{"quest":{"id":"58230ac8-c32","name":"Wiki","description":"NeuroWiki world model integration — rich wiki pages with mermaid, infoboxes, cross-links","layer":"Atlas","priority":75,"status":"active","created_at":"2026-04-02T10:00:57.209491+00:00","updated_at":"2026-04-11T05:44:23.589823+00:00"},"tasks":[{"id":"372681b3-cc0b-4a32-826a-eaffbc643f83","title":"[Wiki] Add mermaid pathway diagrams to top 5 mechanism/disease wiki pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <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 14:42:54","updated_at":"2026-04-13T10:16:02.334119+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/372681b3_cc0_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"d223c98a-2e11-4f88-94d4-eb08d5fb99b0","title":"[Wiki] Reduce stub backlog on high-priority wiki pages","description":"Continuously reduce the backlog of short wiki pages by expanding the highest-value stubs first, using page importance, quality scores, and world-model connectivity to prioritize work.","status":"open","priority":78,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T14:04:32.754570+00:00","updated_at":"2026-04-17T20:30:01.211772+00:00","summary":"","completion_notes":"Auto-release: recurring task had no work this cycle","last_error":"zombie_sweeper: no live slot (assigned='52'), stale heartbeat 2026-04-17 20:07:29.552751+00:00","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d223c98a_2e11_wiki_reduce_stub_backlog_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 6}, \"completion_shas\": [\"7e38fc52258a2a8dcef848aa12f95583cc100fbe\"], \"completion_shas_checked_at\": \"2026-04-13T05:29:04.860620+00:00\", \"completion_shas_missing\": [\"62bc39ddf0facb7827f025add5cfb91a70f34db3\", 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Generate pathway/mechanism diagrams for the 5 most-connected entities.","status":"open","priority":73,"task_type":"recurring","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:56:09.147672+00:00","updated_at":"2026-04-17T10:56:09.147672+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/c4a9a7ae-4d9_wiki_ci_add_mermaid_diagrams_to_next_5_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 6}, \"auto_tagged_at\": \"2026-04-03T22:29:52.501554\", \"completion_shas\": [\"cfeb1a0252230f8cae90cdda8b89215820111667\"], \"completion_shas_checked_at\": \"2026-04-12T23:47:33.814842+00:00\", \"completion_shas_missing\": [\"d9a3ca85b20c0846c33c9e4dde9619fb07dadfb7\", \"bbd022af2698294940761c7d324ddc7ec17beec8\", \"21d7111d457871d778b90f1bb103928762c077d6\", \"a220d10093386a6574dfbd8b50c1ac79201ea994\", \"fc05f82b014ca96a74e79460c907b93746e74538\", \"62f547b283c60785670448fab29dc4d7206af82b\", \"71629e632cffaea38d93f2753f29685e4f41c4d6\", \"a38b54251aa8f35064786dfb78437f9ed2e8030f\", \"f8af773285966361ce357b22bc7c71275c0785f4\", \"9fd43ade52d06a32e60c23cdca126fdf293954f3\", \"930542272d420cebc21f015ef9fffdaa493bace8\", \"ebdbc37d296330b79a063aba9279c730de4e55a8\", \"32171061ab56f13b05be97ea06f4bc0b6b53e20e\", \"1e76ba96fcc564d351376a256494c2b350a4e28d\", \"62870ba733f2e182cc9a1971d9f18b0e8fc6b9ff\", \"d29f4e7efa4bc0cc58d0aa73e0a5029222bc8893\", \"9dc4bb297567ddd34860157c5412df54271f47a9\", \"311c673f505228dab7b61a3fbab0620d7ac5f26b\", \"fa38554625c3d1b1cf69edceed1ce6d90ca89df4\", \"d835f319f51ec3ffd4541d4c48a4221841b27f27\"]}"},{"id":"da354aa6-f7e1-4e2f-b705-5a5e3fbb9b90","title":"[Wiki] Fix 404 on individual wiki entity pages (apoe, trem2, etc.)","description":"Wiki category pages (/wiki/genes, /wiki/all-pages) work but individual entity pages (/wiki/apoe, /wiki/trem2) return 404. These are critical for the demo — visitors click entity links from the wiki homepage and get errors.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's 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":"2026-04-14T03:14:50.008140+00:00","updated_at":"2026-04-14T03:14:50.008140+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/da354aa6_f7e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"4b9fca2292baba63b23bc8c2fed468a037055441\"], \"completion_shas_checked_at\": \"2026-04-14T03:14:49.988394+00:00\"}"},{"id":"5a11482c-8316-4d43-b980-212076868483","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 13639 wiki entities have mermaid diagrams. 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Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 06:27:31","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":"aea37950-f3f3-4be7-b40f-b8bc8af7cada","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6901 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 06:28:09","updated_at":"2026-04-03 15:54:29","summary":"Verified complete by slot 1","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"6de677ab-916c-4068-a6fa-d3cdceb3fc01","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6906 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:12:25","updated_at":"2026-04-03 15:54:29","summary":"Verified complete by slot 1","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"3448dbdf-f2a6-4eea-aee7-302c2a3322b7","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6906 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 06:32:06","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":"90ef91b5-c5b1-464c-a596-16ab67560213","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6911 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 06:39:18","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":"2482305f-b122-40f9-8ad8-761e11bf838e","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6972 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:27:28","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":"10da7745-eb52-4e66-b74e-422b4129cc36","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7010 wiki entities have mermaid diagrams. 