{"quest":{"id":"3aa7ff54-d3c","name":"Exchange","description":"Hypothesis prediction market — score, track, and compare hypotheses","layer":"Exchange","priority":95,"status":"active","created_at":"2026-04-02T10:00:57.209491+00:00","updated_at":"2026-04-10T14:44:10.355870+00:00"},"tasks":[{"id":"1f62e277-c72c-48f3-95f6-49f02b72cca7","title":"[Exchange] Evolve economics, markets, and incentive ecology","description":"Master quest: Continuously improve SciDEX economic infrastructure. Workstreams: (1) threaded comments & voting, (2) generalized multi-asset markets, (3) agent reputation & token economy, (4) market proposal governance, (5) comment-driven price signals. 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Recalculate composite scores incorporating new evidence.\n\n[2026-04-05 update] [Exchange] CI: Update hypothesis scores — consider Elo ratings alongside composite scores","status":"open","priority":96,"task_type":"recurring","frequency":"every-2h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T20:08:20.733355+00:00","updated_at":"2026-04-17T20:08:20.733355+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/9d82cf53-fac_exchange_ci_update_hypothesis_scores_fr_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 5, \"safety\": 9}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"codex\", \"_stall_requeued_at\": \"2026-04-11 03:23:03\", \"completion_shas\": [\"d6e4d69582e1f16c25a89bc2b1ddf5d6e39d0058\", \"c368b80d371327e98bdf552eeec059655714b3af\", \"6b7e0a09a36c9533741ed14f6c3210893e62208e\", \"8b261095c957c22f45ef729fcf3f90ca8a9cb1ce\", \"a9a6f4c38868cc573cf6f8e868f6bacc57eca289\", \"0e216535c287c5b688470bd3230158eeff20cbf1\", \"638dd1b139c7f5567cf5d756639a3d91c23d4aa6\", \"c151b0a2f48833aad22360cea1ac25312c2867a4\", \"024b048bed2ea49f37ef0ab3a1e5bf6bed4465d4\", \"1c01bf952c71491fdb9f2850c8236444aa56a75e\", \"276d122e479b9ca6fa237d2654eeb641d77b0ef1\", \"d08276b46267377147ec9f5529bad97cfd07d6d2\", \"6e06ea7b91064564bc9421c5db7f3251a3ae42c9\", \"797f6d245cdd2f1477161bfc6555f30d6f340787\", \"61337777aca5e61716126a9c7764f30685dc2a7b\", \"14aaff1a7c83892ccb43f259b59cbf31ecf9c649\", \"3e6798b48f6a6a36bf1df444cb73a54f3964339e\", \"86574aa5895201f9d634ecde4c1f3281c8125b58\", \"b1e831f93e33626910bda5085bfd7f25ddf26927\", \"3f6391e0786418991b35ec3d2d3f952939302413\", \"df50463ef976af011c79431fa17446e40e3d6c0e\", \"25173fab7606fefac46007da16c52a4e7c4ff3c2\", \"6886e80b175788a4b4e7224c7cf38da40d0d4daa\", \"652a193482a975d6261286adbaddb6cbdd86ba0e\", \"ce1ec141eeea6e7a6fe9a73f2a805ad033080a05\"], \"completion_shas_checked_at\": \"2026-04-13T05:47:09.348822+00:00\", \"completion_shas_missing\": [\"2d2e5233aaefd0e498ae9c36d290ee29ecb109ef\", \"e4e43aebac98fe4eb5c1fd34f8b0a3ea695aeac8\", \"60a0a1775c2857346603f637f66be8134e18b4a3\", \"a7e011ac5c57bbed1a52484b577790d683aed67a\", \"6849f29c8ea1e343895fb3c3f719c4cd597d2f47\", \"5a04529ae05a8fe829b67208befc06307edbec41\", \"863690a39964adeb2b3658471f35190d634d0640\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"5e1e4ce0-fce2-4c8a-90ac-dd46cf9bb139","title":"[Exchange] Periodic market participant evaluation of top hypotheses","description":"Every 6h: each active market participant evaluates top 20 hypotheses by market volume. Aggregate signals with believability weighting. Apply price adjustments. Track accuracy (did price move in predicted direction within 24h?). Update participant believability scores.","status":"open","priority":95,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T15:03:16.426141+00:00","updated_at":"2026-04-17T15:03:16.426141+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/5e1e4ce0_fce_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 6, \"safety\": 9}, \"completion_shas\": [\"67c8fa936c329d885d467a305137f81adb62b2dc\", \"86e354b16bdc7bf5b9563cd595f3fb8cc3f469ee\", \"029d8c9f770c513362f7b25793d55060a02ce8fa\", \"50d1ab055b181cee6505aa1dfafd6689f9d7504d\"], \"completion_shas_checked_at\": \"2026-04-13T00:41:27.109902+00:00\", \"completion_shas_missing\": [\"9f13dece50d48f21440399d1c58ff94f4d5b002a\", \"979f496b1a9afd2ca0e8574b94e4ae1544709336\", \"079bae9fd8973cde4d7036a2f34cc769a19091fc\", \"af4157e883caf12b9c38ec6a13740ca4d2b03fa3\", \"88f5c14a3fa159e3a8b171b9fc6ddac11d65f420\", \"fa1a745d2fc2087edf98fc1c713190360450686a\", \"1a000c44fbf11ef31a2d5fc84df2e8179d45ecc7\", \"78ba2b7b94eeb40fdbf4c8beeaa10312173f2c94\", \"aff58c892eaa365c2cd0a24181fdf7ba364fa99c\", \"e3535236b74e170c90eb8d8e233924aac65ab0a2\", \"fba7d62be56ecd35b5416ca7ac6b9924a948fdc6\", \"928a836aba9ba683024e700e45819f70dc3a1d12\", \"062e628bad2c7d421448ec5d568e8c49c59dca4d\", \"a341b5f27a885f4bd63fe41a06d7679b2d813b5b\", \"4d6cc1d77132805a6fbfa03b6a36344f92318c8e\", \"167835a4d5f88195a0513a9960449c7ab711593b\", \"76baab518370b68366543b1b103e43c965afaef7\", \"6881fb12f060cebc892976ba191ca8728b158d13\", \"748af5bb3c3719e444fbedf9f5e75e8ca1b70b56\", \"fd5fc1484187f89a9dc802a40b47a4659349dff9\"]}"},{"id":"33803258-84bd-4bde-873b-740f1de9d1c3","title":"[Exchange] CI: Backfill evidence_for/evidence_against with PubMed citations","description":"Find hypotheses missing evidence arrays. Use PubMed API to find relevant papers and populate evidence_for and evidence_against.","status":"open","priority":94,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T16:54:57.825156+00:00","updated_at":"2026-04-17T16:54:57.825156+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/33803258-84b_exchange_ci_backfill_evidence_for_evide_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 9}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"codex\", \"_stall_requeued_at\": \"2026-04-11 03:02:00\", \"completion_shas\": [\"dd83d54fdf0d5cd56fd987305b0279e984fc460b\"], \"completion_shas_checked_at\": \"2026-04-13T07:18:33.787170+00:00\", \"completion_shas_missing\": [\"ee402c0247fe7a5a7ce2173a0f5922b53d7581c1\", 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\"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"24d68b79-e096-48c5-9503-c835ac5e2010","title":"[Exchange] Enrich 7 thin EC Layer II vulnerability hypotheses with deep descriptions and evidence","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"open","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:48:40","updated_at":"2026-04-13T10:16:02.340542+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: NO_COMMITS — No commits found referencing task ID; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/24d68b79_e09_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 9, \"safety\": 10}}"},{"id":"79a35fbd-3e3c-48dc-8462-08498e9bbe96","title":"[Exchange] Add gene expression context to top 5 hypotheses missing it + enrich 2 fully bare hypotheses","description":"REQUEUED — SPEC FILE MISSING: Spec file not found on disk. See original task description for context. Before doing work, verify the spec exists on main or create one.","status":"open","priority":89,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T14:50:37.959770+00:00","updated_at":"2026-04-17T14:50:37.959770+00:00","summary":"","completion_notes":"","last_error":"worker_exit_unclean exit_code=0","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/79a35fbd_3e3_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"a449718f-5325-4a2e-a21f-13fc9affb784","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"623 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"open","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T06:47:21.972781+00:00","updated_at":"2026-04-17T06:47:21.972781+00:00","summary":"","completion_notes":"","last_error":"rate_limit_retries_exhausted:glm","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{}"},{"id":"b634c4b2-1059-487d-bd1f-75526d74dc0f","title":"[Exchange] Enrich evidence citations for top hypotheses with thin evidence","description":"Several high-scoring hypotheses (h-84808267, h-ae1b2beb, h-58e4635a) have minimal or missing evidence_for/evidence_against citations. Enrich these with verified PubMed PMIDs. Directly supports 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"open","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T00:09:37.632157+00:00","updated_at":"2026-04-17T00:09:37.632157+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/b634c4b2_105_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"3f19681e-0f22-4daa-a95b-71956505d642","title":"[Exchange] Enrich 5 thin hypotheses with deep descriptions, evidence, and pathway diagrams","description":"Enrich h-470ff83e, h-a20e0cbb, h-d2722680, h-44195347, h-4113b0e8 with 2000+ word descriptions, PubMed evidence, and mermaid pathway diagrams. These have <300 char descriptions currently.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"open","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:50:16","updated_at":"2026-04-13T10:16:02.320827+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: NO_COMMITS — No commits found referencing task ID; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3f19681e_0f2_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"88e25c11-8f65-49e8-a4c4-ec4432a18ccf","title":"[Exchange] Full enrichment batch 4 — pathway diagrams, clinical trials, gene expression for 5 more hypotheses","description":"Full enrichment for: NAD+ Depletion Rescue (h-cb833ed8), P2Y12 Inverse Agonist (h-f99ce4ca), C1q Mimetic Decoy (h-1fe4ba9b), Lysyl Oxidase Inhibition (h-82922df8), PARP1 Inhibition (h-69919c49). Each gets pathway diagram, clinical trials, gene expression context.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"open","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:51:16","updated_at":"2026-04-13T10:16:02.313929+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: NO_COMMITS — No commits found referencing task ID; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/88e25c11_8f6_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"1eda5888-4f2b-4bd9-b16f-9dbaf6766a8f","title":"[Exchange] Add protocols to 10 experiments","description":"REQUEUED — SPEC FILE MISSING: Spec file not found on disk. See original task description for context. Before doing work, verify the spec exists on main or create one.","status":"open","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:26:25.592595+00:00","updated_at":"2026-04-17T11:05:18.379495+00:00","summary":"","completion_notes":"","last_error":"worker_exit_unclean exit_code=0","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1eda5888_4f2b_exchange_protocols_spec.md","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"68f868ec-c0ab-4081-bbca-b07af2cd4fbb","title":"[Exchange] Enrich 5 thin hypotheses batch 3 — deep descriptions and pathway diagrams","description":"REQUEUED — SPEC FILE MISSING: Spec file not found on disk. See original task description for context. Before doing work, verify the spec exists on main or create one.","status":"open","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:37:51","updated_at":"2026-04-17T11:05:17.781554+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: NO_COMMITS — No commits found referencing task ID; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/68f868ec_c0a_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"1b911c77-4c4e-4dbe-a320-0cb129f1c38b","title":"[Exchange] CI: Enrich thin hypotheses — expand next 5 descriptions","description":"Find hypotheses with description < 500 chars. Pick 5 and expand each to 1000+ words with mechanism details, evidence, and clinical relevance.","status":"open","priority":87,"task_type":"recurring","frequency":"every-2h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T05:41:36.741971+00:00","updated_at":"2026-04-17T05:41:36.741971+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/1b911c77-4c4_exchange_ci_enrich_thin_hypotheses_expa_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 5}, \"completion_shas\": [\"d7ec867726b6f4833a62f16cde1887b95922a268\", \"fd9f849b61daf8be670c71794d777efb497a284b\"], \"completion_shas_checked_at\": \"2026-04-13T06:49:11.443557+00:00\", \"completion_shas_missing\": [\"8e9f12ff3dc5629a5f059a8e8e44fa3ecc3acf6c\", \"d51adece926e970c67e048fffd433ad7df3a8c38\", \"4c98ae8914fba6d2e518e5a19e147d735e1aa55d\", \"20653b8738aafada932e51b19ad73299d8b7a126\", \"7a2c492adb00ac35887f4cceec051a84ae53f0ff\", \"fcafe4ff0d2653d388749b3fdf2f2a31cc414bef\", \"d00be33b06eae212bac4c1211474b25fb2d57c84\", \"e30d29577c3d6cdff0ab462e487455036c70efca\", \"f84074142b0fcc699cd17f7d6357611aaa7f73ce\", \"0c9cae10491e2a043566db0c84591f26e072920c\", \"a6abf1c2028f35d745734781a2c2fb12ee6481de\", \"823687e2c8fb442443f297d9c4d3eeceec774bd7\", \"747d6f1602322c926664a81fda3587cb8b9a055a\", \"39e285e8d62849d1bb9e81f706fd343b83a8221f\", \"d5deccb700955d40c97e4ae2c280d6bb8135ad2b\", \"29628917fc4e7e37d45a984e59d0e9f33a6c6b45\", \"0a5a8fc2707cd05681bc1c6fdcc5a99bb63ec56b\", \"fa7056badc42a4adb2ac00e2a2a29d9cb7e06fe4\", \"f267ccd7a3d93af45af65a869925f4d1233c7f4f\", \"b55a130ace41399e68cf61a3705ee88befd09eaa\", \"555aeb9c86705abca7e1479e81e9a48644addf83\", \"8703f15988bb0f30476622bfeff94a376340c706\", \"b82b87e6883314b17cc4981c4a96180261117063\", \"9464569df5e9672a543504f24029939714269086\", \"f5f146320226b3e2d3a424555b0ee3a2802fc409\", \"80d753188834227a6c7a986c3e61e22e1a192095\"]}"},{"id":"44c29e33-4ef8-4f63-a97a-ff5b66471640","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"open","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"53","started_at":"2026-04-17T10:13:47.170502+00:00","completed_at":"2026-04-17T06:54:58.702264+00:00","updated_at":"2026-04-17 10:19:24","summary":"","completion_notes":"","last_error":"rate_limit_retries_exhausted:glm","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/44c29e33-4ef_exchange_enrich_experiment_descriptions_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 5}}"},{"id":"9455e56c-3e36-44d0-854c-6092020ab3bb","title":"[Exchange] Add protocols to 10 experiments","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\n64 experiments lack detailed protocols. Add methods, controls, expected outcomes, success 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"open","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:38:19.850177+00:00","updated_at":"2026-04-16T22:38:19.850177+00:00","summary":"","completion_notes":"","last_error":"worker_exit_unclean exit_code=0","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"8a0f4dbf-435b-4d49-a121-7351a3af8b3e","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"open","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 05:24:15","updated_at":"2026-04-13T10:15:59.645632+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: NO_COMMITS — No commits found referencing task ID; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8a0f4dbf-435_exchange_bulk_enrich_hypotheses_expand_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 5}}"},{"id":"9b2fabdb-60f4-4130-b1aa-f7694d2ff572","title":"[Exchange] Update hypothesis market prices from recent evidence and debate outcomes","description":"Recalculate market prices for hypotheses that have received new evidence or debate rounds since last pricing.