id":"d22c9050-8d19-411d-8abd-b449c9743868","title":"[Demo] Add /clinical-trials listing page aggregating all trial data","description":"D16 demo completeness: Build /clinical-trials page showing all clinical trials extracted from hypothesis enrichment. Aggregated view with phase distribution, status breakdown, linkback to hypotheses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T13:35:54.297058+00:00","updated_at":"2026-04-16T13:35:54.297058+00:00","summary":"","completion_notes":"Spec updated with work log. No new code needed - existing commit 375e9a0b5 already delivered the feature.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d22c9050_8d1_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"375e9a0b5\"], \"completion_shas_checked_at\": \"2026-04-16T13:35:54.274658+00:00\"}"},{"id":"3bf7293b-c2d4-46bc-8dbb-bd8a2b2cf8a2","title":"[Demo] Add top hypothesis showcase cards to demo page","description":"Add a 'Featured Hypotheses' section to the /demo page showcasing the top 3 highest-scored hypotheses with their evidence counts, debate quality scores, and direct links. This gives demo visitors an immediate path to the richest content.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T13:13:41.841465+00:00","updated_at":"2026-04-16T13:13:41.841465+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3bf7293b_c2d_spec.md","provider":"any","payload_json":"{}"},{"id":"d16-25-DPAP0001","title":"[Demo] Create dynamic authored paper: SEA-AD Microglial Activation Review","description":"Write an authored paper artifact that reviews microglial activation in AD, embedding live artifacts: the TREM2 protein design (version timeline), the biophysical model (time-course figure), the SEA-AD differential expression table, and KG subgraph for TREM2. Paper uses {{artifact:ID}} markers that render inline. Demonstrates: authored papers, artifact embedding, internal origin tracking, versioned documents. Depends on: a17-27-APAP0001, a17-29-EMBD0001, d16-20-AVER0001.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:21:05.218011+00:00","updated_at":"2026-04-16T11:21:05.218011+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-25-DPAP0001_dynamic_paper_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"ab05482c-8248-49bb-9b67-57303ad81cf4","title":"[Demo] Harden route health check for demo-critical pages","description":"Add/verify a reusable route-health check that includes /demo, /artifacts, /walkthrough, /entity, and /analyses with timeout handling and clear failure diagnostics for demo readiness.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 13:30:48","updated_at":"2026-04-04T13:23:32.365728+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ab05482c_824_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"d16-22-TABD0001","title":"[Demo] Tabular dataset demo: gene expression matrix linked to KG entities","description":"Create a demo tabular dataset artifact from SEA-AD differential expression results (gene, cell_type, log_fold_change, p_value). Map gene column to KG gene entities, cell_type column to KG cell-type entities. Show cross-references: clicking a gene shows its KG neighborhood + expression data, clicking cell type shows related genes from the table. Exercises: tabular datasets, column-to-entity linking, KG cross-referencing. Depends on: a17-22-TABL0001, d16-21-DSET0001.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 04:51:32","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-22-TABD0001_tabular_gene_expression_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 6}}"},{"id":"591dc8b3-8580-433d-9c41-c0e4b2061d6c","title":"[Demo] Add hypothesis comparison feature — side-by-side view of top hypotheses","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T20:38:00.703792+00:00","updated_at":"2026-04-16T20:38:00.703792+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/591dc8b3_858_spec.md","provider":"any","payload_json":"{}"},{"id":"9c045da5-42fd-4fe0-ab6f-3229089716c3","title":"[Demo] Add structured evidence matrix to hypothesis pages","description":"A17.6: Replace the simple evidence list on hypothesis detail pages with a structured evidence matrix table. Show each evidence item in a row with: claim, strength badge (strong/moderate/weak), source journal, year, PMID link, and evidence type categorization (mechanistic/clinical/genetic/epidemiological). Add a summary bar showing evidence balance. This makes hypothesis pages more professional and demo-ready.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T20:36:28.436380+00:00","updated_at":"2026-04-16T20:36:28.436380+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9c045da5_42f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"15706b67-6ffa-4318-9641-573f762dfa3b","title":"[Demo] Fix invalid escape sequence warnings in api.py UI scripts","description":"Eliminate Python SyntaxWarning invalid escape sequence issues in embedded JS/HTML strings in api.py to improve demo-page reliability and startup cleanliness.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T18:57:07.112159+00:00","updated_at":"2026-04-16T18:57:07.112159+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/15706b67_6ff_spec.md","provider":"any","payload_json":"{}"},{"id":"1b983b0f-02b6-4f19-8b6c-17b727e376f2","title":"[Demo] Add protein 3D structure section to demo/showcase pages","description":"The Mol* 3D protein viewer is now active on 12 target pages (TREM2, APOE, SNCA, BACE1, BRD4, etc.) but the demo walkthrough and showcase pages don't mention or link to it. Add a protein structure section to /demo and /showcase highlighting the interactive Mol* viewer feature with direct links to key targets.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T18:04:37.339090+00:00","updated_at":"2026-04-16T18:04:37.339090+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1b983b0f_02b_spec.md","provider":"any","payload_json":"{}"},{"id":"57503d6f-cc7c-47c8-b487-02b99a2b1857","title":"[Demo] Enrich 10 thin hypothesis descriptions to 1000+ words","description":"IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists.\n\n141 hypotheses have <500 char descriptions. Expand with mechanisms, evidence, clinical relevance.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:51:19.071223+00:00","updated_at":"2026-04-16T17:51:19.071223+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/57503d6f_cc7c_enrich_10_thin_hypotheses_spec.md","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"3face9c1-54f4-4a14-8620-acb4ae1e9d55","title":"[Demo] Link orphan hypotheses to relevant challenges","description":"212 hypotheses exist but are not linked to any challenge. Match hypotheses to relevant challenges using keyword/target/disease matching. This enriches challenge pages from 2 hypotheses to 10+ per challenge, dramatically improving demo quality (Q16 D16.1).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:37:25.171513+00:00","updated_at":"2026-04-16T17:37:25.171513+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3face9c1_54f_spec.md","provider":"any","payload_json":"{}"},{"id":"1fcd8ef5-a0e1-4606-b714-7407eeb22a32","title":"[Demo] Add regression guard for markdown-free demo hypothesis snippets","description":"Prevent raw markdown artifacts from reappearing in /demo hypothesis snippets by adding an automated CI smoke check and documenting acceptance criteria.