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Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:27:14","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"aa055b86-31d8-42a5-8b9c-5cdae0342c98","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7067 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:11:01","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":"96f17c6a-1d1d-4960-bdcf-4ca2ef5979c8","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7162 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:22:11","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":"28b92dbc-4ed1-47a7-83e1-873985e5cc2a","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7167 wiki entities have mermaid diagrams. 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Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:27:46","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"275fa310-d8f0-4818-aa18-0c4050bf93a6","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7236 wiki entities have mermaid diagrams. 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Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:52:11","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":"339726ca-2299-440d-a319-6c3b8b8c4673","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7236 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:54:49","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":"35561ce7-64f1-4ec6-b1d7-fdaa180ddf4d","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7348 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:27:22","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":"6e9ae8a8-d454-427a-b190-97f1889d7f0d","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7399 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:53:36","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":"d4c8713c-2722-411c-92ba-50409728efbf","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7399 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:53:30","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":"7abe168a-e6e8-408e-8a29-db4851a4ceff","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7399 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 10:08:36","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":"124fd881-8f31-4cdc-ad49-7d1f05287836","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7475 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:58:53","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":"8cf06b47-aaff-48ed-9ccd-177c27678622","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7475 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 10:06:48","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":"249f99df-aa28-462a-93b1-8964873919e3","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7525 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:42:23","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":"a708c4cb-79e8-41b5-9719-8706e1139aa5","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7525 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"q07-w1-1779AC36","title":"[Wiki] Ensure top 20 wiki pages render beautifully","description":"Check rendering of top 20 demo-relevant wiki pages. Fix any broken mermaid, missing TOC, broken links. Ensure infoboxes display. Test: TREM2, APOE, alzheimers-disease, tau-propagation, microglia, neuroinflammation, alpha-synuclein, autophagy, blood-brain-barrier, glymphatic-system.","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:53:31","updated_at":"2026-04-02 09:43:32","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"860a1796-f5d4-4860-bf37-7e5b94bb9bd2","title":"[Wiki] Add mermaid diagrams to next batch of 100 wiki pages with KG edges","description":"5,209 wiki pages have mermaid diagrams. Many more pages have matching KG edges but no diagrams yet. Generate mermaid flowcharts for the next 100 most-connected wiki pages. Use slug-based matching for wiki_pages to knowledge_edges. Write directly to DB with retry logic for lock handling.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's 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":"2026-04-16T21:00:39.392500+00:00","updated_at":"2026-04-16T21:00:39.392500+00:00","summary":"Verified complete by slot 1","completion_notes":"Work log commit already on branch: cf312dca5. Mermaid diagrams verified in DB (11245 pages with mermaid, up from 11169 before work). No code changes needed — only spec work log update.