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"open","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 09:09:24","updated_at":"2026-04-13T10:14:01.108439+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: NO_COMMITS — No commits found referencing task ID; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"b13f71fa-4650-4cde-972d-879789a6b47b","title":"[Exchange] Update hypothesis market prices from recent evidence and debate outcomes","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\nRecalculate market prices for hypotheses that have received new evidence or debate rounds since last pricing.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"open","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-09 01:51:01","updated_at":"2026-04-13T10:12:59.548783+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: ORPHAN_BRANCH — 1 commit(s) found but none on main; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"992a786c-5fa3-4bc0-9b63-7fe40d01391d","title":"[Exchange] Enrich top 3 hypotheses 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-13T19:00:25.500281+00:00","updated_at":"2026-04-13T19:00:25.500281+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/992a786c_5fa_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"3520762bd3b8ac1c9d017e3676a1808faa1ab85a\"], \"completion_shas_checked_at\": \"2026-04-13T19:00:25.479198+00:00\", \"completion_shas_missing\": [\"c6e8e08af16a417dc7e3f8e453bb893ca3a883c4\", \"bc8a157c3fa87ac83ff6aadbce872ecff4d6ad58\"]}"},{"id":"7f2937e4-5a23-40c3-afaa-0b6753e8cfdc","title":"[Exchange] Enrich top-scoring thin hypotheses — APOE4-Lipidation, APOE4-to-APOE2, Stress Granule","description":"Enrich the top 3 highest-scoring hypotheses that still have thin descriptions (<300 chars) and no evidence. Target: h-11ba42d0 (APOE4-Lipidation, score 0.845), h-81949907 (APOE4-to-APOE2, score 0.76), h-14c98fa1 (Stress Granule Dissolution, score 0.71). Each should get: 2000+ word description with mechanism details, evidence_for with PubMed citations, evidence_against, pathway context.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T10:42:54.558650+00:00","updated_at":"2026-04-16T10:42:54.558650+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7f2937e4_5a2_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 11:59:32\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"fd48d578a\"], \"completion_shas_checked_at\": \"2026-04-16T10:42:54.540447+00:00\"}"},{"id":"0ba4bce7-a8f5-459f-8b20-797e10e95464","title":"[Exchange] Enrich top 5 unenriched hypotheses with pathway diagrams, evidence, clinical trials","description":"D16.1 priority: Hypotheses h-51e7234f (APOE Autophagy, 0.80), h-3d545f4e (Butyrate Microglia, 0.79), h-5d943bfc (Proteostasis APOE, 0.745), h-d4f71a6b (TG2 Inhibition, 0.725), h-f3fb3b91 (TLR4 Modulation, 0.71) all lack pathway_diagram, clinical_trials, evidence_for, evidence_against. Enrich them.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-13T20:45:19.728019+00:00","updated_at":"2026-04-13T20:45:19.728019+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/0ba4bce7_a8f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"d62ee7aa63caf10ebe328c9dd1774b92bae16822\", \"7de1a879afa901c7bbd2a81870e98359dc40bcfb\"], \"completion_shas_checked_at\": \"2026-04-13T20:45:19.708854+00:00\"}"},{"id":"3b1eaa64-00a1-40ef-95b3-3224af316fb6","title":"[Exchange] Enrich top SEA-AD hypothesis with PubMed citations and evidence","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-13T20:42:31.869898+00:00","updated_at":"2026-04-13T20:42:31.869898+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/3b1eaa64_00a_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"a0d6837fda53163464ea15eff0be42df91aca094\"], \"completion_shas_checked_at\": \"2026-04-13T20:42:31.849682+00:00\"}"},{"id":"82243992-25c7-462c-b306-dbd5d07c6585","title":"[Exchange] Enrich hypotheses 4-10 to demo quality","description":"Expand descriptions and evidence for hypotheses ranked 4-10 to match the quality of top 3.\n\nCurrent state:\n- Top 3 hypotheses have 8000-12000 char descriptions with detailed mechanisms\n- Hypotheses 4-10 have only 200-300 char descriptions\n\nHypotheses to enrich:\n4. CYP46A1 Overexpression Gene Therapy (201 chars) → 8000+ chars\n5. Gamma entrainment therapy to restore hippocampal-cortical synchrony (298 chars)\n6. Membrane Cholesterol Gradient Modulators (203 chars)\n7. SASP-Mediated Complement Cascade Amplification (307 chars)\n8. AMPK hypersensitivity in astrocytes (287 chars)\n9. Transcriptional Autophagy-Lysosome Coupling (221 chars)\n10. TREM2-mediated microglial tau clearance enhancement (224 chars)\n\nFor each hypothesis, expand description to include:\n- Mechanistic foundation (2-3 paragraphs on biological mechanism)\n- Supporting evidence from multiple lines (genetics, cell culture, animal models, human data)\n- Therapeutic rationale and design principles\n- Clinical translation pathway (Phase 1/2/3 roadmap)\n- Challenges and risk mitigation\n- Resource requirements and timeline\n- Competitive landscape\n\nAlso enrich evidence_for/evidence_against:\n- Add 8-10 PubMed citations per hypothesis with abstracts\n- Include strength ratings (high/medium/low)\n- Cover supporting AND contradicting evidence\n\nTest: Visit /exchange and /hypothesis/{id} pages to verify rich content displays correctly.\n\nThis is Quest 16 (Demo Showcase) priority - these become the hero pages visitors explore first.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-17T04:13:09.838274+00:00","updated_at":"2026-04-17T04:13:09.838274+00:00","summary":"","completion_notes":"Enrichment is a database content operation performed by prior agent (commit 91a577751, orphaned). Data persists in scidex.db across main resets. Verified 4 independent times (minimax:56, glm-5:50, glm-5:51, glm-5:51-2nd). No code changes possible — the enrichment targets are DB rows, not source files.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/82243992_25c_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"fc09221ec748bad79ba1448ba2c34cc85083c3e2\", \"91a5777512e8186dfbf243b3a2e152a6bb49e64f\", \"c9de6aba1c64eaa1ab719bad6bdfbfdcf69f44ba\"], \"completion_shas_checked_at\": \"2026-04-13T22:43:26.139126+00:00\"}"},{"id":"06d452a0-87b3-423a-96ed-c84c6fa59188","title":"[Exchange] Enrich top hypothesis h-61196ade — evidence, gene expression","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-15T21:38:40.240704+00:00","updated_at":"2026-04-15T21:38:40.240704+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/06d452a0_87b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 23:45:49\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"26550570-5abe-42bf-9253-74fd337df610","title":"[Exchange] Enrich top thin hypotheses with rich descriptions, mermaid diagrams, and citations","description":"Enrich the highest-scoring hypotheses that have thin descriptions (<500 chars) with 2000+ word descriptions including mechanism details, PubMed citations, evidence chains, and mermaid pathway diagrams. Focus on top 5 by composite_score: h-51e7234f (0.8), h-3d545f4e (0.79), h-5d943bfc (0.745), h-d4f71a6b (0.725), h-f3fb3b91 (0.71).\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-15T20:09:36.342424+00:00","updated_at":"2026-04-15T20:09:36.342424+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/26550570_5ab_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 23:32:35\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"33c114fa-1a5f-42ac-a50b-9c468cd5548d","title":"[Exchange] Add mermaid pathway diagrams to top 10 hypothesis descriptions","description":"Add mermaid pathway diagrams to hypothesis descriptions for the top 10 scoring hypotheses that don't have them yet. Each diagram should show the mechanistic pathway (gene -> protein interaction -> cellular process -> disease outcome). Update the description field in the hypotheses table. This enriches the hypothesis detail pages which render mermaid diagrams.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-13T23:21:13.687352+00:00","updated_at":"2026-04-13T23:21:13.687352+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/33c114fa_1a5_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"86af224b2345c60cb393fcc7aa27eb34e2bade96\", \"ac276bbeda744255afef431d00b585a049272956\"], \"completion_shas_checked_at\": \"2026-04-13T23:21:13.670581+00:00\"}"},{"id":"25810cf2-e80a-4733-86ca-0654d1198894","title":"[Exchange] Enrich top thin hypotheses batch 2 — deep descriptions for 5 high-scoring hypotheses","description":"Enrich 5 high-scoring hypotheses that have thin descriptions (<300 chars) with deep 2000+ word descriptions, mechanism details, PubMed evidence, and pathway context. Target: h-3a901ec3 (Connexin-43, 0.72), h-d2722680 (TET2 Epigenetic, 0.70), h-019ad538 (Circadian Clock Reset, 0.70), h-4fabd9ce (Cryptic Exon Silencing, 0.70), h-8196b893 (Axonal RNA Transport, 0.70)\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-13T23:02:49.938381+00:00","updated_at":"2026-04-13T23:02:49.938381+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/25810cf2_e80_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"8818f0b27aa60967199bb11ebe0b14c5291a54aa\"], \"completion_shas_checked_at\": \"2026-04-13T23:02:49.921380+00:00\"}"},{"id":"36c7841f-59ed-4dba-adb1-dfbf7a145d25","title":"[Exchange] Enrich thin high-scoring hypotheses with rich descriptions","description":"Enrich hypotheses h-f3fb3b91 (TLR4, score 0.71) and h-180807e5 (APOE-TREM2, score 0.695) with rich 2000+ word descriptions, mechanism details, evidence chains, and pathway diagrams. These are top-scoring hypotheses with descriptions under 500 chars.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T00:21:07.109134+00:00","updated_at":"2026-04-16T00:21:07.109134+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/36c7841f_59e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 02:21:45\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"f570d8bf-ea77-4e6c-a06f-293c0b0b0070","title":"[Exchange] Enrich next batch of thin hypotheses (batch 2)","description":"Enrich hypotheses: h-180807e5 (APOE-TREM2, 0.695), h-54b9e0f5 (GAG Template, 0.665), h-a4e259e0 (Vagal Cholinergic, 0.66), h-16ee87a4 (Cx43 Mito Transfer, 0.63), h-63b7bacd (CRISPR Activation, 0.6). Skip h-2f43b42f (corrupt data).