{"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":"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":"running","priority":48,"task_type":"one_shot","frequency":"","assigned_slot":"996","started_at":"2026-04-25T22:05:26.931228+00:00","completed_at":null,"updated_at":"2026-04-25T22:05:26.931228+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"open","priority":71,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:18.498973+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","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}, \"completion_shas\": [\"00cdc6574367f99622496d63ab5b6105f96bf613\"], \"completion_shas_checked_at\": \"2026-04-21T02:58:37.512584+00:00\"}"},{"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":"open","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-25T16:10:08.428746+00:00","updated_at":"2026-04-25T16:10:08.428746+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":"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":"open","priority":68,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:18.166711+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"q02-e2-E3B0F52A","title":"[Exchange] Back-fill tokens_used and citations_count for all hypotheses","description":"Calculate and populate tokens_used, kg_edges_generated, citations_count for all 139 hypotheses. Derive from debate_rounds tokens, knowledge_edges by analysis_id, and evidence citation parsing. Essential for Resource Economics quest.","status":"open","priority":68,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:17.942752+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"71c5877e-b7a5-4591-ac6d-207b6862fb24","title":"[Exchange] Backfill price_history from market_transactions","description":"price_history table has 0 rows but market_transactions has 8. Create initial price_history entries for all 118 hypotheses using their current composite_score. The /api/hypothesis/{id}/history endpoint exists but returns empty data. Each hypothesis should have at least an initial_listing event.","status":"open","priority":68,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:16.997160+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","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":"open","priority":67,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:18.192826+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"599b596b-ccb2-48b8-88f2-1138dd3f1fff","title":"[Exchange] Add clinical-trial context to 20 hypotheses missing trial signals","description":"Duplicate check","status":"open","priority":65,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-25T07:47:20.399767+00:00","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","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":"open","priority":65,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:17.303160+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","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":"open","priority":65,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:16.637228+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","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":"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":"open","priority":60,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:16.641402+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","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":"open","priority":58,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:17.104573+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","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":"open","priority":58,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:16.904281+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","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":"open","priority":55,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:16.645438+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","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":"open","priority":52,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:16.908840+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","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":"open","priority":50,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:17.346510+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","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":"open","priority":40,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:16.375599+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","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}}"},{"id":"t-percentile-rankings","title":"Show