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/860a1796_f5d_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}}"},{"id":"9cb9abc8-b15e-4791-bcb9-cef347a5d8d2","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's 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":"2026-04-16T21:00:25.976052+00:00","updated_at":"2026-04-16T21:00:25.976052+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/9cb9abc8-b15_wiki_add_structured_infoboxes_to_gene_p_spec.md","provider":"any","payload_json":"{}"},{"id":"df0dfc3d-221c-434b-a5d3-5f34f8c7fd0b","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, 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Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 13:56:28","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":"3b819176-4455-4d4e-8f8b-f11a6fb1d8e1","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:01:22","updated_at":"2026-04-03 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15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"8f05b049-bd18-4873-bb73-556c9d512b81","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:06:51","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"dc31f90b-c56e-4e50-9266-9758d2605a61","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:12:44","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":"9ec2756f-44a9-4072-b8d0-b84774228134","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:20:33","updated_at":"2026-04-03 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function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:36:41","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":"584e4928-189f-45cb-be34-0f5e207074a3","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:43:59","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":"394c3108-9d58-4160-82f7-06af46772c5c","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:37:06","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":"a172770f-b497-4804-af4e-ac7dff680a44","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:49:07","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"2a3a4859-957b-4f68-a667-7488bc5d0044","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:53:41","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":"84e658e7-16a5-4b16-96f1-58f642d29bac","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:43:00","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":"98916e82-1d55-4fd2-8e0b-8004365197d9","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:56:43","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":"e1a7eadb-599b-4537-8e80-6c1cdc2f95f7","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:59:07","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c6898219-384a-4f51-9695-1b2bed143228","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:39:24","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":"2b514270-9048-4511-8aff-67e1455bed19","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:39:35","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":"7571f88f-4b7b-46b6-b3cc-a5e7ed37ce83","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:53:51","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"9f80cb3b-c98f-4edc-9322-22eca4e58c50","title":"[Wiki] Add mermaid diagrams to next batch of high-connectivity entities","description":"Generate mermaid pathway/relationship diagrams for top-connected wiki entities that don't have them yet. Target: 50+ entities.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's 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":"2026-04-16T22:55:31.527085+00:00","updated_at":"2026-04-16T22:55:31.527085+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/9f80cb3b_c98_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}, \"completion_shas\": [\"cb945b20c\"], \"completion_shas_checked_at\": \"2026-04-16T22:55:12.945058+00:00\"}"},{"id":"c14f691d-665d-443f-a25a-d43bd2dfd3fb","title":"[Wiki] Expand 10 stub wiki pages to 500+ words (297/17399 are stubs)","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\n297 wiki pages have <200 words. Expand with descriptions, related entities, references.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's 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":78,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:09:03.323306+00:00","updated_at":"2026-04-17T10:09:03.323306+00:00","summary":"","completion_notes":"Verification: All 10 target pages (ai-tool-ai2-autodiscovery, ai-tool-science-beach, ai-tool-skillclaw, ai-tool-pask, ai-tool-searl, ai-tool-pask-memory, ai-tool-clinical-world-model, ai-tool-eigentsearch, ai-tool-variant-bio, ai-tool-owkin-k-navigator) now have 600+ words in the live DB.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"8d1469e2-4482-4a36-b89f-f1a0080c2aa2","title":"[Wiki] Expand 10 stub wiki pages to 500+ words (254/17333 are stubs)","description":"254 wiki pages have <200 words. Expand with descriptions, related entities, references.