\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-14T02:28:41.614221+00:00","updated_at":"2026-04-14T02:28:41.614221+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/f570d8bf_ea7_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"e17583d8ce2419bd91a1f4362a635bbe73fbb22c\"], \"completion_shas_checked_at\": \"2026-04-14T02:28:41.586168+00:00\", \"completion_shas_missing\": [\"e6d2905705466f44075140c0411e29c242fa5881\"]}"},{"id":"ec517533-aa24-4aa5-94d3-38fcbe4ff812","title":"[Exchange] Wire threaded comment API endpoints — POST/GET/vote on any entity","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T01:07:07.009282+00:00","updated_at":"2026-04-16T01:07:07.009282+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/exch-ws1-01-CAPI_comment_api_endpoints_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 04:31:11\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"89595f0aae6a1b5be3144fabaa21f4021e79e918\"], \"completion_shas_checked_at\": \"2026-04-16T01:07:06.988541+00:00\"}"},{"id":"6958f72c-2a29-41a8-ad0e-dbc6a0b3a107","title":"[Exchange] Insert SEA-AD notebook hypotheses into DB","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T01:02:04.964218+00:00","updated_at":"2026-04-16T01:02:04.964218+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/6958f72c_2a2_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 03:48:21\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"4b454bbe85ab7e6b07c9315227e1f0dbee8cfca7\"], \"completion_shas_checked_at\": \"2026-04-16T01:02:04.947628+00:00\"}"},{"id":"7439ebbb-59c6-4e17-972b-6826f1bdb7cd","title":"[Exchange] Enrich top 5 zero-citation hypotheses with PubMed evidence and clinical context","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-14T03:45:15.449447+00:00","updated_at":"2026-04-14T03:45:15.449447+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/7439ebbb_59c_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"26c19ba0333f35921d3fd59ab3ed9ba28d33eb1f\"], \"completion_shas_checked_at\": \"2026-04-14T03:45:15.422565+00:00\"}"},{"id":"5d05dab9-df5e-4d9e-9bd9-7b332f2c16f5","title":"[Exchange] Enrich thin hypotheses batch 3 (scores 0.46-0.50)","description":"Enrich 5 hypotheses: h-075f1f02 (Brain Insulin Resistance), h-4b517512 (Glial Ketone Shunt), h-29ef94d5 (Epigenetic Memory), h-9adb5c9e (Gap Junction Hemichannels), h-8bd89d90 (PHB2 Cross-Seeding Hub)\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-14T03:38:45.313200+00:00","updated_at":"2026-04-14T03:38:45.313200+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/5d05dab9_df5_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"96ac20ce04ac982281b0b5a3ef862901a29a9f5a\"], \"completion_shas_checked_at\": \"2026-04-14T03:38:45.292536+00:00\"}"},{"id":"c391c064-887c-4d2b-8b0b-36257f8216a6","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"121 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:13:35","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":"","provider":"any","payload_json":"{}"},{"id":"9a8031be-5c18-462b-85c4-34443cfcbb9c","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"119 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:15:28","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":"9cb3e20a-97bf-44f0-bacf-7b8e5577f842","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"117 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:54:13","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":"","provider":"any","payload_json":"{}"},{"id":"80dfccac-07ad-42dd-8f69-5bafe69ec1ba","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"86 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:14:49","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":"","provider":"any","payload_json":"{}"},{"id":"4c26d99c-5b4c-4f01-911e-749d080be6be","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"75 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:23:52","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":"39edf99f-20ef-446b-ba90-7821c39fc147","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"44 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:52:19","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":"9522557b-13fc-4a8d-b6bd-117ba3d0689d","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. 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Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 06:58:27","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":"134b016f-9b33-4b9f-88e6-cdf1a9ce4210","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:02:52","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":"e9251c47-92ef-4608-8d1c-cd9f49d173ea","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:08:41","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":"f57b2fbb-8ea9-4dc3-a94e-60099d86e1b4","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:12:00","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":"91f2ae99-d78f-4e70-8ba2-b36341767370","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:17:21","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":"8f2abee8-e356-463f-b9b7-1f79b59de89e","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:22:30","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":"bcb7d3b4-0d5a-4219-81eb-9bd14974bc14","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:34:01","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":"658e9772-296a-4f27-a6e9-162536a9e6ba","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:41:55","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":"ceff6986-714e-4524-92c2-7c8b89c2fa4a","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:57:59","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":"083eedc6-b37f-476e-8c45-1e7415d95e23","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:19:08","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":"e263cc04-1375-4db4-b5b4-c5a661ae14fb","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:31:42","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":"37374fcb-623b-4fde-878c-7ccb257cef1a","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:45:09","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":"053aba7b-6d4d-463f-8a1f-bae2d10cc8fc","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:55:59","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":"e44d9125-5c1c-4e42-8105-8927306d7366","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:58:01","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":"1c598820-d20b-4e24-9049-ec29bed2a496","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 10:05:12","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":"035c49c1-cbb0-4649-8caa-c71ba21bd8d9","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:38:59","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":"8f5e0da9-1091-43a3-bba3-2a1d353f432a","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"0 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"archived","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:43:37","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":"3b5b67ec-fb13-4e11-bded-ca7d8d98e0b7","title":"[Senate] SALVAGE: review lost commit 7946e9fb (Exchange discovery dividend backprop cre)","description":"On 2026-04-11 the push_main race silently dropped 6 substantive commits from main. Each was independently implemented by another agent in parallel with mine. Today's audit recovered them as salvage branches on the remote so the work isn't lost. This task asks an agent to review one such commit and decide whether to merge it, reconcile it with the existing implementation, or close it as a duplicate.\n\nCommit: 7946e9fb (834+ lines)\nBranch: salvage/lost-2026-04-11-7946e9fb\nTitle:  Exchange discovery dividend backprop credit #14\n\nSteps: \n  1. git fetch origin salvage/lost-2026-04-11-7946e9fb\n  2. git log -p 7946e9fb | less   # review the diff\n  3. Compare against the current code in main (mine landed too — search for the relevant economics_drivers/*.py file)\n  4. Decide: (a) cherry-pick if it adds something mine doesn't, (b) close as duplicate if mine is the canonical, (c) reconcile both implementations into one\n  5. Document the decision in the task summary, citing the chosen path\n\nContext: see incident_push_main_ambiguous_ref_2026-04-11.md in agent memory.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T10:13:31.276823+00:00","updated_at":"2026-04-16T10:13:31.276823+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/3b5b67ec_fb1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"e91b404c1ea1694cba3887f07cf1a4ef0d56f783\", \"3249a370b511c0d98cd1c35366a9e5069bad013b\", \"21fe78b65cf40c44e3a3910d19dd9ccc027b64e9\", \"078fcde2352e56c0a5deb0022ae9668538009034\", \"3828029ec0f75276a1b5b760eaa1715d52af75f6\", \"cd0cc9d7c15e00ddbed94639aec27b46053a1004\", \"39975bae410e0f625128ac0fa0d393377aba85c5\"], \"completion_shas_checked_at\": \"2026-04-16T10:13:31.258191+00:00\", \"completion_shas_missing\": [\"874a952dcea88489d1dae18caa7fbc8cfe0a72eb\", \"3cc4707f3ef75e906af2129f2bd70f77cf704456\", \"a4b8610f25ef1f5932e77e7a04e91ad25dae8bbc\", \"2aa17bdc264b0b86ce883fa95d1d83c87f2325e6\", \"a7bdf0ad4ebdb86d39245bd86a11a6fc80be89d9\", \"224360aff9fe36e65fdf59e5c784ddf2f45f85fb\", \"09dec0bddb7d48f8dc51079f415be2d735540dc2\", \"2dfb138239199eae39aea9b329cf536c310d91cf\", \"2057b72b16d2b1a91d9ef45b0c81b5ef8ae1cfbe\", \"98d190fcbb7019ff3435078c9a503dd2d25c8b9f\", \"3e29f012fd795cc28a6cf60c6d8146e576e548b6\", \"b30b9c064e47e2688f1f489ada933abe5e5147e1\", \"bff7e52167d5008951e0a05a0fd99b71194d30a2\", \"6c170f68779597553232d320234641be7e46eab4\", \"dd620ea60d73510fb04f2f41517ead96dad32f56\", \"c066fc8660639ac4062a4c417eaf81c587729ce8\", \"3c3faef4c21e1f68745d590ae59ce7d66a2bb305\", \"289e4cfcea02d6568d361e6ccbc8c50ed0acd416\", \"9eac45550e7ff833408c42633ea24db9cbe3fed8\", \"02bad0d624eff6a10a8d95edb391f2277114371b\", \"827b0d668ab4a16d6af78ca72ee58085c9b14329\", \"7f74869404c9c48acb6ac2377e02d2c3e03f5499\", \"378ccc70d89a2644d7fcff52e1229d080686c49e\", \"7681b001d73e6dd6cd68232de12fa289bfcfb0b8\", \"bfcf08c8cde9ffb90f1631501bd614fd55289287\", \"7faa96c4c65c17054dbeec76553cca9062e786a9\", \"98b150bbedfe36cceb77e6adba064ff684a66aae\", \"8386b07752c5a0fcb776e0f4bcf2a59f0ba27ab4\", \"03b5e34fbe3e762547252370a0a25a449fd7dd52\", \"5282e3b8e847425bc71404797681309f3e7ecd6e\", \"8d8e43df50250af0e677e99e8765238633442629\", \"fff42988c22bd3bed17447de4f34de42fa75b585\", \"7aeae62bdd68a4e01b3ef89967516eeb2b42606c\", \"3d7e7a78c8f9023b7414cc89f8d3deb16ed1f5db\", \"3a0a246797647ada5a17c0d0e7e9eb57679e851f\", \"f67b9587d2db656320982c31ab62f55fa26efd77\", \"c4b6612499e933dad0ce81f920f61132a05655dc\"]}"},{"id":"d08a5755-1cbf-4bf9-918e-f67d5b08c160","title":"[Exchange] Implement 3 market participant trading strategies (Methodologist, Replication Scout, Freshness Monitor)","description":"Implement evaluate() methods for Methodologist (study design scoring), Replication Scout (PubMed replication search), Freshness Monitor (recency detection) in market_participants.py. Each produces buy/sell/hold signals with magnitude 0-1. Integrate with exchange.py price updates. Track accuracy. See agent_ecosystem_activation_spec.md Phase 1a.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T09:54:25.400967+00:00","updated_at":"2026-04-16T09:54:25.400967+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/agent_ecosystem_activation_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"analysis\": 7}}"},{"id":"c50018a8-3304-4adb-9140-95c71be388f1","title":"[Exchange] Enrich final 7 thin hypotheses to eliminate all thin descriptions","description":"Final batch: enrich all remaining hypotheses with <500 char descriptions to reach 0 thin hypotheses platform-wide.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T09:43:57.035088+00:00","updated_at":"2026-04-16T09:43:57.035088+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c50018a8_330_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"e881d7bb-9f71-4f02-af2c-bbfbdab1def3","title":"[Exchange] Enrich top hypotheses with PubMed citations — batch 2 (0-citation high-scorers)","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T07:26:43.703722+00:00","updated_at":"2026-04-16T07:26:43.703722+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/e881d7bb_9f7_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"9a09ab7be9ad3f6d0e6fefe8b9649ebf4f525501\"], \"completion_shas_checked_at\": \"2026-04-16T07:26:43.681590+00:00\"}"},{"id":"facbd5d5-d554-4918-82d7-7dd422be407a","title":"[Exchange] Enrich next 20 hypotheses with PubMed abstracts in evidence","description":"Continuing from top 3, fetch PubMed abstracts for evidence citations of the next 20 hypotheses by score. 129/149 still lack abstracts.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T04:49:57.577405+00:00","updated_at":"2026-04-16T04:49:57.577405+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/facbd5d5_d55_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"3a812945-8394-402b-8756-681f03fe49c7","title":"[Exchange] Enrich thin-evidence hypotheses with PubMed citations","description":"15 hypotheses with composite_score > 0.42 have only 3-4 evidence items each. Enrich top 5 by score (h-1e564178, h-b0cda336, h-0e0cc0c1, h-072b2f5d, h-1a34778f) with PubMed evidence using tools.py search_pubmed. Each should have 10+ evidence_for and 5+ evidence_against items with real PMIDs and abstracts.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T03:52:23.064806+00:00","updated_at":"2026-04-16T03:52:23.064806+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/3a812945_839_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"8d91b08b8ae7538410c072773a768c6ce5646197\"], \"completion_shas_checked_at\": \"2026-04-16T03:52:23.049810+00:00\"}"},{"id":"f9b8996d-a553-43c4-8419-06400012800a","title":"[Exchange] Enrich top hypotheses #4-#10 with 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T02:49:15.930566+00:00","updated_at":"2026-04-16T02:49:15.930566+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/f9b8996d_a55_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"b24444e68b676a19b705bd5ac72a527dcde9a65e\"], \"completion_shas_checked_at\": \"2026-04-16T02:49:15.904777+00:00\"}"},{"id":"a490095e-4f38-4eb5-8c03-718ba076db4b","title":"[Exchange] Enrich top 10 thin high-score hypotheses with deep descriptions and pathway diagrams","description":"95 hypotheses still have <500 char descriptions. Enrich the top 10 by composite_score with 2000+ word descriptions, mechanism details, pathway diagrams, and evidence context. Target: h-62f9fc90, h-ee1df336, h-fb56c8a0, h-8ef34c4c, h-3d993b5d, h-5e68b4ad, h-fd1562a3, h-19003961, h-fdb07848, h-e12109e3\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T02:34:14.568036+00:00","updated_at":"2026-04-16T02:34:14.568036+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a490095e_4f3_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"q02-e1-36718F69","title":"[Exchange] Enrich hypotheses 4-10 with deep descriptions","description":"Enrich hypotheses ranked 4-10 (CYP46A1, Membrane Cholesterol, SASP Complement, AMPK Astrocytes, Autophagy-Lysosome, TREM2 Tau Clearance, Circadian Melatonin) with 1000+ word descriptions, mechanism details, 5+ PubMed citations each, evidence chains. Update DB fields.","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T05:01:34.382299+00:00","updated_at":"2026-04-17T05:01:34.382299+00:00","summary":"","completion_notes":"DB corruption blocking: PRAGMA integrity_check shows extensive errors in the live scidex.db. The running API (uvicorn, PID 3532999) has the DB locked in WAL mode. UPDATE operations fail with \"database disk image is malformed\". The enrich_hypotheses.py script was written but cannot execute the DB update due to the lock. Hypotheses h-0f025d94 (129 chars) and h-3481330a (363 chars) were identified as needing enrichment with 9,662 and 5,847 char descriptions respectively ready to be written. Cannot proceed without either (a) sudo access to stop the API and fix the DB, or (b) the DB corruption being resolved by another agent.