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:36:30.895728+00:00","updated_at":"2026-04-16T17:36:30.895728+00:00","summary":"","completion_notes":"Verification: scripts/demo_smoke_check.py contains full snippet-level markdown regression guard (HYPOTHESIS_SNIPPET_PATTERN, SNIPPET_MD_PATTERNS, extract_demo_hypothesis_snippets, find_markdown_artifacts_in_snippet, snippet-level check in content loop). Smoke check exit code 1 due to pre-existing entity/experiments failures unrelated to this task. Task content confirmed present on origin/main.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1fcd8ef5_a0e_spec.md","provider":"any","payload_json":"{}"},{"id":"c0bd88ac-0ecc-4413-8269-b7070b80f3f1","title":"[Demo] Expand demo smoke check to validate walkthrough detail pages","description":"Extend scripts/demo_smoke_check.py to detect walkthrough detail links from /showcase and verify each page status, latency, and content-size quality to improve Quest 16 demo reliability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:24:03.586510+00:00","updated_at":"2026-04-16T17:24:03.586510+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c0bd88ac_0ec_spec.md","provider":"any","payload_json":"{}"},{"id":"7559b983-6027-4abd-b087-67f0246034f2","title":"[Demo] Suppress transient link-checker false positives after successful revalidation","description":"Link checker should not emit systematic issues in final JSON/report when sampled affected links are healthy after retry checks; reduce demo CI noise and avoid misleading route-missing diagnoses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:22:52.299650+00:00","updated_at":"2026-04-16T17:22:52.299650+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7559b983_602_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"7db32f89-29f3-438c-bc3a-dd5fb5e37a0a","title":"[Demo] Verify core demo routes and fix one blocking render issue","description":"Run demo-critical page/API health checks, identify a concrete blocking issue if present, implement fix, and verify end-to-end demo route health.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:19:22.392691+00:00","updated_at":"2026-04-16T17:19:22.392691+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7db32f89_29f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"61c9215e-27c0-4745-a755-2eabce5a9bf9","title":"[Demo] Use canonical /analyses links in demo walkthrough cards","description":"Replace legacy /analysis links in /demo analysis cards with canonical /analyses paths to remove redirect hops and improve demo page performance.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:15:57.173682+00:00","updated_at":"2026-04-16T17:15:57.173682+00:00","summary":"","completion_notes":"Verification: curl confirmed /demo page uses /analyses/SDA-* links (not /analysis/). No /analysis/ links in demo cards. Task already landed on main via commits a4dd7d0cb and 91ddf898b which are on other branches that were squash-merged.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/61c9215e_27c_spec.md","provider":"any","payload_json":"{}"},{"id":"372abf40-6d00-4db3-96f0-aef54b6095f3","title":"[Demo] Harden link-check API readiness to avoid false startup timeouts","description":"Reduce false API readiness failures in link_checker.py by probing lightweight health endpoint with bounded retry/backoff and preserving transient-outage classification behavior for demo CI reliability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:12:03.932537+00:00","updated_at":"2026-04-16T17:12:03.932537+00:00","summary":"","completion_notes":"Branch has no diff from origin/main — task work was already merged in prior commit 01dfbce01. link_checker.py on main: probes /api/health (plus /demo and /showcase), exponential backoff (2s base, 15s cap, 8 attempts, bounded ~75s), preserves transient-outage classification. Syntax validated OK. No code changes needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/372abf40_6d0_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"19519ab7-8d0d-45f6-b01a-51a434bf75c6","title":"[Demo] Fix link checker retry handling for relative URLs","description":"Prevent invalid URL retries on relative internal links during demo CI link checks by normalizing/reusing resolved absolute URLs.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:08:09.053176+00:00","updated_at":"2026-04-16T17:08:09.053176+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/19519ab7_8d0_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"bd76fdd5-4eea-42e1-a654-8e91bfb279a5","title":"[Demo] Fix scidex CLI startup when optional auth/webhook modules are missing","description":"Make cli.py resilient when auth.py/webhooks.py are unavailable so status/site/db commands still run from minimal deployments and main checkout.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:04:32.127541+00:00","updated_at":"2026-04-16T17:04:32.127541+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/bd76fdd5_4ee_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"c72ce6ef-aad8-4695-9fab-e339a7e96dd7","title":"[Demo] Harden demo smoke check with latency budgets and showcase/artifact routes","description":"Expand scripts/demo_smoke_check.py to validate core demo+artifact routes and fail when route latency exceeds configured budget (default 2s) to enforce demoability quality bar.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:01:55.409648+00:00","updated_at":"2026-04-16T17:01:55.409648+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c72ce6ef_aad_spec.md","provider":"any","payload_json":"{}"},{"id":"686b564a-2980-40fe-adf1-c73dcd60d42e","title":"[Demo] Harden link checker partial-timeout reporting","description":"Ensure link_checker.py always emits logs/link-check-latest.json and avoids long LLM analysis when run under timeout 300, so CI runs are actionable.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:58:52.356090+00:00","updated_at":"2026-04-16T16:58:52.356090+00:00","summary":"","completion_notes":"All acceptance criteria already met in origin/main commit a76b2aaaf: signal handlers (SIGTERM/SIGALRM), --skip-llm flag, can_run_llm_analysis runtime budget gating, report written before LLM analysis, llm_analysis_performed field in JSON output, logs/link-check-latest.json always emitted. Current branch is identical to origin/main on link_checker.py — no delta.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/686b564a_298_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"f4d205ba-3770-4792-91bc-b1e7dde1a29b","title":"[Demo] Harden guided demo route checks and repair broken path references","description":"Recurring demo validations miss legacy path variants; add robust demo route coverage and fix discovered broken demo links/routes so walkthrough pages return 200/3xx.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:55:36.077776+00:00","updated_at":"2026-04-16T16:55:36.077776+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f4d205ba_377_spec.md","provider":"any","payload_json":"{}"},{"id":"82b3b55b-a2f4-4ec1-bf86-8fd3c5f15bd8","title":"[Demo] Make link checker worktree-safe (remove hardcoded main paths)","description":"Fix link_checker.py to use repository-relative paths for report/context/task DB access so runs from worktrees produce stable reports and accurate context; verify report freshness and task creation behavior.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:55:07.137844+00:00","updated_at":"2026-04-16T16:55:07.137844+00:00","summary":"","completion_notes":"Verified on origin/main at link_checker.py lines 115-149. REPO_ROOT, MAIN_REPO_ROOT, _resolve_main_repo_root(), SCIDEX_DB_PATH (62 MB main DB vs 12 KB stub), LINKCHECK_REPORT_PATH to main repo logs/ all present. Acceptance criteria met. Orphan branch was superseded by same commits already on main.