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's 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":78,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T08:56:31.644976+00:00","updated_at":"2026-04-17T08:56:31.644976+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":"0d37548c-12fe-4d8e-9f71-08504ce3bf89","title":"[Wiki] Add structured infoboxes to 10 gene/protein entity pages","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\n42 wiki entities lack infoboxes. Add gene symbol, function, associated diseases, known drugs.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's 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":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T11:55:19.789920+00:00","updated_at":"2026-04-17T11:55:19.789920+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"069264cf-e37e-4c7b-af99-0c314fc52de2","title":"[Wiki] Add structured infoboxes to 10 gene/protein entity pages","description":"52 wiki entities lack infoboxes. Add gene symbol, function, associated diseases, known drugs.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's 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":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:44:30.513391+00:00","updated_at":"2026-04-17T10:44:30.513391+00:00","summary":"","completion_notes":"Infoboxes already implemented and working. Gene/protein wiki pages render structured infoboxes with Gene Symbol, Function, Chromosome, Associated Diseases, Known Drugs, Interactions, and KG connection counts. The system was built by task 2a3a4859-957b-4f68-a667-7488bc5d0044 (complete on main). Confirmed via live curl of /wiki/genes-chchd3 and /wiki/genes-chmp5. No code changes needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"}],"reviews":[],"effectiveness":{},"spec_content":"---\ntitle: \"Quest: Wiki\"\ndescription: \"SciDEX world model — rich wiki pages with inline citations, mermaid diagrams, infoboxes, and cross-links to the knowledge graph\"\ntype: quest\nlayer: Atlas\npriority: 85\nstatus: active\nquest_id: 58230ac8-c32\nspec_path: docs/planning/specs/quest_wiki_spec.md\n---\n\n# Quest: Wiki\n\n**Layer:** Atlas  \n**Priority:** P85 (raised from P75 — inline citations now primary focus)  \n**Status:** active\n\n## Vision\n\nSciDEX wiki pages are the human-readable face of the knowledge graph. The target state: every factual claim is inline-cited with a hoverable popover showing the supporting paper's title, key claim, and a quoted excerpt. Pages are structurally complete (infoboxes, mermaid diagrams, cross-links) and continuously improved by background agents.\n\nFOXP1 and FOXP2 are the current pilot focus: demonstrating best-practice inline citation, paralog cross-referencing, and speech/language disorder representation.\n\n## Current Tracks\n\n### Track A: Inline Citations (P85 — Primary)\nSee full spec: `docs/planning/specs/quest_wiki_citations_spec.md`\n\n- Rich hover popovers with claim + excerpt + figure reference\n- FOXP1 and FOXP2 pilot pages fully cited (≥8 inline citations each)\n- Recurring citation enrichment task (every 6h)\n- Paper-to-wiki backlink governance (every 12h)\n- Citation coverage report (daily)\n\n### Track B: Structural Quality (P82 — Ongoing)\n\n- Structured infoboxes on all gene/protein/disease pages\n- Mermaid pathway diagrams on mechanism pages\n- H1 headings present on all pages\n- No boilerplate \"Background\" / \"The study of X has evolved...\" filler sections\n\n### Track C: Cross-links (P78 — Ongoing)\n\n- All pages linked to related hypotheses via artifact_links\n- All pages linked to supporting analyses\n- Paralog/homolog see-also links (e.g. FOXP1 ↔ FOXP2)\n- Disease pages link to gene pages and vice versa\n\n### Track D: SciDEX Rebrand (P70)\n\nReplace all \"NeuroWiki\" references with \"SciDEX Wiki\":\n- quest_wiki_spec.md (this file — done)\n- specs: 22c4c017, 48c44e67, a7e9909f, 6391cf49 (mark as legacy)\n- api.py: HTML comments, footer text, CSS class names\n- wiki_pages.source_repo UI label\n\n## Open Tasks\n\n- [ ] [Atlas] Rich hover popover for wiki citations — claim + excerpt + figure_ref (P88)\n- [ ] [Atlas] FOXP1 page: rewrite with ≥8 inline citations, speech/language featured (P86)\n- [ ] [Atlas] FOXP2 page: rewrite with ≥8 inline citations, all disease associations cited (P85)\n- [ ] [Atlas] Create recurring wiki-citation-enrichment task (every 6h) (P82)\n- [ ] [Atlas] Create paper-to-wiki-backlink governance task (every 12h) (P80)\n- [ ] [Atlas] Add wiki_citations table migration (P75)\n- [ ] [Wiki] Add structured infoboxes to gene/protein wiki pages (P82)\n- [ ] [Wiki] CI: Add mermaid diagrams to next 5 entity pages (P78)\n- [ ] [Atlas] Replace NeuroWiki references with SciDEX in UI-facing code (P70)\n\n## Success Criteria\n\n- [ ] FOXP1 and FOXP2 pages have ≥8 inline citations each, speech/language role prominently featured\n- [ ] Hover popovers show full citation context (claim, excerpt, figure)\n- [ ] Citation coverage ≥80% for pages with linked papers\n- [ ] Recurring enrichment task runs and adds ≥5 citations per 6h pass\n- [ ] Zero \"NeuroWiki\" in active UI-facing