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"7e4d8f56-540c-4c11-9068-18710b38d6a4","title":"[Exchange] Add evidence_for/evidence_against to all hypotheses","description":"Many hypotheses lack structured evidence. Add PubMed-cited evidence_for and evidence_against arrays. Target: all 142 hypotheses should have at least 3 evidence items 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T10:54:28.395814+00:00","updated_at":"2026-04-16T10:54:28.395814+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/7e4d8f56-540_exchange_add_evidence_for_evidence_agai_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"b56814975\"], \"completion_shas_checked_at\": \"2026-04-16T10:54:05.917320+00:00\"}"},{"id":"46210eb2-bd0a-497c-98cd-b3b97ca47bae","title":"[Exchange] Implement comment sort algorithms — Hot, Top, New, Best, Controversial","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T10:51:47.286116+00:00","updated_at":"2026-04-16T10:51:47.286116+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/exch-ws1-02-SORT_comment_sort_algorithms_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}}"},{"id":"494862e6-194d-448e-bd64-421f08042d59","title":"[Exchange] Quality-verify top 30 hypotheses — validate evidence, scores, and content","description":"Run quality verification on the top 30 unverified hypotheses: validate that evidence_for/against contain real PMIDs, descriptions are substantive, scores are reasonable, and mark quality_verified=1. This advances Quest 2 (Exchange) and 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T10:47:19.685785+00:00","updated_at":"2026-04-16T10:47:19.685785+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/494862e6_194_spec.md","provider":"any","payload_json":"{}"},{"id":"3db1ad5d-e487-4cf2-bf45-c4ef2d297b88","title":"[Exchange] Build hypothesis comparison panel with side-by-side scores","description":"Quest 2: The Exchange page has compare checkboxes but the comparison panel/modal is not built. Add a floating comparison tray that appears when hypotheses are selected, and a full comparison view showing dimension scores, evidence balance, and key metrics side by side.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T10:36:13.436289+00:00","updated_at":"2026-04-16T10:36:13.436289+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3db1ad5d_e48_spec.md","provider":"any","payload_json":"{}"},{"id":"e835bb37-4160-4672-8d43-fda11633b23c","title":"[Exchange] Add hypothesis comparison view with side-by-side scores and evidence","description":"Quest 2/16: Add a comparison modal/page to the Exchange where users can select 2-3 hypotheses and see their scores, evidence, and pathway diagrams side-by-side. This is a key demo feature showing the market-style evaluation system.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T10:33:59.947950+00:00","updated_at":"2026-04-16T10:33:59.947950+00:00","summary":"","completion_notes":"Feature already exists at /compare route (api.py line 27186). Original work landed on orphan branch; confirmed via git history: commits 0efaf3988, 6a1b609ad, d72b86cbc address this. Route is live and healthy.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e835bb37_416_spec.md","provider":"any","payload_json":"{}"},{"id":"6ee4ab08-a221-4478-ac0d-a79d644303db","title":"[Exchange] Enrich 5 more thin-evidence hypotheses (batch 2)","description":"Second batch of evidence enrichment: h-7e0b5ade (LRP1 circadian), h-82922df8 (LOX matrix), h-db6aa4b1 (PIEZO1 ion channel), h-637a53c9 (APOE4 chaperone), h-1acdd55e (MMP cholinergic). Each has <8 evidence items.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T10:27:39.539611+00:00","updated_at":"2026-04-16T10:27:39.539611+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6ee4ab08_a22_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"97230db6-6785-4b12-8a73-67b8d5be28da","title":"[Exchange] Enrich top 7 highest-scored thin hypotheses with deep descriptions","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T10:20:43.394942+00:00","updated_at":"2026-04-16T10:20:43.394942+00:00","summary":"","completion_notes":"Verified: commit 3884f83d5 on origin/main contains enrich_top7_thin.py (399 lines) + spec update. 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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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T10:19:44.507003+00:00","updated_at":"2026-04-16T10:19:44.507003+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/eeca3a31_d6f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"d1c66637d84235e7e3ed77d2821ceb38d941ed44\", \"870f458d9ef74acd8d638c28986b74a81a5c2cad\", \"0384af14c6b1ce42e03cfa801cc68ac201614f43\"], \"completion_shas_checked_at\": \"2026-04-16T10:19:44.468764+00:00\"}"},{"id":"285d9a8e-bfc4-4c12-a948-577ef88856f4","title":"[Exchange] Add evidence_for/evidence_against to all hypotheses","description":"Many hypotheses lack structured evidence. 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See spec Phase 1c.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T15:47:34.130940+00:00","updated_at":"2026-04-16T15:47:34.130940+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/agent_ecosystem_activation_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 7}}"},{"id":"bf70b637-cd7a-4346-a9ce-b34d7e690771","title":"[Exchange] Activate token earning mechanics — mint on debate/evidence/hypothesis actions","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T15:02:51.777759+00:00","updated_at":"2026-04-16T15:02:51.777759+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/exch-ws3-02-EARN_token_earning_mechanics_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}}"},{"id":"ec2aec08-b3b9-4e51-8632-7cbbfe56f0de","title":"[Exchange] Enrich TREM2 hypothesis with mermaid pathway diagram and PubMed evidence","description":"The top-scoring hypothesis (h-61196ade, TREM2-Dependent Microglial Senescence Transition, score 0.85) has only 5 papers and no mermaid diagram. Add a pathway diagram showing the TREM2 signaling cascade, microglial senescence transition, and therapeutic intervention points. Also fetch additional PubMed evidence to strengthen the evidence base.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T14:08:49.995329+00:00","updated_at":"2026-04-16T14:08:49.995329+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/ec2aec08_b3b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"2ee3753f-d474-4f31-be42-ab88c7b3ab23","title":"[Exchange] Add pathway diagrams to 5 high-scoring hypotheses missing them","description":"Add mermaid pathway diagrams to top 5 hypotheses that currently lack them. Target: h-2f43b42f, h-16ee87a4, h-63b7bacd, h-8b7727c1, h-c9c79e3e\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T14:03:52.037966+00:00","updated_at":"2026-04-16T14:03:52.037966+00:00","summary":"","completion_notes":"Task completed via equivalent work in commit 1cc2280e5 [Exchange] Bulk-add mermaid pathway diagrams to 97 hypotheses [task:dbc05d86]. All 5 target hypotheses (h-2f43b42f, h-16ee87a4, h-63b7bacd, h-8b7727c1, h-c9c79e3e) confirmed to have valid pathway diagrams with proper mermaid syntax. Original task commits (2a76db90b, 7fa54c2bd) were orphaned but equivalent work landed on main via bulk-add.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/2ee3753f_d47_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"1cc2280e5\"], \"completion_shas_checked_at\": \"2026-04-16T14:03:52.021709+00:00\"}"},{"id":"0aa736f8-ac1c-4369-858f-b79b45d7113f","title":"[Exchange] Enrich 3 thin SEA-AD v4 hypotheses to demo quality","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T13:44:17.195142+00:00","updated_at":"2026-04-16T13:44:17.195142+00:00","summary":"","completion_notes":"Verified on main via db query. The 3 SEA-AD v4 hypotheses are fully enriched:\n- h-seaad-v4-26ba859b: 18,012 char description, 31,053 evidence_for, 5,050 evidence_against, pathway diagram, clinical trials, gene expression context\n- h-seaad-v4-5a7a4079: 10,539 char description, 15,477 evidence_for, 1,706 evidence_against, pathway diagram, clinical trials, gene expression context\n- h-seaad-v4-29e81bbc: 11,800 char description, 14,371 evidence_for, 2,202 evidence_against, pathway diagram, clinical trials, gene expression context\n\nThe work was done in commit bf9141a4f which landed on origin/main. Branch was up to date with origin/main when checked - no new commits needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0aa736f8_ac1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"dbc05d86-940c-49ca-8e93-cecb18f96c6d","title":"[Exchange] Bulk add mermaid diagrams to remaining 100+ hypotheses","description":"Generate mermaid pathway diagrams for the ~109 hypotheses scoring above 0.35 that don't have them yet. Use template-based approach matching target gene families to known pathway patterns. This enriches hypothesis detail pages significantly.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T13:43:44.489577+00:00","updated_at":"2026-04-16T13:43:44.489577+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/dbc05d86_940_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}}"},{"id":"850e3b86-6908-4c96-b659-5534e877fc50","title":"[Exchange] Auto-link target genes to wiki pages on hypothesis detail pages","description":"When rendering hypothesis detail pages, auto-detect gene/protein names in the description and link them to their wiki pages. For example, if the description mentions TREM2, make it a clickable link to /wiki/genes-trem2. This connects the Exchange and Atlas layers visually.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T13:36:53.918199+00:00","updated_at":"2026-04-16T13:36:53.918199+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/850e3b86_690_spec.md","provider":"any","payload_json":"{}"},{"id":"1a4a55ae-53a8-45ce-abbd-1b1a6103c27c","title":"[Exchange] Create hypothesis_papers table and link hypotheses to their cited papers","description":"The hypothesis detail page queries hypothesis_papers table which doesn't exist. Create it and populate from evidence_for/evidence_against PMIDs. This enables the 'Linked Papers' section 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T13:34:09.557446+00:00","updated_at":"2026-04-16T13:34:09.557446+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/1a4a55ae_53a_spec.md","provider":"any","payload_json":"{}"},{"id":"0511c4b1-1be6-44dc-86c4-d8220a761dcf","title":"[Exchange] Enrich 5 more thin-evidence hypotheses (batch 3)","description":"Third batch: h-23a3cc07, h-bb518928, h-69919c49, h-b948c32c, h-fd1562a3. Each has <8 evidence items.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T13:25:20.008853+00:00","updated_at":"2026-04-16T13:25:20.008853+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/0511c4b1_1be_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"408c42ab-98d1-43c1-99ee-5a67e5362fe9","title":"[Exchange] Backfill PubMed citations for top 10 hypotheses","description":"Top hypotheses have 0-6 citations. Enrich with real PubMed references to improve demo quality. Use tools.py pubmed_search to find relevant papers and update citations_count and evidence fields.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T13:14:36.302744+00:00","updated_at":"2026-04-16T13:14:36.302744+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/408c42ab_98d_spec.md","provider":"any","payload_json":"{}"},{"id":"14245b33-d3c9-468b-8b30-92fee7c7c005","title":"[Exchange] Enrich top hypotheses batch 3 — add clinical trials and pathway diagrams to 5 high-scoring hypotheses","description":"Enrich 5 high-scoring hypotheses (AMPK, Purinergic, BBB SPM, Senescent Microglia, HSP70) with clinical trial data and pathway diagrams. These are in the top 20 by market_price but lack enrichment. 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T13:13:48.961391+00:00","updated_at":"2026-04-16T13:13:48.961391+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/14245b33_d3c_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"5b39913a-645b-430e-96ca-0d0971dc0d49","title":"[Exchange] Add pathway diagrams to CYP46A1 and Ganglioside hypotheses + enrich Dual-Receptor","description":"Add mermaid pathway diagrams to h-2600483e (CYP46A1 Gene Therapy, score 0.82) and h-12599989 (Ganglioside Rebalancing, score 0.71) which are missing them. Also fully enrich h-48d1115a (Dual-Receptor Antibody Shuttling, score 0.64) which has only 183 chars 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T13:01:53.404025+00:00","updated_at":"2026-04-16T13:01:53.404025+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/5b39913a_645_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"fcf6e752-7c9a-4f2b-b9a0-2dde81742c9e","title":"[Exchange] Add /experiments page — browsable experiment library with protocols","description":"Create an /experiments HTML page showing all 188 experiments with search, type filtering, and expandable protocols. Complements the /api/experiments endpoint. Essential for demo completeness.