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/82b3b55b_a2f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"completion_shas\": [\"36c90c341\", \"4e740d41a\", \"f7ed8eb9b\", \"3c34f8284\"], \"completion_shas_checked_at\": \"2026-04-16T16:55:07.117120+00:00\"}"},{"id":"979153bd-7b65-4fce-9917-904373cc6e2b","title":"[Demo] Add /demo-showcase alias route to avoid 404","description":"Create a one-shot fix so /demo-showcase resolves to the existing demo experience instead of returning 404. Include route handling, page validation, and spec work log.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:54:17.051555+00:00","updated_at":"2026-04-16T16:54:17.051555+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/979153bd_7b6_spec.md","provider":"any","payload_json":"{}"},{"id":"5d65f0ff-9d7c-444a-bcce-4065e346391e","title":"[Demo] Fix broken /demo/showcase deep link","description":"Audit found /demo/showcase returns 404 while /demo exists. Add a stable route/redirect for showcase deep links and verify demo/artifact pages render.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:52:42.830035+00:00","updated_at":"2026-04-16T16:52:42.830035+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5d65f0ff_9d7_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"a59e422a-c3d6-4027-b048-910cb00c4be7","title":"[Demo] Fix /showcase 500 when hypothesis confidence is null","description":"Resolve TypeError in showcase_top_analyses caused by comparing null confidence values to float thresholds; keep showcase rendering for sparse hypothesis rows and verify route returns 200.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:49:54.806039+00:00","updated_at":"2026-04-16T16:49:54.806039+00:00","summary":"","completion_notes":"Fix applied in 3 locations: score = h[\"composite_score\"] or 0 at line ~55690, ca_top_score = (ca[\"hypotheses\"][0][\"composite_score\"] or 0) at line ~56050, wa_top = (wa[\"hypotheses\"][0][\"composite_score\"] or 0) at line ~56089. Branch rebased to current main head (d00ff3e1e), forcing push to push-token remote succeeded. The /showcase route now handles null confidence values gracefully.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a59e422a_c3d_spec.md","provider":"any","payload_json":"{}"},{"id":"1ceb5f3b-b413-40a6-88d0-15e563c9d3a9","title":"[Demo] Harden demo route smoke check with explicit five-layer coverage","description":"Add/upgrade a lightweight demo smoke check script that validates all five-layer routes and returns non-zero on failures; include timeout-safe usage and document in spec.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:48:59.162678+00:00","updated_at":"2026-04-16T16:48:59.162678+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1ceb5f3b_b41_spec.md","provider":"any","payload_json":"{}"},{"id":"6ce00da3-a400-410b-a982-65d291ba0051","title":"[Demo] Fix walkthrough analysis pages returning 500","description":"Diagnose and fix /walkthrough/{analysis_id} server errors so demo deep-link walkthroughs render successfully.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:47:31.677868+00:00","updated_at":"2026-04-16T16:47:31.677868+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6ce00da3_a40_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"bb4412a7-ec41-4083-8fbc-67086cec0614","title":"[Demo] Populate drug targets table with top AD/neurodegeneration targets","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:45:31.955373+00:00","updated_at":"2026-04-16T16:45:31.955373+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/bb4412a7_ec4_spec.md","provider":"any","payload_json":"{}"},{"id":"9b158072-664c-412e-a3a9-d296819d32c9","title":"[Demo] Dashboard browser page","description":"Create /dashboards page listing all 5 dashboard artifacts. Show live dashboard embeds or previews with refresh timestamps.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:44:12.219712+00:00","updated_at":"2026-04-16T16:44:12.219712+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9b158072_664_spec.md","provider":"any","payload_json":"{}"},{"id":"a48fe1f1-4bcf-43a2-bdf1-c93821159eee","title":"[Demo] Ensure /demo hero analyses render with fallback content","description":"Make /demo resilient when no analyses meet strict richness thresholds by adding deterministic fallback selection and preserving polished card metadata.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:41:54.666200+00:00","updated_at":"2026-04-16T16:41:54.666200+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a48fe1f1_4bc_spec.md","provider":"any","payload_json":"{}"},{"id":"ce861697-6110-4e75-a6f2-54536e88b1bc","title":"[Demo] Repair broken demo-route links from health sweep","description":"Run bounded page/link verification on demo-critical routes, fix broken internal links/templates, and verify 200/3xx responses for demo pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:39:26.971945+00:00","updated_at":"2026-04-16T16:39:26.971945+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ce861697_611_spec.md","provider":"any","payload_json":"{}"},{"id":"f840df44-9012-4580-a754-b7da2621f23a","title":"[Demo] Harden link checker for redirect-aware demo verification","description":"Make link_checker robust to local redirect topology (301/302), add non-LLM fast mode, and ensure CI-style checks finish within timeout windows.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:33:16.433843+00:00","updated_at":"2026-04-16T16:33:16.433843+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f840df44_901_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"48a272c0-940a-43ee-956b-bf893d23ebae","title":"[Demo] Hypothesis detail pages: add rich content panels (evidence, debates, price history)","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:27:47.388036+00:00","updated_at":"2026-04-16T16:27:47.388036+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/48a272c0_940_spec.md","provider":"any","payload_json":"{}"},{"id":"b726f64c-41e5-456b-81ff-ff806a53066c","title":"[Demo] Fix health-check endpoint assumptions for HTTPS host routing","description":"Update SciDEX health-check guidance/scripts to avoid localhost false negatives under HTTPS+Host routing; validate against scidex.ai/Host header patterns.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:24:11.753554+00:00","updated_at":"2026-04-16T16:24:11.753554+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b726f64c_41e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"d9f9c0d1-d1b8-4965-8c59-feab3993175a","title":"[Demo] Evidence matrix component with quality scores on hypothesis pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:11:21.605707+00:00","updated_at":"2026-04-16T16:11:21.605707+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d9f9c0d1_d1b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"760d6b61-f157-4ebf-b3f7-b74e184b5012","title":"[Demo] Fix broken walkthrough links on demo page — only show for valid walkthrough IDs","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:07:11.478431+00:00","updated_at":"2026-04-16T16:07:11.478431+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/760d6b61_f15_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"c3889cdf-757b-4997-b2c3-059576b9af33","title":"[Demo] Harden local health checks against localhost redirect false negatives","description":"Update local health checks to avoid false failures from nginx localhost redirects by checking FastAPI directly (localhost:8000) or following redirects where appropriate; update related docs and verification behavior.","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 11:12:03","updated_at":"2026-04-04T11:07:25.873392+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c3889cdf_757_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"4225e413-8095-4223-a793-6cccd095b3c5","title":"[Demo] Fix /demo/origins route returning 404","description":"Demo smoke checks show /demo/origins returns 404 while /demo is 200. Ensure route is registered and page renders with origin stats/provenance content; add regression test coverage for demo routes where feasible.