code\n- [ ] All gene/protein pages have structured infoboxes\n\n## Work Log\n\n### 2026-04-09 — Quest Refresh\n\n- Elevated priority to P85 based on user feedback: inline citations are the #1 missing feature\n- Added inline citation quest spec (quest_wiki_citations_spec.md)\n- Identified FOXP1/FOXP2 as pilot pages — both have refs_json but zero inline markers\n- Tooltip currently shows only `authors (year)` — upgrading to rich popover with claim/excerpt\n- Renamed \"NeuroWiki\" → \"SciDEX Wiki\" throughout this spec\n- Added 4 governance/recurring task patterns for continuous citation improvement\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: Wiki</h2></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><strong style=\"color:#e0e0e0\">Layer:</strong> Atlas  \n<strong style=\"color:#e0e0e0\">Priority:</strong> P85 (raised from P75 — inline citations now primary focus)  \n<strong style=\"color:#e0e0e0\">Status:</strong> active</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\">SciDEX wiki pages are the human-readable face of the knowledge graph. The target state: every factual claim is inline-cited with a hoverable popover showing the supporting paper&#x27;s title, key claim, and a quoted excerpt. Pages are structurally complete (infoboxes, mermaid diagrams, cross-links) and continuously improved by background agents.</p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\">FOXP1 and FOXP2 are the current pilot focus: demonstrating best-practice inline citation, paralog cross-referencing, and speech/language disorder representation.</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\">Current Tracks</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\">Track A: Inline Citations (P85 — Primary)</h4>\nSee full spec: <code style=\"background:#1a1a2e;color:#ce93d8;padding:0.1rem 0.3rem;border-radius:3px;font-size:0.85em\">docs/planning/specs/quest_wiki_citations_spec.md</code></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><ul style=\"padding-left:1.5rem;margin:0.4rem 0\"><li style=\"margin:0.15rem 0;color:#bbb\">Rich hover popovers with claim + excerpt + figure reference</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">FOXP1 and FOXP2 pilot pages fully cited (≥8 inline citations each)</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">Recurring citation enrichment task (every 6h)</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">Paper-to-wiki backlink governance (every 12h)</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">Citation coverage report (daily)</li>\n</ul>\n<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\">Track B: Structural Quality (P82 — Ongoing)</h4></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><ul style=\"padding-left:1.5rem;margin:0.4rem 0\"><li style=\"margin:0.15rem 0;color:#bbb\">Structured infoboxes on all gene/protein/disease pages</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">Mermaid pathway diagrams on mechanism pages</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">H1 headings present on all pages</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">No boilerplate &quot;Background&quot; / &quot;The study of X has evolved...&quot; filler sections</li>\n</ul>\n<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\">Track C: Cross-links (P78 — Ongoing)</h4></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><ul style=\"padding-left:1.5rem;margin:0.4rem 0\"><li style=\"margin:0.15rem 0;color:#bbb\">All pages linked to related hypotheses via artifact_links</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">All pages linked to supporting analyses</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">Paralog/homolog see-also links (e.g. FOXP1 ↔ FOXP2)</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">Disease pages link to gene pages and vice versa</li>\n</ul>\n<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\">Track D: SciDEX Rebrand (P70)</h4></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\">Replace all &quot;NeuroWiki&quot; references with &quot;SciDEX Wiki&quot;:\n<ul style=\"padding-left:1.5rem;margin:0.4rem 0\"><li style=\"margin:0.15rem 0;color:#bbb\">quest_wiki_spec.md (this file — done)</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">specs: 22c4c017, 48c44e67, a7e9909f, 6391cf49 (mark as legacy)</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">api.py: HTML comments, footer text, CSS class names</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">wiki_pages.source_repo UI label</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\"><div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Atlas] Rich hover popover for wiki citations — claim + excerpt + figure_ref (P88)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Atlas] FOXP1 page: rewrite with ≥8 inline citations, speech/language featured (P86)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Atlas] FOXP2 page: rewrite with ≥8 inline citations, all disease associations cited (P85)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Atlas] Create recurring wiki-citation-enrichment