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T12:59:44.761023+00:00","updated_at":"2026-04-16T12:59:44.761023+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/fcf6e752_7c9_spec.md","provider":"any","payload_json":"{}"},{"id":"97164433-b038-4327-af70-e295fd8750c0","title":"[Exchange] Price history tracking","description":"E2.1: Create price_history table (hypothesis_id, price, score, event_type, event_source, created_at). Insert a row whenever composite_score changes in post_process.py. Backfill initial prices for all hypotheses. Add GET /api/hypothesis/{id}/history.\n\nAcceptance: price_history populated. API returns time series data.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:51:13","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/97164433_b03_price_history_tracki_spec.md","provider":"any","payload_json":"{}"},{"id":"8f89b059-ffed-4d20-9210-54961706d78b","title":"[Exchange] Add evidence matrix component to hypothesis pages","description":"Add structured evidence quality matrix to hypothesis detail pages showing each citation's quality score, relevance to claim, and evidence type (for/against). Quest 17 task A17.6. Currently 50 hypotheses have low validation scores — this component helps users understand evidence strength.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T23:12:49.199803+00:00","updated_at":"2026-04-16T23:12:49.199803+00:00","summary":"","completion_notes":"Task was reopened due to NO_COMMITS audit, but the feature was delivered under different task IDs (5a22b3a8, 6483159a). All evidence matrix functionality exists on origin/main.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8f89b059_ffe_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"73c462fa-a55e-40f3-acab-7a7c4e4361e4","title":"[Exchange] Build /targets page and /api/targets endpoint — browse 150 drug targets","description":"Build /targets listing page with druggability filtering, target class breakdown, and composite scores. Also add /api/targets JSON endpoint. 150 targets exist with rich data but no browsing UI or API.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T22:40:27.850449+00:00","updated_at":"2026-04-16T22:40:27.850449+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/73c462fa_a55_spec.md","provider":"any","payload_json":"{}"},{"id":"3f3e59db-18c4-4ed0-ab53-0006b33638ba","title":"[Exchange] Add hypothesis clustering visualization to /exchange page","description":"Add a visual clustering of hypotheses by target gene/domain showing relationships. Use SVG or canvas to render clusters of related hypotheses, helping visitors see the landscape of discoveries.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T22:35:00.936487+00:00","updated_at":"2026-04-16T22:35:00.936487+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3f3e59db_18c_spec.md","provider":"any","payload_json":"{}"},{"id":"a320aaa1-bbf3-452f-ad5b-118ad721c3d3","title":"[Exchange] Backfill gene_expression_context for top 20 hypotheses","description":"138 of 149 hypotheses are missing gene_expression_context. This task enriches the top 20 by composite_score with Allen Brain Atlas gene expression data, linking target genes to brain region expression patterns relevant to Alzheimer's disease.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T19:48:58.550030+00:00","updated_at":"2026-04-16T19:48:58.550030+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/a320aaa1_bbf_spec.md","provider":"any","payload_json":"{}"},{"id":"6b97f89c-f560-4c7d-8b56-f7a7dd69980f","title":"[Exchange] Enrich thin hypotheses batch — expand descriptions and add evidence","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T19:19:44.545711+00:00","updated_at":"2026-04-16T19:19:44.545711+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/6b97f89c_f56_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"a5406a19-8a19-41a4-887b-423d1c5223a4","title":"[Exchange] Bulk enrich thin hypotheses — expand next 10 highest-scoring to 1000+ words","description":"Run bulk enrichment on the 10 highest-scoring hypotheses with descriptions under 300 chars. Use Claude via Bedrock to generate deep descriptions.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T19:08:30.234365+00:00","updated_at":"2026-04-16T19:08:30.234365+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a5406a19_8a1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"cd9f3624-703f-41ec-8787-4120b21ec488","title":"[Exchange] Enrich thin hypotheses batch — 5 mid-tier hypotheses with deep descriptions and evidence","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T18:05:27.223560+00:00","updated_at":"2026-04-16T18:05:27.223560+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/cd9f3624_703_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"1290fb13-d11d-4f40-ac4e-e7660809159d","title":"[Exchange] Enrich top 5 hypotheses with clinical trials data via ClinicalTrials.gov API","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T18:03:08.603510+00:00","updated_at":"2026-04-16T18:03:08.603510+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/1290fb13_d11_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"279265710\", \"1b312da69\"], \"completion_shas_checked_at\": \"2026-04-16T18:02:51.154278+00:00\"}"},{"id":"37b0cbc5-93b3-4f5f-9ad8-45add440d2a9","title":"[Exchange] Backfill empty evidence arrays for h-84808267 and h-7e0b5ade","description":"Hypotheses h-84808267 (Synthetic Biology BBB) and h-7e0b5ade (Circadian LRP1) have empty evidence_for=[] and evidence_against=[]. Run backfill to populate with PubMed citations. Quest 16 D16.1 priority.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T16:54:19.940084+00:00","updated_at":"2026-04-16T16:54:19.940084+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/37b0cbc5_93b_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"4fbf04e53dffa428602cb58bcdb23beedd435e55\"], \"completion_shas_checked_at\": \"2026-04-16T16:54:19.920177+00:00\"}"},{"id":"c89ba1df-e514-41c4-96e9-70001b2dd9cd","title":"[Exchange] Backfill gene_expression_context for 15 high-scoring hypotheses missing it","description":"36 hypotheses are missing gene_expression_context. Fill the top 15 by composite_score with structured gene expression data including Allen Brain Atlas expression patterns, cell-type specificity, regional distribution, and disease-associated expression changes. Target hypotheses start with h-e3e8407c (score 0.75) down to h-58e655ee (score 0.57).\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T16:31:21.316950+00:00","updated_at":"2026-04-16T16:31:21.316950+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/c89ba1df_e51_spec.md","provider":"any","payload_json":"{}"},{"id":"c153f3a4-dde4-443f-a870-fb0602aa908b","title":"[Exchange] Fill evidence validation scores for top hypotheses with missing data","description":"8 hypotheses with composite_score >= 0.7 have NULL evidence_validation_score. Compute and fill based on PMID coverage and evidence strength ratings.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T16:11:34.013590+00:00","updated_at":"2026-04-16T16:11:34.013590+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/c153f3a4_dde_spec.md","provider":"any","payload_json":"{}"},{"id":"24d79ce1-78dc-483f-bcc3-6a002a117023","title":"[Exchange] Add pathway diagrams to next 10 hypotheses missing them","description":"Add mermaid pathway diagrams to 10 hypotheses that currently lack them. Targets: h-27bc0569, h-3a4f2027, h-a87702b6, h-15336069, h-24e08335, h-61196ade, h-a8165b3b, h-e5a1c16b, h-06cb8e75, h-e3e8407c\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T16:09:06.274811+00:00","updated_at":"2026-04-16T16:09:06.274811+00:00","summary":"","completion_notes":"Verified: all 10 target hypotheses already have mermaid pathway diagrams in the database (confirmed via direct SQL query). Commit 50a70c639 is an ancestor of 8d2e6b111 which is on origin/main.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/24d79ce1_78d_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"6b514069-515c-479f-8288-9d5a4e270475","title":"[Exchange] Add mermaid pathway diagrams to remaining 16 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T16:08:02.109454+00:00","updated_at":"2026-04-16T16:08:02.109454+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/6b514069_515_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"7e6fb135-2306-48b2-b5d7-426eeb43bb72","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03T05:49:53.380811","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"81a417e3-b31e-4eca-93d6-919940d6fe66","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:12:19","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":"","provider":"any","payload_json":"{}"},{"id":"07c8d21a-9f6c-4517-bfd8-89a3f0dc8c2a","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:50:48","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":"","provider":"any","payload_json":"{}"},{"id":"c89f18d3-0d1f-456c-b94c-c0ce6e696d7b","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:38:35","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":"","provider":"any","payload_json":"{}"},{"id":"b50f8dfd-d50a-4008-9021-2c9a9cc885d2","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:09:20","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":"","provider":"any","payload_json":"{}"},{"id":"997c7176-8e08-4853-9722-487433888462","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:06:50","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":"","provider":"any","payload_json":"{}"},{"id":"351f4edc-9d7d-4bf9-af96-576dca39fc69","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:25:23","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":"","provider":"any","payload_json":"{}"},{"id":"10237655-b334-4205-9e9f-fd9da56a08d3","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:28:20","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":"4514f997-9751-4a91-b097-782a19cb8cd5","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:17:56","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":"5d3e8a70-9f29-4b42-96f5-1b2e102624a7","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:26:26","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":"de91aec4-e835-410e-8d45-6670d7048c38","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:54:54","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":"5c38c571-7f31-43bb-8229-2b850a91c7c8","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:55:33","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":"994da43f-1077-4179-80ab-b4c582f47b8a","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:07:42","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":"2910df89-e620-4727-b2f8-d7ad3fdaeeb5","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:35:52","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":"f0236e27-f85a-4175-85df-01d7f7d7a6bf","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:36:06","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":"bf943bfe-56d5-4d2f-815d-015d7d465450","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 18:15:13","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":"f0199fd5-7e45-4d3a-a20a-dc2f36d465ca","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 18:18:38","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":"d532e8be-8afd-4ce2-a3a7-eacbb0011a29","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 18:27:54","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":"be7ecd1f-c007-473b-9987-1899ff30f50e","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. Add experimental protocols, expected outcomes, success criteria, and link to parent hypotheses.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 18:34:54","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":"caa00771-9960-49ea-96fe-f22bcf7566e5","title":"[Exchange] Enrich experiment descriptions — add protocols and expected outcomes","description":"188 experiments exist but most have thin descriptions. 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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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:50:05.928834+00:00","updated_at":"2026-04-17T10:50:05.928834+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/c0825bd0-a0b_exchange_enrich_target_profiles_add_dru_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 5}}"},{"id":"da5b7995-f00d-46df-9d52-49a3076fe714","title":"[Exchange] WS3: Agent Reputation & Token Economy","description":"Implement agent reputation and token economy per docs/planning/specs/agent_reputation_tokens_spec.md. Creates actor_reputation and token_ledger tables, backfills from existing data, adds token earning/spending APIs and reputation endpoints.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:22:47.350655+00:00","updated_at":"2026-04-17T10:22:47.350655+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/da5b7995_f00_spec.md","provider":"any","payload_json":"{}"},{"id":"8bb32dae-0818-4705-bd2b-152fa77e7c72","title":"[Exchange] Implement generalized market framework (Economics WS2)","description":"Extend market system beyond hypotheses to support 6+ artifact types: analyses, agents, tools, KG entities, knowledge gaps, tasks. Unified pricing API, volume tracking, trade history, sparklines. Enables Phase 2 of task prioritization quest and unblocks Contributor Network quest. See generalized_markets_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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:20:57.113861+00:00","updated_at":"2026-04-17T10:20:57.113861+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/generalized_markets_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"57b36a06b3b3a90bce9c7a91ca87bedd21a05abb\"], \"completion_shas_checked_at\": \"2026-04-17T10:20:57.055538+00:00\"}"},{"id":"4de30635-b07f-42dc-8977-e84c6f7c0b06","title":"[Exchange] Update hypothesis KG connectivity scores from actual edge data","description":"Recalculate kg_connectivity_score for all hypotheses based on actual knowledge graph edge counts for their target genes. Currently uses default values.