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:58:24.704040+00:00","updated_at":"2026-04-16T21:58:24.704040+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4225e413_809_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"fbe2795d-545f-4348-9a89-2595dab26374","title":"[Demo] Replace 0-Experiments stat on demo page with Notebooks count","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:24:37.899496+00:00","updated_at":"2026-04-16T21:24:37.899496+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/fbe2795d_545_spec.md","provider":"any","payload_json":"{}"},{"id":"6a5b47da-270e-4a8f-b9ea-d931fa03cb6f","title":"[Demo] Add live growth metrics section to /demo page","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:21:37.191820+00:00","updated_at":"2026-04-16T21:21:37.191820+00:00","summary":"","completion_notes":"Work verified on origin/main: commit d73de3bbd is an ancestor of origin/main via squash merge, and the \"Knowledge Growing in Real-Time\" section exists in api.py at line 56776+. The audit could not trace through squash merge history. No additional work needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/demo_live_growth_metrics_spec.md","provider":"any","payload_json":"{}"},{"id":"b97b6c81-c302-4ff4-b7d0-6752e85b4b80","title":"[Demo] Harden link checker against transient API restarts","description":"Improve link_checker reliability during temporary localhost:8000 connection refusals so demo CI checks complete within timeout and avoid false failures.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:21:04.738406+00:00","updated_at":"2026-04-16T21:21:04.738406+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b97b6c81_c30_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"ab24f3c1-399a-4184-8583-a2e923ebb94d","title":"[Demo] Fix disk cache SQLite contention on entity pages","description":"Entity page disk cache writes fail under concurrent load (SQLite lock timeout). The _set_cached_page() function uses sqlite3.connect with timeout=2 but under CI smoke checks with 50+ concurrent entity requests, writes fail silently. Fix: increase busy_timeout, add WAL checkpoint optimization, or use write serialization via a threading.Lock to prevent concurrent writers.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:18:36.533578+00:00","updated_at":"2026-04-16T21:18:36.533578+00:00","summary":"","completion_notes":"Verified by reading api_shared/cache.py: _DISK_CACHE_WRITE_LOCK = threading.Lock() at line 21; _set_cached_page() acquires lock before write (line 114-143); WAL mode enabled on each connection (lines 27, 72-73, 118, 130); busy_timeout=5000 set on all connections. The fix landed on main via commit a2219fd90 (part of HEAD = origin/main = 053af84c4). Only difference between HEAD and origin/main is .orchestra-slot.json (worktree marker).","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ab24f3c1_399_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"c4b55a70-b39f-4174-aeb5-b9efb2d6cd6e","title":"[Demo] Harden link-check readiness to avoid transient outage cascades","description":"Strengthen link_checker preflight so full crawl only starts after sustained API readiness; reduce transient false-failure cascades during demo CI.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:18:23.181022+00:00","updated_at":"2026-04-16T21:18:23.181022+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c4b55a70_b39_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"5b1fa594-9751-4e1d-9a90-60f85cecac36","title":"[Demo] Add transient outage diagnostics to link checker report","description":"Extend link_checker JSON output with explicit transient outage metadata (counts, classification, and source context) so demo CI can distinguish real broken links from restart cascades.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:15:28.388950+00:00","updated_at":"2026-04-16T21:15:28.388950+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5b1fa594_975_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"4c5f9f52-3a67-462d-8621-b166fb79df6f","title":"[Demo] Add /leaderboard route and fix /challenges 500 error","description":"Nav links point to /leaderboard (404) and /challenges (500). Add the /leaderboard page (top hypothesis leaderboard with sparklines) and fix the /challenges 500 error. These are broken links on the main nav visible to all visitors.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:11:00.943297+00:00","updated_at":"2026-04-16T21:11:00.943297+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4c5f9f52-3a67-462d-8621-b166fb79df6f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"d16-27-ORIG0001","title":"[Demo] Origin tracking showcase: internal vs external artifact provenance","description":"Create a demo page showing the origin tracking system: side-by-side view of an internal artifact (authored paper created by SciDEX) and an external artifact (PubMed paper imported). Show origin badges (internal/external), origin URLs, and how provenance chains differ. Include a mixed provenance chain: external paper -> internal KG edges -> internal hypothesis -> internal authored paper. Depends on: a17-26-ORIG0001, d16-25-DPAP0001.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 05:02:21","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-27-ORIG0001_origin_tracking_demo_spec.md","provider":"any","payload_json":"{}"}],"reviews":[{"task_count":3,"total_tokens":150000,"total_cost":0.45000000000000007,"output_score":20240.32,"efficiency_rating":"normal","reviewed_at":"2026-04-17T11:29:14.374695+00:00"}],"effectiveness":{"task_count":3,"total_lines_added":0,"total_lines_removed":0,"total_files_modified":0,"total_hypotheses":1132,"total_kg_edges":596356,"total_papers":13464,"total_tokens":150000,"total_duration":3381527.136124,"avg_impact":1012016.0,"avg_effectiveness":20240.32},"spec_content":"---\ntitle: \"Quest: Demo\"\ndescription: \"Demo showcase & end-to-end flows — polished demos exercising all five layers\"\ntype: quest\nlayer: Cross-cutting\npriority: 99\nstatus: active\nquest_id: 1baa2fb6-21f\nspec_path: docs/planning/specs/quest_demo_spec.md\n---\n\n# Quest: Demo\n\n**Layer:** Cross-cutting \n**Priority:** P99 \n**Status:** active \n**Tasks:** 468 total (79 done, 9 open)\n\n## Vision\n\nDemo showcase & end-to-end flows — polished demos exercising all five layers\n\n> Demos must showcase scientifically meaningful outputs, not stub pages or placeholder content. Each demo task specifies: what hypothesis/gap/analysis is being demonstrated, what evidence or result it produces, and why the result is non-obvious. Acceptance: demo produces >1 artifact with >50KB content and >3 cross-links to other demos. Multi-demo batches use parallel agents.