task (every 6h) (P82)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Atlas] Create paper-to-wiki-backlink governance task (every 12h) (P80)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Atlas] Add wiki_citations table migration (P75)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Wiki] Add structured infoboxes to gene/protein wiki pages (P82)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Wiki] CI: Add mermaid diagrams to next 5 entity pages (P78)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Atlas] Replace NeuroWiki references with SciDEX in UI-facing code (P70)</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; FOXP1 and FOXP2 pages have ≥8 inline citations each, speech/language role prominently featured</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Hover popovers show full citation context (claim, excerpt, figure)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Citation coverage ≥80% for pages with linked papers</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Recurring enrichment task runs and adds ≥5 citations per 6h pass</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Zero &quot;NeuroWiki&quot; in active UI-facing code</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; All gene/protein pages have structured infoboxes</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\"><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\">2026-04-09 — Quest Refresh</h4></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><ul style=\"padding-left:1.5rem;margin:0.4rem 0\"><li style=\"margin:0.15rem 0;color:#bbb\">Elevated priority to P85 based on user feedback: inline citations are the #1 missing feature</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">Added inline citation quest spec (quest_wiki_citations_spec.md)</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">Identified FOXP1/FOXP2 as pilot pages — both have refs_json but zero inline markers</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">Tooltip currently shows only <code style=\"background:#1a1a2e;color:#ce93d8;padding:0.1rem 0.3rem;border-radius:3px;font-size:0.85em\">authors (year)</code> — upgrading to rich popover with claim/excerpt</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">Renamed &quot;NeuroWiki&quot; → &quot;SciDEX Wiki&quot; throughout this spec</li>\n<li style=\"margin:0.15rem 0;color:#bbb\">Added 4 governance/recurring task patterns for continuous citation improvement</li>\n</ul></p></div>","spec_file":"quest_wiki_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; 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SciDEX already has a PaperCorpus abstraction layer with adapter classes — this quest extends it with new adapters, strengthens the citation/reference model beyond PMID as primary key, refactors legacy PubMed-only pipelines to use the generic layer, and integrates Paperclip MCP for agent-native deep-dive capabilities (search, grep, map, ask-image, sql). Goal: any SciDEX component that searches literature or cites papers goes through a unified multi-source interface.","task_count":0,"done_count":0},{"name":"Gap Factory","layer":"Atlas","priority":85,"status":"active","description":"Automated knowledge gap generation, decomposition, and value-scoring pipeline.\n\nCore principles:\n- Gaps are almost never \"resolved\" — they represent open questions that require extraordinary convergent evidence (5+ analyses, 2+ debates, composite score ≥0.85) to close.\n- Gaps have VALUE proportional to: importance × log(1 + dependent_hypotheses) × tractability.\n- Gaps decompose into subproblems (gap_subproblems table) and form dependency networks (gap_dependencies: blocks / informs / subsumes / requires / contradicts).\n- New gaps are identified by: debate transcript analysis, KG contradiction detection, paper frontier scanning, hypothesis-gap mismatch analysis.\n\nStatus model (graduated evidence thresholds):\n  open → investigating → partially_addressed → substantially_addressed → resolved\n\nInfrastructure delivered (2026-04-06):\n- Migration 054: gap_dependencies, gap_subproblems, value_if_resolved column, resolution_criteria\n- update_gap_statuses() with graduated thresholds\n- Dashboard shows \"Active Gaps\" (non-resolved) instead of \"Open Gaps\"\n\nOpen workstreams:\n1. Gap identification: scan new papers/debates for unresolved questions\n2. Gap decomposition: LLM-driven subproblem extraction from gap descriptions\n3. Gap dependency mapping: connect gaps to hypotheses and other gaps\n4. Gap value scoring: count downstream impact on hypothesis portfolios\n5. Gap tournaments: Elo-rank gaps by \"most important to solve\" via LLM judge\n6. Gap-hypothesis matching: surface which hypotheses address which gaps","task_count":9,"done_count":6},{"name":"Atlas","layer":"Atlas","priority":80,"status":"active","description":"Living knowledge graph + world model — multi-representation scientific knowledge. Includes automated gap detection pipeline, gap prioritization, and continuous knowledge frontier expansion.","task_count":504,"done_count":107}]}