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:06:38.732588+00:00","updated_at":"2026-04-17T10:06:38.732588+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/4de30635_b07_spec.md","provider":"any","payload_json":"{}"},{"id":"05eb41f8-d96a-4a88-95d5-0c5f6aa44037","title":"[Exchange] Validate evidence quality and mark top hypotheses as verified","description":"Only 3/149 hypotheses are quality_verified. Validate PMIDs in evidence_for/evidence_against, check citation relevance, and mark hypotheses that pass quality gates. This adds credibility badges to 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T05:50:52.592887+00:00","updated_at":"2026-04-17T05:50:52.592887+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/05eb41f8_d96_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"8fe7350db\"], \"completion_shas_checked_at\": \"2026-04-17T00:11:07.241977+00:00\"}"},{"id":"3aad1a29-9588-4cbd-855f-141ff9d0ccb5","title":"[Exchange] Hypothesis scoring recalibration","description":"Recalibrate hypothesis composite scores using updated evidence. For each hypothesis: count confirmed papers, count KG edges, measure convergence with related hypotheses. Adjust scores and record price changes in price_history and market_transactions tables.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T05:50:25.549894+00:00","updated_at":"2026-04-17T05:50:25.549894+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":"{}"},{"id":"884a8b9e-bc05-4db0-ba24-780b25b870c7","title":"[Exchange] Implement hypothesis versioning — track how scores change over time","description":"Create hypothesis_versions table. On each re-score, save previous state. Show version diff on detail page.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T05:46:53.964922+00:00","updated_at":"2026-04-17T05:46:53.964922+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"656d1328-1794-4b3d-8b82-5ab36482e544","title":"[Exchange] Add evidence validation — check if cited PMIDs actually support claims","description":"For each hypothesis, verify that PubMed citations actually discuss the claimed evidence. Use abstract text matching against evidence claims. Flag low-relevance citations.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T05:16:37.665017+00:00","updated_at":"2026-04-17T05:16:37.665017+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":"{}"},{"id":"2319bf98-c44b-41d1-90be-be65cf60e04c","title":"[Exchange] Enrich 6 thin-evidence hypotheses with PubMed citations","description":"Several high-value hypotheses have fewer than 3 evidence_for or 2 evidence_against citations: h-7e0b5ade, h-82922df8, h-1e564178, h-1a34778f, h-b0cda336, h-0e0cc0c1. Enrich with targeted PubMed searches. Quest 16 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T18:24:16.151151+00:00","updated_at":"2026-04-16T18:24:16.151151+00:00","summary":"","completion_notes":"Verified via API: all 6 hypotheses have sufficient evidence (≥3 evidence_for, ≥2 evidence_against). Commits 1ccb5fde1 and 156fbab59 exist on token/main (canonical main) but not on origin/main — sync issue between remotes. Task goal achieved.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/2319bf98_c44_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"d46d9ad2-64b9-4654-b33e-724049c3f708","title":"[Exchange] Enrich thin hypotheses batch 6 — expand next 5 thinnest descriptions","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T18:11:55.321711+00:00","updated_at":"2026-04-16T18:11:55.321711+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/d46d9ad2_64b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"bdce957a-6b7d-445a-89e7-f2a9d38e0a72","title":"[Exchange] Cross-link hypothesis pages with wiki entities and KG edges","description":"For top 20 hypotheses by score, ensure each hypothesis page links to relevant wiki entities mentioned in its description. Add sidebar or footer section showing related wiki pages, KG neighbors, and linked analyses. This enriches the demo by connecting hypotheses to the broader knowledge graph.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T18:05:20.677149+00:00","updated_at":"2026-04-16T18:05:20.677149+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/bdce957a_6b7_spec.md","provider":"any","payload_json":"{}"},{"id":"9d6a9404-a856-47fd-addb-d1d47c509f49","title":"[Exchange] Backfill evidence_for/evidence_against for top hypotheses missing them","description":"Many hypotheses have empty evidence_for/evidence_against fields. Use KG edges and paper citations to populate these for the top-scoring 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:51:28.677141+00:00","updated_at":"2026-04-16T17:51:28.677141+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/9d6a9404_a85_spec.md","provider":"any","payload_json":"{}"},{"id":"bf02bab7-a4a4-4876-aa53-13843ba397e0","title":"[Exchange] Backfill hypothesis_type, cost, and timeline for 42 hypotheses","description":"42 hypotheses are missing hypothesis_type, estimated_cost_usd, and estimated_timeline_months. Backfill based on their target pathways, experiment types, and disease context.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:48:56.996857+00:00","updated_at":"2026-04-16T17:48:56.996857+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/bf02bab7_a4a_spec.md","provider":"any","payload_json":"{}"},{"id":"ea545379-544d-4893-8118-8a6b63be2545","title":"[Exchange] Enrich next 5 thin hypotheses with descriptions, pathways, 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:37:13.734798+00:00","updated_at":"2026-04-16T17:37:13.734798+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ea545379_544_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"28a7c19e-3224-46d9-b93c-d13f154155cd","title":"[Exchange] Enrich target profiles — add druggability analysis and clinical context","description":"155 targets exist. 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Enrich with druggability scores, known drugs, clinical trial status, structural biology data.","status":"archived","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03T05:43:13.871254","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"50d49b1a-e2c4-4ec6-9940-390f5fe502f4","title":"[Exchange] Enrich target profiles — add druggability analysis and clinical context","description":"149 targets exist. Enrich with druggability scores, known drugs, clinical trial status, structural biology data.","status":"archived","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 13:59:59","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":"829aa18c-7cab-47f3-b50b-9141d4199405","title":"[Exchange] Enrich target profiles — add druggability analysis and clinical context","description":"149 targets exist. 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Enrich with druggability scores, known drugs, clinical trial status, structural biology data.","status":"archived","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:26:28","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":"616f0dcf-3ee5-4389-83f6-abe604d22bce","title":"[Exchange] Enrich target profiles — add druggability analysis and clinical context","description":"149 targets exist. Enrich with druggability scores, known drugs, clinical trial status, structural biology data.","status":"archived","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:28:57","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":"d4c85391-3c68-4ffe-8eb5-b84b2f1fe211","title":"[Exchange] Enrich target profiles — add druggability analysis and clinical context","description":"149 targets exist. Enrich with druggability scores, known drugs, clinical trial status, structural biology data.","status":"archived","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:23:06","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":"20680de5-9b79-4008-85bb-56acf1722a6d","title":"[Exchange] Enrich target profiles — add druggability analysis and clinical context","description":"149 targets exist. 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Enrich with druggability scores, known drugs, clinical trial status, structural biology data.","status":"archived","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:08:25","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":"75f7ac75-4387-4a8c-9ef4-a9c904a30787","title":"[Exchange] Enrich target profiles — add druggability analysis and clinical context","description":"155 targets exist. 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Enrich with druggability scores, known drugs, clinical trial status, structural biology data.","status":"archived","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:43:42","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":"2ac8e1b9-88f9-458b-806f-1bc09821373c","title":"[Exchange] Enrich target profiles — add druggability analysis and clinical context","description":"155 targets exist. 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Enrich with druggability scores, known drugs, clinical trial status, structural biology data.","status":"archived","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 10:09:38","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":"2cf41ad3-8625-4dd7-a516-000a1c504a8a","title":"[Exchange] Enrich target profiles — add druggability analysis and clinical context","description":"155 targets exist. 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Enrich with druggability scores, known drugs, clinical trial status, structural biology data.","status":"archived","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:42:13","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":"78e3970e-9ce6-47b6-a08f-6aab3ccc586d","title":"[Exchange] Enrich target profiles — add druggability analysis and clinical context","description":"155 targets exist. 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Use Chart.js which is already loaded on the /compare page.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T19:17:56.688583+00:00","updated_at":"2026-04-16T19:17:56.688583+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1d94dc96_898_spec.md","provider":"any","payload_json":"{}"},{"id":"78fa87d7-c5ca-44b2-87c8-4f2849ceb1d5","title":"[Exchange] Enrich evidence_against for 15 hypotheses with 0 contradicting citations","description":"15 high-value hypotheses have 0 evidence_against citations. Add 2 contradicting PubMed citations each using target-gene specific limitation/challenge queries. Quest 16 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T19:16:25.390464+00:00","updated_at":"2026-04-16T19:16:25.390464+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/78fa87d7_c5c_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"20f506a4-ec9b-4e2d-bfaa-730de689c0f8","title":"[Exchange] Backfill target_pathway for 41 hypotheses missing pathway data","description":"41 of 199 hypotheses have NULL or empty target_pathway. Fill with structured pathway names (e.g. 'Classical complement cascade', 'TREM2/TYROBP signaling') to enable pathway-based filtering and cross-hypothesis linking on the 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T19:15:50.682491+00:00","updated_at":"2026-04-16T19:15:50.682491+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/20f506a4_ec9_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"9e96afa1-b9c5-44c7-b571-721cf63534c7","title":"[Exchange] Enrich thin hypotheses batch 7 — expand next 5 thinnest","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T18:33:27.104472+00:00","updated_at":"2026-04-16T18:33:27.104472+00:00","summary":"","completion_notes":"Verified via local DB: all 5 hypotheses are enriched (12K-30K chars each). Commit 0926d55f3 exists but was orphan (not on main lineage). Task work was completed — only the push/merge failed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9e96afa1_b9c_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"36fe85eb-ea87-4a4c-87fa-255fa73a361c","title":"[Exchange] Add mermaid pathway diagrams to next 5 high-scoring hypotheses missing them","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T18:24:32.621371+00:00","updated_at":"2026-04-16T18:24:32.621371+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/36fe85eb_ea8_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"64a5f1e5-c7ba-474d-bce8-10f5223970af","title":"[Exchange] Add protocols to 10 experiments","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\n69 experiments lack detailed protocols. Add methods, controls, expected outcomes, success 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T22:19:09.845604+00:00","updated_at":"2026-04-16T22:19:09.845604+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":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"fd1a3168-129c-4367-894f-abb6e244d21b","title":"[Exchange] Add protocols to 10 experiments","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\n71 experiments lack detailed protocols. Add methods, controls, expected outcomes, success 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T21:57:48.933254+00:00","updated_at":"2026-04-16T21:57:48.933254+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":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"f6d9d091-e0e9-41ab-81e6-8f989ac1a848","title":"[Exchange] Add protocols to 10 experiments","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\n64 experiments lack detailed protocols. Add methods, controls, expected outcomes, success 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T21:41:19.096007+00:00","updated_at":"2026-04-16T21:41:19.096007+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/fd1a3168_add_protocols_experiments_spec.md","provider":"codex","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"7c5fe235-47fd-43df-bd7b-24b71005642a","title":"[Exchange] Implement agent reputation and token economy","description":"Token ledger with earning/spending rules, reputation scoring from contribution history, believability-weighted voting. Backfill from 243 agent_performance records. See docs/planning/specs/agent_reputation_tokens_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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T21:20:07.452954+00:00","updated_at":"2026-04-16T21:20:07.452954+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/7c5fe235_47f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}}"},{"id":"2e4601bb-c535-4f2f-8ef5-9e75800aa296","title":"[Exchange] Add mermaid pathway diagrams to 10 hypotheses missing them","description":"27 hypotheses lack mermaid pathway diagrams. Add scientifically accurate mechanism diagrams to the top 10 by composite_score. Each diagram should illustrate the key molecular pathway or mechanism cascade described in the hypothesis.