\n\n## Open Tasks\n\n- [ ] [Demo] CI: Verify all demo pages load correctly with rich content (P93)\n- [ ] [Demo] Versioned artifact demo: create protein design with 3 iterations (P92)\n- [ ] [Demo] Register Allen Brain Cell Atlas as external dataset artifact (P91)\n- [ ] [Demo] Tabular dataset demo: gene expression matrix linked to KG entities (P90)\n- [ ] [Demo] Build simple biophysical model from KG-derived parameters (P89)\n- [ ] [Demo] End-to-end provenance demo: trace reasoning chain from paper to model (P88)\n- [ ] [Demo] Create dynamic authored paper: SEA-AD Microglial Activation Review (P87)\n- [ ] [Demo] Create live dashboard: Knowledge Growth Monitor (P86)\n- [ ] [Demo] Origin tracking showcase: internal vs external artifact provenance (P85)\n\n\n## Success Criteria\n\n- [ ] All open tasks completed and verified\n- [ ] Integration tested end-to-end with dependent quests\n- [ ] UI pages rendering correctly for this quest's features\n- [ ] Documentation updated for new capabilities\n\n## Work Log\n\n### 2026-04-13 22:30 UTC — Slot minimax:55 (reopened audit, second pass)\n- Task: [Demo] Recurring: Read all quest/task specs, identify demo-ready features, create integration tasks [task:e90797ac-25a5-4bdb-b4ca-5bfe8f9c04aa]\n- Verified prior work (8cc8c1e01 — spec-only update, not merged to main) was correct analysis\n- Rebased against latest origin/main (5440bf99b)\n- Created two integration task specs to unblock P88 and P85:\n\n**Created:**\n- `docs/planning/specs/e90797ac_p88_provenance_infra_spec.md` — P88 infrastructure: pinned_artifacts column in analyses table + GET /api/analysis/{id}/provenance endpoint exposing verify_reproducibility()\n- `docs/planning/specs/e90797ac_p85_origin_tracking_spec.md` — P85 frontend: origin badges (INTERNAL/EXTERNAL) on artifact detail pages at /artifacts/{id}\n\n**Key findings from spec sweep:**\n- 1693 spec files across all quests\n- Quest:Agora (2 open), Quest:Forge (6 open), Quest:Atlas (3 open), Quest:Exchange (5 open), Quest:Sender (9 open)\n- P86 (Dashboard): Dashboard already registered (`dashboard-knowledge-growth-monitor`) with full data_sources (paper_count, hypothesis_count, kg_edge_count, analysis_count, wiki_count SQL queries). `render_dashboard()` and `/api/dashboard/{id}/refresh` both fully implemented. **Unblocked — needs only verification that the dashboard page at /dashboard/{id} renders correctly**\n- P88 (Provenance): `verify_reproducibility()` exists in `scripts/test_reproducibility.py` but not exposed via API. `pinned_artifacts` column missing from analyses table. assemble_provenance_demo.py exists but wasn't run.\n- P85 (Origin): `origin_type`/`origin_url` columns exist in DB. Frontend badges NOT rendered on artifact detail page. Need to add to api.py artifact detail page.\n- P89 (Biophysical model): Commit f5f36ad25 on branch `forge-startup-logging-20260413041942` — model code exists but NOT on main yet (f5f36ad25 is on a non-main branch). Verified in worktree that `forge/biophysical_models/microglial_activation.py`, `site/figures/models/microglial_activation/time_course.png`, `site/figures/models/microglial_activation/sensitivity_tornado.png` exist.\n- P92 (Versioned protein design): COMPLETED per prior audit\n- P87 (Dynamic authored paper): COMPLETED per prior audit\n\n**Recommended next steps:**\n1. Run assemble_provenance_demo.py to create the provenance chain artifact\n2. Execute the two new integration task specs (e90797ac_p88 and e90797ac_p85)\n3. Verify P86 dashboard page renders at /dashboard/dashboard-knowledge-growth-monitor\n4. Re-verify P89 (biophysical model) on main by checking forge/biophysical_models/ path\n\n### 2026-04-13 20:15 UTC — Slot minimax:55 (reopened audit)\n- Task: [Demo] Recurring: Read all quest/task specs, identify demo-ready features, create integration tasks [task:e90797ac-25a5-4bdb-b4ca-5bfe8f9c04aa]\n- Hard-reset to origin/main to clear prior worktree state; re-investigated from first principles\n- Live system stats (2026-04-13 20:15 UTC): 414 hypotheses, 291 analyses, 701K KG edges (from DB), 405 notebooks\n- Cross-checked P88/P86/P85/P91 dependencies against live API and artifact_registry code\n\n**Detailed dependency verification:**\n\n| Priority | Task | Status | Verified blockers |\n|---|---|---|---|\n| P93 | CI: Verify demo pages | Ongoing recurring CI | None |\n| P92 | Versioned artifact demo | COMPLETED | None |\n| P91 | Register Allen Brain Cell Atlas | UNSTARTED | Independent; no infra blockers |\n| P90 | Tabular gene expression demo | PARTIAL | KG integration not verified via code inspection |\n| P89 | Biophysical model | PARTIAL | Code not verified |\n| P88 | End-to-end provenance demo | UNSTARTED | See analysis below |\n| P87 | Dynamic authored paper | COMPLETED | None |\n| P86 | Knowledge Growth Dashboard | UNSTARTED | **UNBLOCKED** — see below |\n| P85 | Origin tracking showcase | UNSTARTED | See analysis below |\n\n**P88 (Provenance Demo) — Detailed analysis:**\n- `GET /api/artifacts/{id}/provenance` → returns `build_provenance_chain()` from artifact_links (WORKS, 6-entry chain for h-seaad-v4-26ba859b)\n- `GET /api/artifacts/{id}/provenance-graph` → returns graph with 4 nodes, 6 edges (WORKS)\n- `render_dashboard()` in `scidex/atlas/artifact_registry.py:811` fully implements `{{data:KEY}}` substitution via sql_query, artifact_ref, api_endpoint sources (WORKS)\n- `pinned_artifacts` field NOT in analysis metadata — provenance is computed live from artifact_links, not from pre-pinned versions\n- `verify_reproducibility()` NOT implemented anywhere — script exists in `scripts/test_reproducibility.py` but is not exposed via API\n- **What P88 actually needs**: (1) `pinned_artifacts` column in `analyses` table, (2) `verify_reproducibility()` function exposed at `GET /api/analysis/{id}/provenance`, (3) artifact link chain connecting 8 chain nodes\n\n**P86 (Dashboard Demo) — UNBLOCKED:**\n- `render_dashboard()` fully implemented with `{{data:KEY}}` substitution supporting sql_query, artifact_ref, api_endpoint (artifact_registry.py:811)\n- `/api/dashboard/{id}/refresh` → calls `artifact_registry.render_dashboard()` → evaluates SQL → persists rendered_html → returns JSON (WORKS)\n- Frontend polling auto-refresh wired in dashboard_standalone page (api.py:17758)\n- **No missing infrastructure** — only needs a registered dashboard artifact with the right data_sources/metadata\n- `a17-30-DREF0001` (data source refresh engine) is already implemented — `render_dashboard()` IS the refresh engine\n- Recommended: Register \"SciDEX Knowledge Growth Monitor\" dashboard artifact with data_sources = paper_count, hypothesis_count, kg_edge_count, analysis_count, wiki_count SQL queries\n\n**P85 (Origin Tracking) — Needs verification:**\n- `origin_type` and `origin_url` columns exist in artifacts table\n- Origin badges mentioned in prior work log but NOT visible in artifact detail page grep check\n- `a17-26-ORIG0001` may need a frontend component on artifact detail pages to show \"INTERNAL\"/\"EXTERNAL\" badges\n- d16-25 (authored paper) is DONE, providing an internal artifact example\n- Recommended: Verify origin badges appear on `/artifacts/{id}` detail page; if missing, add frontend rendering\n\n**P91 (Allen Brain Cell Atlas) — Independent, no blockers:**\n- d16-03 (aging mouse atlas) is a SEPARATE task, not a blocker\n- Allen Brain Atlas API access needs verification but infrastructure is ready\n- Could bootstrap from SEA-AD MTG 10x dataset already registered\n\n**Recommended integration tasks to spawn (one-shot):**\n\n1. **[Atlas] Expose verify_reproducibility via API + pinned_artifacts in analysis metadata**\n - Priority: P88\n - Spec: `docs/planning/specs/e90797ac_p88_provenance_infra_spec.md`\n - Details: Add pinned_artifacts column to analyses table, expose verify_reproducibility() at GET /api/analysis/{id}/provenance\n\n2. **[Atlas] Add origin tracking badges to artifact detail pages**\n - Priority: P85\n - Spec: `docs/planning/specs/e90797ac_p85_origin_tracking_spec.md`\n - Details: Add INTERNAL/EXTERNAL badges to /artifacts/{id} page, wire origin_type and origin_url\n","spec_html":"

Quest: Demo

Layer: Cross-cutting \nPriority: P99 \nStatus: active \nTasks: 468 total (79 done, 9 open)

Vision

Demo showcase & end-to-end flows — polished demos exercising all five layers

> Demos must showcase scientifically meaningful outputs, not stub pages or placeholder content. Each demo task specifies: what hypothesis/gap/analysis is being demonstrated, what evidence or result it produces, and why the result is non-obvious. Acceptance: demo produces >1 artifact with >50KB content and >3 cross-links to other demos. Multi-demo batches use parallel agents.

Open Tasks

☐ [Demo] CI: Verify all demo pages load correctly with rich content (P93)
\n
☐ [Demo] Versioned artifact demo: create protein design with 3 iterations (P92)
\n
☐ [Demo] Register Allen Brain Cell Atlas as external dataset artifact (P91)
\n
☐ [Demo] Tabular dataset demo: gene expression matrix linked to KG entities (P90)
\n
☐ [Demo] Build simple biophysical model from KG-derived parameters (P89)
\n
☐ [Demo] End-to-end provenance demo: trace reasoning chain from paper to model (P88)
\n
☐ [Demo] Create dynamic authored paper: SEA-AD Microglial Activation Review (P87)
\n
☐ [Demo] Create live dashboard: Knowledge Growth Monitor (P86)
\n
☐ [Demo] Origin tracking showcase: internal vs external artifact provenance (P85)

Success Criteria

☐ All open tasks completed and verified
\n
☐ Integration tested end-to-end with dependent quests
\n
☐ UI pages rendering correctly for this quest's features
\n
☐ Documentation updated for new capabilities

Work Log

2026-04-13 22:30 UTC — Slot minimax:55 (reopened audit, second pass)

\n
  • Task: [Demo] Recurring: Read all quest/task specs, identify demo-ready features, create integration tasks [task:e90797ac-25a5-4bdb-b4ca-5bfe8f9c04aa]
    • \n
  • Verified prior work (8cc8c1e01 — spec-only update, not merged to main) was correct analysis
    • \n
  • Rebased against latest origin/main (5440bf99b)
    • \n
  • Created two integration task specs to unblock P88 and P85:
    • \n
\nCreated:\n
  • docs/planning/specs/e90797ac_p88_provenance_infra_spec.md — P88 infrastructure: pinned_artifacts column in analyses table + GET /api/analysis/{id}/provenance endpoint exposing verify_reproducibility()
    • \n
  • docs/planning/specs/e90797ac_p85_origin_tracking_spec.md — P85 frontend: origin badges (INTERNAL/EXTERNAL) on artifact detail pages at /artifacts/{id}
    • \n
\nKey findings from spec sweep:\n
  • 1693 spec files across all quests
    • \n
  • Quest:Agora (2 open), Quest:Forge (6 open), Quest:Atlas (3 open), Quest:Exchange (5 open), Quest:Sender (9 open)
    • \n
  • P86 (Dashboard): Dashboard already registered (dashboard-knowledge-growth-monitor) with full data_sources (paper_count, hypothesis_count, kg_edge_count, analysis_count, wiki_count SQL queries). render_dashboard() and /api/dashboard/{id}/refresh both fully implemented. Unblocked — needs only verification that the dashboard page at /dashboard/{id} renders correctly
    • \n
  • P88 (Provenance): verify_reproducibility() exists in scripts/test_reproducibility.py but not exposed via API. pinned_artifacts column missing from analyses table. assemble_provenance_demo.py exists but wasn't run.
    • \n
  • P85 (Origin): origin_type/origin_url columns exist in DB. Frontend badges NOT rendered on artifact detail page. Need to add to api.py artifact detail page.
    • \n
  • P89 (Biophysical model): Commit f5f36ad25 on branch forge-startup-logging-20260413041942 — model code exists but NOT on main yet (f5f36ad25 is on a non-main branch). Verified in worktree that forge/biophysical_models/microglial_activation.py, site/figures/models/microglial_activation/time_course.png, site/figures/models/microglial_activation/sensitivity_tornado.png exist.
    • \n
  • P92 (Versioned protein design): COMPLETED per prior audit
    • \n
  • P87 (Dynamic authored paper): COMPLETED per prior audit
    • \n
\nRecommended next steps:\n
  • Run assemble_provenance_demo.py to create the provenance chain artifact
    • \n
  • Execute the two new integration task specs (e90797ac_p88 and e90797ac_p85)
    • \n
  • Verify P86 dashboard page renders at /dashboard/dashboard-knowledge-growth-monitor
    • \n
  • Re-verify P89 (biophysical model) on main by checking forge/biophysical_models/ path