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T21:18:19.914297+00:00","updated_at":"2026-04-16T21:18:19.914297+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/2e4601bb_c53_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"0c020210-bfe4-4ec5-929b-91a9af621882","title":"[Exchange] Implement threaded comments & voting system (Economics WS1)","description":"Implement Reddit/StackOverflow-style threaded comment system with voting for all SciDEX artifacts (hypotheses, analyses, agents, tools, etc.). Supports sort modes: Hot, Top, New, Best, Controversial. Enables community discussion and quality signals. Foundational for Economics quest WS1. See threaded_comments_voting_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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T21:09:53.928894+00:00","updated_at":"2026-04-16T21:09:53.928894+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/threaded_comments_voting_spec.md","provider":"any","payload_json":"{}"},{"id":"d3d06124-5830-4215-8084-bfc72439c824","title":"[Exchange] WS1: Threaded Comments & Voting System","description":"Build Reddit/StackOverflow-inspired threaded comment and voting system for any SciDEX entity. See docs/planning/specs/threaded_comments_voting_spec.md for full spec. Parent quest: Economics Quest (P88). Foundational workstream - unblocks WS3, WS5.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T21:06:32.878121+00:00","updated_at":"2026-04-16T21:06:32.878121+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/threaded_comments_voting_spec.md","provider":"any","payload_json":"{}"},{"id":"009635d2-9369-41d8-9e14-d84b2cc6c046","title":"[Exchange] WS2: Generalized Market Framework","description":"Extend market system from hypotheses-only to multi-asset (6 types: hypothesis, analysis, agent, tool, entity, gap). See docs/planning/specs/generalized_markets_spec.md. Parent quest: Economics Quest (P88). Foundational workstream - unblocks WS3, WS4, WS5.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T21:06:23.367682+00:00","updated_at":"2026-04-16T21:06:23.367682+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/generalized_markets_spec.md","provider":"any","payload_json":"{}"},{"id":"006b1dd7-2323-437d-8623-4aab5ae7aa6a","title":"[Exchange] Implement threaded comments and voting system","description":"Build Reddit/SO-inspired comment threading and voting on any SciDEX entity. Tables: comments (threaded), votes (reputation-weighted). Sort modes: hot, top, new, best, controversial. See docs/planning/specs/threaded_comments_voting_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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T21:02:46.875599+00:00","updated_at":"2026-04-16T21:02:46.875599+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/006b1dd7_232_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}}"},{"id":"9cd222f8-6345-436a-8f80-8acda0cde081","title":"[Exchange] Build generalized market framework for multi-asset pricing","description":"Extend hypothesis-only markets to 6 asset types: hypothesis, analysis, agent, tool, entity, gap. Unified markets table, generalized LMSR pricing, multi-asset exchange page. See docs/planning/specs/generalized_markets_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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T21:01:57.159700+00:00","updated_at":"2026-04-16T21:01:57.159700+00:00","summary":"","completion_notes":"Verified: migration 050 (markets + market_trades tables), all API endpoints, multi-asset exchange page, 415 markets backfilled — all already on main from economics quest WS2 (commit 66ea51893). Task ID was not tagged in that commit, which is why audit flagged it. Work is done, not duplicate.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9cd222f8_634_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"completion_shas\": [\"04db0509b\"], \"completion_shas_checked_at\": \"2026-04-16T21:01:57.135663+00:00\"}"},{"id":"b9e735c4-58d8-4c5b-a696-8a6bb9858db3","title":"[Exchange] Enrich thin hypotheses batch 8 — expand next 5 thinnest","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T20:36:50.480702+00:00","updated_at":"2026-04-16T20:36:50.480702+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/b9e735c4_58d_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"fa89d516-0a71-458f-a2b8-4498627ec68c","title":"[Exchange] Backfill gene_expression_context batch 2 — next 30 hypotheses","description":"Continuing gene_expression_context enrichment. 118 hypotheses still missing. Batch 2 covers next 30 by composite_score.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T20:33:35.528148+00:00","updated_at":"2026-04-16T20:33:35.528148+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/fa89d516_0a7_spec.md","provider":"any","payload_json":"{}"},{"id":"152b6cde-6ed2-402f-9463-a108aed21b28","title":"[Exchange] Enrich next batch of thin-evidence hypotheses (batch 2)","description":"Continue enriching thin-evidence hypotheses. 56 total with <8 evidence_for or <4 evidence_against. First batch of 5 done. Enrich next 5 by score: h-23a3cc07, h-ee1df336, h-bb518928, h-82922df8, h-69919c49.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T20:29:43.849779+00:00","updated_at":"2026-04-16T20:29:43.849779+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/152b6cde_6ed_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"0c378120-9118-4763-ac59-8936b735111a","title":"[Exchange] Add /api/experiments JSON endpoint with pagination and filtering","description":"The /api/experiments endpoint doesn't exist yet. Add it with support for ?limit, ?offset, ?type, ?disease filters. Return experiment data including the newly enriched protocols and 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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":"2026-04-16T20:22:00.621220+00:00","updated_at":"2026-04-16T20:22:00.621220+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0c378120_911_spec.md","provider":"any","payload_json":"{}"},{"id":"0bc09c92-ba30-4d2c-bde8-228b89266e8f","title":"[Exchange] Priority-weighted task generation from hypothesis scores","description":"Connect Exchange scores to task generation:\n1. Higher-scoring hypotheses should get more follow-up analyses, more tool invocations, more validation\n2. Implement a scoring function: allocation_weight = composite_score * evidence_freshness * gap_coverage\n3. When generating new tasks, weight task priority by the allocation_weight of the target hypothesis/entity\n4. Add allocation_weight column to hypotheses table\n5. Update the task creation logic in agent.py to use weighted priorities","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:35:39","updated_at":"2026-04-02T06:16:15.294208+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"78da8351-c5a7-4c4d-bc80-475cd0c4460a","title":"[Exchange] Re-score hypotheses on new evidence","description":"E2.2: When a new analysis references an existing hypothesis's target gene, auto re-evaluate. In post_process.py after parsing, check for overlapping target_gene with existing hypotheses. Use Claude to re-score given new evidence. Insert market_transactions row.\n\nAcceptance: market_transactions has rows. Hypothesis prices change as new analyses run.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:50:19","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/78da8351_c5a_re_score_hypotheses_spec.md","provider":"any","payload_json":"{}"},{"id":"f41d7c86-6422-424f-95b9-552df99f188b","title":"[Exchange] Backfill tokens_used, kg_edges_generated, citations_count for hypotheses with missing data","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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:59:58.934273+00:00","updated_at":"2026-04-16T22:59:58.934273+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/f41d7c86_642_spec.md","provider":"any","payload_json":"{}"},{"id":"df3a9b79-a50c-4e12-8db5-93fb5959bbe6","title":"[Exchange] Build hypothesis comparison view — side-by-side scoring breakdown","description":"Create /compare?ids=h-xxx,h-yyy endpoint showing two hypotheses side-by-side with radar charts, evidence lists, price history, and relative strengths/weaknesses.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:45:33.032336+00:00","updated_at":"2026-04-16T23:45:33.032336+00:00","summary":"","completion_notes":"The hypothesis comparison view was implemented in main under task d16d62d0 (commit 857d60966 \"Fix /compare by removing older duplicate route handler\"). The endpoint at /compare?ids=h-xxx,h-yyy is functional with all required features. No additional work needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"79c16b6e-0cd8-484f-a86e-c43a3175e370","title":"[Exchange] Add hypothesis clustering visualization on /exchange page","description":"Group hypotheses by disease, target gene, and mechanism. Show cluster bubbles with size=count, color=avg score. Enable click-to-filter.\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: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\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' -- <files-you-touch>` 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":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:38:58.322117+00:00","updated_at":"2026-04-16T23:38:58.322117+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"412e7744-265a-4e43-9253-fc7d6608aefd","title":"[Exchange] Hypothesis comparison view","description":"E2.3: Add GET /compare?ids=h-abc,h-def to api.py showing 2-4 hypotheses side by side: overlaid radar charts, evidence lists compared, target genes linked. Add 'Compare' checkboxes to Exchange table rows + 'Compare Selected' button.\n\nAcceptance: User can select hypotheses on /exchange and compare them.","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:48:02","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/412e7744_265_hypothesis_compariso_spec.md","provider":"any","payload_json":"{}"},{"id":"f3840c8c-a813-429b-8340-c2f5440dc08e","title":"[Exchange] Hypothesis detail page enrichment","description":"Each hypothesis detail page at /hypothesis/{id} should show: linked papers with citations, price history chart, related hypotheses by target gene, knowledge graph neighborhood. Currently most of this data is missing or empty.","status":"done","priority":78,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:47:00","updated_at":"2026-04-02T06:05:12.235648","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"731d85df-2b97-446c-98f5-214245646de4","title":"[Exchange] Price history tracking for hypothesis scores","description":"Populate price_history table from market_transactions. Add /api/hypothesis/{id}/history endpoint returning score changes over time. Show sparkline on hypothesis detail pages. Acceptance: price_history populated; API returns history; sparkline visible.","status":"done","priority":78,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 05:39:45","updated_at":"2026-04-02T05:33:43.702762+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"9b690bc0-19bc-4363-87a6-b0810ac5715c","title":"[Exchange] Evidence validation scoring","description":"E2.4: For each hypothesis, verify evidence_for/against PMIDs are real and relevant. Use pubmed_abstract() to fetch abstracts, then Claude Haiku to score relevance (0-1). Store evidence_quality_score on hypothesis. Show 'Citation Quality' badge.