    • 2026-04-13 20:15 UTC — Slot minimax:55 (reopened audit)

    \n
    • Task: [Demo] Recurring: Read all quest/task specs, identify demo-ready features, create integration tasks [task:e90797ac-25a5-4bdb-b4ca-5bfe8f9c04aa]
      • \n
    • Hard-reset to origin/main to clear prior worktree state; re-investigated from first principles
      • \n
    • Live system stats (2026-04-13 20:15 UTC): 414 hypotheses, 291 analyses, 701K KG edges (from DB), 405 notebooks
      • \n
    • Cross-checked P88/P86/P85/P91 dependencies against live API and artifact_registry code
      • \n
    \nDetailed dependency verification:

    PriorityTaskStatusVerified blockers
    P93CI: Verify demo pagesOngoing recurring CINone
    P92Versioned artifact demoCOMPLETEDNone
    P91Register Allen Brain Cell AtlasUNSTARTEDIndependent; no infra blockers
    P90Tabular gene expression demoPARTIALKG integration not verified via code inspection
    P89Biophysical modelPARTIALCode not verified
    P88End-to-end provenance demoUNSTARTEDSee analysis below
    P87Dynamic authored paperCOMPLETEDNone
    P86Knowledge Growth DashboardUNSTARTEDUNBLOCKED — see below
    P85Origin tracking showcaseUNSTARTEDSee analysis below
    \nP88 (Provenance Demo) — Detailed analysis:\n

    • GET /api/artifacts/{id}/provenance → returns build_provenance_chain() from artifact_links (WORKS, 6-entry chain for h-seaad-v4-26ba859b)
      • \n
    • GET /api/artifacts/{id}/provenance-graph → returns graph with 4 nodes, 6 edges (WORKS)
      • \n
    • render_dashboard() in scidex/atlas/artifact_registry.py:811 fully implements {{data:KEY}} substitution via sql_query, artifact_ref, api_endpoint sources (WORKS)
      • \n
    • pinned_artifacts field NOT in analysis metadata — provenance is computed live from artifact_links, not from pre-pinned versions
      • \n
    • verify_reproducibility() NOT implemented anywhere — script exists in scripts/test_reproducibility.py but is not exposed via API
      • \n
    • What P88 actually needs: (1) pinned_artifacts column in analyses table, (2) verify_reproducibility() function exposed at GET /api/analysis/{id}/provenance, (3) artifact link chain connecting 8 chain nodes
      • \n
    \nP86 (Dashboard Demo) — UNBLOCKED:\n
    • render_dashboard() fully implemented with {{data:KEY}} substitution supporting sql_query, artifact_ref, api_endpoint (artifact_registry.py:811)
      • \n
    • /api/dashboard/{id}/refresh → calls artifact_registry.render_dashboard() → evaluates SQL → persists rendered_html → returns JSON (WORKS)
      • \n
    • Frontend polling auto-refresh wired in dashboard_standalone page (api.py:17758)
      • \n
    • No missing infrastructure — only needs a registered dashboard artifact with the right data_sources/metadata
      • \n
    • a17-30-DREF0001 (data source refresh engine) is already implemented — render_dashboard() IS the refresh engine
      • \n
    • Recommended: Register "SciDEX Knowledge Growth Monitor" dashboard artifact with data_sources = paper_count, hypothesis_count, kg_edge_count, analysis_count, wiki_count SQL queries
      • \n
    \nP85 (Origin Tracking) — Needs verification:\n
    • origin_type and origin_url columns exist in artifacts table
      • \n
    • Origin badges mentioned in prior work log but NOT visible in artifact detail page grep check
      • \n
    • a17-26-ORIG0001 may need a frontend component on artifact detail pages to show "INTERNAL"/"EXTERNAL" badges
      • \n
    • d16-25 (authored paper) is DONE, providing an internal artifact example
      • \n
    • Recommended: Verify origin badges appear on /artifacts/{id} detail page; if missing, add frontend rendering
      • \n
    \nP91 (Allen Brain Cell Atlas) — Independent, no blockers:\n
    • d16-03 (aging mouse atlas) is a SEPARATE task, not a blocker
      • \n
    • Allen Brain Atlas API access needs verification but infrastructure is ready
      • \n
    • Could bootstrap from SEA-AD MTG 10x dataset already registered
      • \n
    \nRecommended integration tasks to spawn (one-shot):

  • [Atlas] Expose verify_reproducibility via API + pinned_artifacts in analysis metadata
    • \n - Priority: P88
    - Spec: docs/planning/specs/e90797ac_p88_provenance_infra_spec.md
    - Details: Add pinned_artifacts column to analyses table, expose verify_reproducibility() at GET /api/analysis/{id}/provenance

  • [Atlas] Add origin tracking badges to artifact detail pages
    • \n - Priority: P85
    - Spec: docs/planning/specs/e90797ac_p85_origin_tracking_spec.md
    - Details: Add INTERNAL/EXTERNAL badges to /artifacts/{id} page, wire origin_type and origin_url

    ","spec_file":"quest_demo_spec.md","commits":[{"hash":"abc8d0179","message":"[Exchange] Verify /challenge broken links are false positives: all 36 pages return 200 [task:e5a1490f-9ab6-4275-a96b-bd34ceb84fcf]","date":"2026-04-17"},{"hash":"440d6072c","message":"[Senate] Final work log update: document branch push to remote [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"8eefea2c0","message":"[Atlas] Add redirects in api.py for /site/notebooks/ and root-level .ipynb URLs to /notebooks/ path [task:f92194bf-f23c-4bf3-97d4-676c02f5fb42]","date":"2026-04-17"},{"hash":"bdf2e04e8","message":"[Atlas] Document /mission HTTP 0 fix: already addressed in c5d7a696 [task:e50f7fed-ccde-4104-b98a-205bb500e792]","date":"2026-04-17"},{"hash":"f39b5d3b0","message":"[Atlas] Fix broken /entity links: clean corrupted data + add cleanup script [task:326c7abd-3ad2-4ae5-9a0e-e9981d611890]","date":"2026-04-17"},{"hash":"a4954541c","message":"Squash merge: orchestra/task/09b3a393-broken-links-in-api-http-0-30-links (1 commits)","date":"2026-04-17"},{"hash":"40b62c4b8","message":"[Atlas] Verify /api broken links: all 10 endpoints HTTP 200, no code changes needed [task:09b3a393-777f-4379-85c6-2bf55f6e69c0]","date":"2026-04-17"},{"hash":"6e54e1ccc","message":"On orchestra/task/326c7abd-broken-links-in-entity-http-400-64-links: stash unrelated changes","date":"2026-04-17"},{"hash":"53f087f8e","message":"index on orchestra/task/326c7abd-broken-links-in-entity-http-400-64-links: f3b466710 [Atlas] Add /mission→/missions redirect in api.py; confirm /mission broken links are false positives [task:c0d66faa-91be-41e3-909d-d6359c5b936e]","date":"2026-04-17"},{"hash":"58b5eb786","message":"[Atlas] Verify /analysis broken links: all 10 pages HTTP 200, false positive [task:a7c6d6d2-17bb-4e1c-b131-10677c65e9d0]","date":"2026-04-17"},{"hash":"0be6ce64a","message":"[Senate] Update spec work log: service verified operational, no code changes needed [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"53c7da02f","message":"Squash merge: orchestra/task/c13f680a-broken-links-in-site-http-404-198-links (1 commits)","date":"2026-04-17"},{"hash":"20a14e537","message":"[Atlas] Fix /site/notebooks/ 404 in api.py: add redirect to /notebooks/ route [task:c13f680a-60bf-49f3-aa42-a05602d77405]","date":"2026-04-17"},{"hash":"52e043bda","message":"Squash merge: orchestra/task/c5d7a696-broken-links-in-target-http-0-765-links (3 commits)","date":"2026-04-17"},{"hash":"aead3c46d","message":"[Atlas] Restore nb-top5- prefix-stripping fallback removed in prior commit [task:c5d7a696-2296-468a-83a2-2d3cabc6901e]","date":"2026-04-17"},{"hash":"1786c8cc4","message":"[Atlas] Wire up suppress_transient_http0_noise() in link checker to prevent false-positive tasks [task:c5d7a696-2296-468a-83a2-2d3cabc6901e]","date":"2026-04-17"},{"hash":"13c833f16","message":"[Atlas] Add redirects for /site/notebooks/ and root-level .ipynb URLs to /notebooks/ path [task:f92194bf-f23c-4bf3-97d4-676c02f5fb42]","date":"2026-04-17"},{"hash":"25d912117","message":"[Senate] Update spec work log: document MERGE GATE rebase fix [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"06151c073","message":"[Senate] Update spec: verify service operational, no code changes needed [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"dc15730ae","message":"[Atlas] Fix /notebook top5-SDA-* broken links: add prefix-stripping fallback in notebook_detail [task:c13f680a-60bf-49f3-aa42-a05602d77405]","date":"2026-04-17"}],"related_quests":[{"name":"Epistemic Rigor","layer":"Cross-cutting","priority":95,"status":"active","description":"Evolve SciDEX toward rigorous scientific epistemology: 6-tier epistemic classification (T0 axiom → T5 contested) with asymmetric promotion/demotion (Gödel Machine principle), adversarial Falsifier persona as 5th debate round, proof-gated KG updates with contradiction checking against established knowledge, GFlowNet-inspired diverse hypothesis portfolio maintenance (anti-monoculture rules), pre-registration of predictions before analysis, replication status tracking (unreplicated/replicated/failed_replication), and calibration-adjusted believability weights. Every claim must be traceable to ground truth.","task_count":14,"done_count":14},{"name":"Search","layer":"Cross-cutting","priority":95,"status":"active","description":"Universal search across all SciDEX content with autocomplete","task_count":200,"done_count":13},{"name":"Economics","layer":"Cross-cutting","priority":94,"status":"active","description":"Resource economics — token/cost tracking, belief evolution, impact scoring. Extends to quadratic staking (agents stake reputation quadratically for high-confidence assertions), calibration tracking (per-persona hit rate on predictions vs outcomes), GFlowNet-inspired diversity bonuses (reward-proportional resource allocation preserving competing hypotheses), and contested claim prediction markets.","task_count":196,"done_count":9},{"name":"Evolutionary Arenas","layer":"Cross-cutting","priority":73,"status":"active","description":"Elo tournaments × LMSR markets × evolutionary operators for scientific artifacts. Pairwise LLM-judged matches produce quality signals that fuse with market prices; top-ranked artifacts spawn mutate/crossover/refine variants; adaptive loops dig deeper on winners. Bridges Bradley-Terry ≡ Elo ≡ LMSR via shared functional form. Spec: docs/planning/specs/q-evolutionary-arenas_spec.md","task_count":8,"done_count":7},{"name":"Resources","layer":"Cross-cutting","priority":70,"status":"active","description":"Resource tracking — Bedrock costs, API call logging, budget monitoring","task_count":1,"done_count":1},{"name":"Artifacts","layer":"Cross-cutting","priority":68,"status":"active","description":"Rich artifacts & computational notebooks. Artifact lifecycle governance: git-like versioning (version_number, parent_version_id, changelog), lifecycle states (active/deprecated/cold/superseded), supersession chains with forward reference resolution, dependency tracking, never-delete policy. Deduplication agent scans for duplicates and produces merge recommendations for governance review.","task_count":466,"done_count":89}]}