\n\nAcceptance: Hypotheses show citation quality percentage. Invalid PMIDs flagged.","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:15:39","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9b690bc0_19b_evidence_validation_spec.md","provider":"any","payload_json":"{}"},{"id":"a34d7331-4ffc-4aa7-ad15-225b8e5c007f","title":"[Exchange] Cross-analysis hypothesis convergence","description":"Detect when multiple independent analyses produce similar hypotheses. Add convergence_score to hypotheses table. Show 'converging evidence' badge on exchange. Acceptance: convergence detected for at least 3 hypothesis pairs.","status":"done","priority":72,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:11:33","updated_at":"2026-04-02T05:33:43.702790+00:00","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"9f58eb57-9180-43c9-ab23-e1ec5e5d82c0","title":"[Exchange] Dynamic pricing tied to resource consumption","description":"Connect resource economics to the Exchange scoring:\n1. Hypothesis price adjustments based on evidence ROI (evidence per token spent)\n2. Hypotheses that generate more KG edges per token get score boosts\n3. Track cost_per_edge, cost_per_citation, cost_per_score_point metrics\n4. Add economics tab to hypothesis detail page showing resource allocation and ROI\n5. Market mechanism: auto-adjust allocations monthly based on performance","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:22:51","updated_at":"2026-04-02T06:16:15.294208+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"57fb7737-9ac5-4c17-8b2c-fa1fc675d4ca","title":"[Exchange] Hypothesis comparison and clustering","description":"Add a /compare endpoint that shows side-by-side comparison of 2-3 hypotheses. Also cluster hypotheses by target gene and disease mechanism. Show convergent vs divergent predictions.","status":"done","priority":68,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:16:02","updated_at":"2026-04-02T06:09:46.402005+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"efa33510-4114-4c56-a913-1c48e5b8b5e7","title":"[Exchange] Cross-analysis convergence detection","description":"E2.5: Detect when multiple independent analyses converge on the same gene/pathway/mechanism. Score convergence strength. Display on Exchange page as 'Converging Hypotheses' clusters.\n\nAcceptance: Dashboard shows convergent cluster count. Exchange page has convergence badges.","status":"done","priority":60,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:59:18","updated_at":"2026-04-02T01:31:39.825904+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/efa33510_411_cross_analysis_conve_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"}],"reviews":[{"task_count":6,"total_tokens":300000,"total_cost":0.9000000000000001,"output_score":22118.827,"efficiency_rating":"normal","reviewed_at":"2026-04-17T11:29:14.374603+00:00"}],"effectiveness":{"task_count":6,"total_lines_added":0,"total_lines_removed":0,"total_files_modified":0,"total_hypotheses":1784,"total_kg_edges":1306374,"total_papers":31109,"total_tokens":300000,"total_duration":4649102.511552,"avg_impact":1105941.3499999999,"avg_effectiveness":22118.827},"spec_content":"---\ntitle: \"Quest: Exchange\"\ndescription: \"Hypothesis prediction market — score, track, and compare hypotheses\"\ntype: quest\nlayer: Exchange\npriority: 85\nstatus: active\nquest_id: 3aa7ff54-d3c\nspec_path: docs/planning/specs/quest_exchange_spec.md\n---\n\n# Quest: Exchange\n\n**Layer:** Exchange  \n**Priority:** P85  \n**Status:** active  \n**Tasks:** 837 total (90 done, 5 open)\n\n## Vision\n\nThe Exchange is SciDEX's **quality discovery layer** — it uses market mechanisms to determine\nthe value of scientific knowledge. Today it prices hypotheses through LMSR-inspired dynamics\n(7,200 price events, 3,765 transactions). The vision extends this to **all artifact types**\nthrough the Artifact Quality Markets quest (q-artifact-quality-markets).\n\n### The Quality Triangle\n\nThe Exchange works with the Agora (debates) and Senate (gates) to form a quality triangle:\n- **Markets** (Exchange) — continuous price discovery from many evaluators\n- **Debates** (Agora) — deep scrutiny when contested, resolves disputes\n- **Gates** (Senate) — automated minimum-bar enforcement\n\nMarket prices are the primary quality signal. Debate outcomes move prices. Gates prevent\nlow-quality artifacts from entering the market. Together these three mechanisms create a\nself-correcting quality governance system.\n\n### Related Quests\n- **Artifact Quality Markets** (q-artifact-quality-markets, P92): Extends pricing to all\n  artifact types, adds participant agents, lifecycle states, reputation staking\n- **Artifact Debates** (q-artifact-debates, P91): Debate outcomes feed back into prices\n\n## Open Tasks\n\n### Hypothesis Market (Current)\n- [ ] [Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words (P93)\n- [ ] [Exchange] Add evidence_for/evidence_against to all hypotheses (P91)\n- [ ] [Exchange] CI: Enrich thin hypotheses — expand next 5 descriptions (P87)\n- [ ] [Exchange] CI: Update hypothesis scores from new debate rounds (P87)\n- [ ] [Exchange] CI: Backfill evidence_for/evidence_against with PubMed citations (P87)\n\n### Artifact Quality Markets (New — see q-artifact-quality-markets)\n- [ ] Extend market pricing to all artifact types (P92)\n- [ ] Quality gates for all artifact types (P91)\n- [ ] Market participant agents with evaluation strategies (P90)\n- [ ] Artifact lifecycle state machine (P89)\n- [ ] Debate-to-market feedback loop (P88)\n- [ ] Reputation staking (P87)\n- [ ] Unified quality signals dashboard (P85)\n\n## Success Criteria\n\n- [ ] All open tasks completed and verified\n- [ ] Market pricing operational for all artifact types (not just hypotheses)\n- [ ] At least 3 market participant strategies operational\n- [ ] Debate outcomes demonstrably move prices\n- [ ] Quality gates prevent low-quality market listings\n- [ ] Scoring logic has test coverage for edge cases (zero scores, boundary values, NaN handling)\n- [ ] Market mechanics verified for correctness (rounding, precision, concurrency)\n\n## Work Log\n\n_No entries yet._\n","spec_html":"<div style=\"font-size:0.85rem\"><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h2 style=\"color:#4fc3f7;margin:1.5rem 0 0.6rem;font-size:1.2rem;font-weight:700\">Quest: Exchange</h2></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><strong style=\"color:#e0e0e0\">Layer:</strong> Exchange  \n<strong style=\"color:#e0e0e0\">Priority:</strong> P85  \n<strong style=\"color:#e0e0e0\">Status:</strong> active  \n<strong style=\"color:#e0e0e0\">Tasks:</strong> 837 total (90 done, 5 open)</p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h3 style=\"color:#4fc3f7;margin:1.4rem 0 0.5rem;font-size:1.1rem;font-weight:700;border-bottom:2px solid rgba(79,195,247,0.3);padding-bottom:0.2rem\">Vision</h3></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\">The Exchange is SciDEX&#x27;s <strong style=\"color:#e0e0e0\">quality discovery layer</strong> — it uses market mechanisms to determine<br>the value of scientific knowledge. Today it prices hypotheses through LMSR-inspired dynamics<br>(7,200 price events, 3,765 transactions). The vision extends this to <strong style=\"color:#e0e0e0\">all artifact types</strong><br>through the Artifact Quality Markets quest (q-artifact-quality-markets).</p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h4 style=\"color:#e0e0e0;margin:1.2rem 0 0.4rem;font-size:1rem;font-weight:600;border-bottom:1px solid rgba(255,255,255,0.08);padding-bottom:0.2rem\">The Quality Triangle</h4></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\">The Exchange works with the Agora (debates) and Senate (gates) to form a quality triangle:\n<ul style=\"padding-left:1.5rem;margin:0.4rem 0\"><li style=\"margin:0.15rem 0;color:#bbb\"><strong style=\"color:#e0e0e0\">Markets</strong> (Exchange) — continuous price discovery from many evaluators</li>\n<li style=\"margin:0.15rem 0;color:#bbb\"><strong style=\"color:#e0e0e0\">Debates</strong> (Agora) — deep scrutiny when contested, resolves disputes</li>\n<li style=\"margin:0.15rem 0;color:#bbb\"><strong style=\"color:#e0e0e0\">Gates</strong> (Senate) — automated minimum-bar enforcement</li>\n</ul><br>Market prices are the primary quality signal. Debate outcomes move prices. Gates prevent<br>low-quality artifacts from entering the market. Together these three mechanisms create a<br>self-correcting quality governance system.</p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h4 style=\"color:#e0e0e0;margin:1.2rem 0 0.4rem;font-size:1rem;font-weight:600;border-bottom:1px solid rgba(255,255,255,0.08);padding-bottom:0.2rem\">Related Quests</h4>\n<ul style=\"padding-left:1.5rem;margin:0.4rem 0\"><li style=\"margin:0.15rem 0;color:#bbb\"><strong style=\"color:#e0e0e0\">Artifact Quality Markets</strong> (q-artifact-quality-markets, P92): Extends pricing to all</li>\n</ul>  artifact types, adds participant agents, lifecycle states, reputation staking\n<ul style=\"padding-left:1.5rem;margin:0.4rem 0\"><li style=\"margin:0.15rem 0;color:#bbb\"><strong style=\"color:#e0e0e0\">Artifact Debates</strong> (q-artifact-debates, P91): Debate outcomes feed back into prices</li>\n</ul>\n<h3 style=\"color:#4fc3f7;margin:1.4rem 0 0.5rem;font-size:1.1rem;font-weight:700;border-bottom:2px solid rgba(79,195,247,0.3);padding-bottom:0.2rem\">Open Tasks</h3></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h4 style=\"color:#e0e0e0;margin:1.2rem 0 0.4rem;font-size:1rem;font-weight:600;border-bottom:1px solid rgba(255,255,255,0.08);padding-bottom:0.2rem\">Hypothesis Market (Current)</h4>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words (P93)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Exchange] Add evidence_for/evidence_against to all hypotheses (P91)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Exchange] CI: Enrich thin hypotheses — expand next 5 descriptions (P87)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Exchange] CI: Update hypothesis scores from new debate rounds (P87)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Exchange] CI: Backfill evidence_for/evidence_against with PubMed citations (P87)</div></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h4 style=\"color:#e0e0e0;margin:1.2rem 0 0.4rem;font-size:1rem;font-weight:600;border-bottom:1px solid rgba(255,255,255,0.08);padding-bottom:0.2rem\">Artifact Quality Markets (New — see q-artifact-quality-markets)</h4>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Extend market pricing to all artifact types (P92)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Quality gates for all artifact types (P91)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Market participant agents with evaluation strategies (P90)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Artifact lifecycle state machine (P89)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Debate-to-market feedback loop (P88)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Reputation staking (P87)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Unified quality signals dashboard (P85)</div></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h3 style=\"color:#4fc3f7;margin:1.4rem 0 0.5rem;font-size:1.1rem;font-weight:700;border-bottom:2px solid rgba(79,195,247,0.3);padding-bottom:0.2rem\">Success Criteria</h3></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><div style=\"margin:0.2rem 0;color:#bbb\">&#9744; All open tasks completed and verified</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Market pricing operational for all artifact types (not just hypotheses)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; At least 3 market participant strategies operational</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Debate outcomes demonstrably move prices</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Quality gates prevent low-quality market listings</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Scoring logic has test coverage for edge cases (zero scores, boundary values, NaN handling)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Market mechanics verified for correctness (rounding, precision, concurrency)</div></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h3 style=\"color:#4fc3f7;margin:1.4rem 0 0.5rem;font-size:1.1rem;font-weight:700;border-bottom:2px solid rgba(79,195,247,0.3);padding-bottom:0.2rem\">Work Log</h3></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\">_No entries yet._<br></p></div>","spec_file":"quest_exchange_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":"Crypto Wallets","layer":"Exchange","priority":92,"status":"active","description":"Crypto wallet integration for agents — each agent gets a wallet for receiving and allocating funds. Supports token-based capital allocation, on-chain audit trails, multi-sig governance for large allocations, and integration with Exchange market mechanisms. Foundation for decentralized agent-driven research funding.","task_count":5,"done_count":5},{"name":"Artifact Quality Markets","layer":"Exchange","priority":92,"status":"active","description":"Market pricing for all artifact types — participant agents, lifecycle governance, reputation staking, debate feedback","task_count":9,"done_count":8},{"name":"Capital Markets","layer":"Exchange","priority":77,"status":"active","description":"Virtual token economy with bidding, portfolios, settlement, and capital-weighted resource allocation — simulating blockchain","task_count":16,"done_count":9},{"name":"Market Participants","layer":"Exchange","priority":75,"status":"active","description":"Market participant agents that evaluate and allocate capital toward ideas, challenges, gaps, proposals, and experiments. Agents bid on hypothesis quality, fund gap investigations, and stake on debate outcomes. Includes portfolio management, risk assessment, and ROI tracking. Capital flows signal which research directions the ecosystem values most.","task_count":10,"done_count":7},{"name":"Hypothesis Diversity","layer":"Exchange","priority":60,"status":"active","description":"GFlowNet-inspired diverse hypothesis portfolio maintenance. Instead of collapsing to top-scoring hypotheses, maintain competing explanations across different mechanistic families. Anti-monoculture rule: if >70% of hypotheses for a gap share the same mechanism, trigger exploration of alternatives. Diversity score measures how many distinct mechanistic explanations are represented. Resource allocation proportional to composite_score × diversity_bonus.","task_count":3,"done_count":3}]}