percentile rankings on hypothesis detail pages","description":"","status":"open","priority":30,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:19.398554+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:00:25.500281+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":"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. See docs/planning/specs/economics_quest_spec.md\n\n[2026-04-05 update] [Exchange] Evolve economics, markets, and incentive ecology — now has Elo-tournament counterpart in q-evolutionary-arenas","status":"blocked","priority":97,"task_type":"recurring","frequency":"every-2h","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T23:22:32.882431+00:00","updated_at":"2026-04-24T13:13:26.517172+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/1f62e277_c72_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 7, \"safety\": 7}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"codex\", \"_stall_requeued_at\": \"2026-04-11 02:38:58\", \"completion_shas\": [\"95fcb170474aca19cbe0f3cd16132c727019cff4\", \"e22896857d809b2f6d260de649b2f75c86eb4472\", \"47182caf2a789e2180d30df090c31c777d95467b\", \"43a418b5ddc584ca7bccc98585798e48bc06645e\", \"d11e5b1b63bf13d5eb9b2cfcf65fb3b1e513503d\", \"923c8d26d90622eaf192d7743c35d4e7a65840c6\", \"dcaa815516ed3cb6d165093ae3a99d879e9e57d0\", \"b4c98fd9107e440648947eed673cdc4e10d13e29\", \"80516d2cc29761933de5c7c320c777cd8aacb0b1\", \"c3f2b5aca5ade73fc64d7d2271dc532dbdaf3ff2\", \"c7a8d2aadc4264ae57b4a588bb58a39beaf4704b\", \"e37188fa9a232f9e15398b026db0fd2b796f437e\", \"581844e23f078f2b2f1867fb10341fad0ec7d956\", \"0fd474081008f7111a56cb17fb7c1711617ff2f3\", \"e9f6043727a34cdc94b1e8064c31b2569c9fe470\", \"3b857c6d1cb48664ce5a27c62d8047de18e53612\", \"7b186846ac481d90d16054ef6ee13d7e4d32a644\", \"bdb28ea3ad3f8b380bdfd090f429e135e7b5193e\", \"948096af5dd5d7562af8198fc2bea39824f276e7\", \"0bb51340753ebbd5b393b1ce1182eb332df2f82d\", \"349c8db85c2fd82129ea912a4f36898ccbac2ddf\", \"d6a8d83a969ea85dc62b4caf7cd0d9fe4a754155\", \"cd27c717d3d5a9079ca0d62b2038852d708ced7a\", \"24f8b76c9dff34501ed52f754ea24bbf9424491d\", \"2969877810c3a0112612ce9e5effddebd24d6887\", \"71b367fe506243ccdf2619d89d442ae6eae5736d\", \"56720038e6d040b51fbd7be4f763efcb007643e5\", \"97d4bb4e9bd937fd1de933334ae5b27f14d1f9d5\", \"1f15606736afd350dc5f3dceed21042a9d4deefd\", \"66ea51893d8458c9d92ddaa16f4f77bf241725b0\", \"790e973cec13d3febf98dd2b8c0a6b3436300101\", \"272f622f6711e0cd490b7602e2da1500f2c5e8f0\", \"a5bbf358b42d3b1c22095ec5fdeb56fe6ffbc672\", \"5c2ff01ded50ed5fe19cdaa9ebf3bd5e19d2aa75\"], \"completion_shas_checked_at\": \"2026-04-13T04:53:44.251723+00:00\", \"completion_shas_missing\": [\"2d0e90975b9199e57de3d4a44d300ee10b3189b2\", \"33f562b99c13879bd2021ba318788c6ca623f95c\", \"c4e0f09f21c11899b5d8fdf3cdc53f19a7b58867\", \"549e6828077c7106686f506219c33310c75bcc7b\", \"5fa514a1879858c0fca7203ca087599bac494d6a\", \"57bd8760f37d9af30ebb4f7a1b04a07124565cf6\", \"32464ae7a4e1f7a052cb0e1a5dd8529fdcbd5785\", \"7ff6c7a1abe5b4fdb735d29c7da522a279cec361\", \"735cc029abc78af9975fc0210e5489cfdcd9b62a\", \"1385b2b3853042d5f9f2b9adb4fa620ded0b5c58\", \"74d5fbf8f034c6ff6c98ddebd60299452705dad5\", \"91f8a6fa731354aa2a75620ca3f0b3d59a958bb6\", \"916b8d727293083aa3c1a31312b2629227e89b8c\", \"4bc05738c40dfb916b8648c25b70af1c1e588587\", \"45a2784ab8581c850ed620317e16b3259c73a36f\", \"fb39fb2fa13318ccca7228ebf1633201109bcda8\", \"e74549b596a6bc6f1ac7ea720e380d9f321bf703\", \"5de6a2dbb39178ab6f38a5d6a76e7d0deb482103\", \"590b7efd1d94cfc34895b76f018c3a8b041f9a1f\", \"58f295c2a3dd930469fc8396636f3865669a0b37\", \"6369b32900d30ab65e0eb5d7dfee08ae6db1c600\", \"37f668b48090e365bf730be028fb3b5584233205\", \"37ffbee0222f53fd04e76230e81ce3bed2ffd604\", \"8040a8f4d1975bad3238d797739d3449db0537c9\", \"e7667ac5d94707ef898f30a72c564b1e7dc3e711\", \"42e143f92caa31243c327a3b9bad1a89ee1fb94c\", \"1574bf77a18c909ba6f8ab5b56168a5c8b3691b1\", \"ce816296a18132d70db4b6f98898edde34ce7fab\", \"e6a88118ed613813837f752b5e549e3e0fefdff4\", \"d59daedca517fdf7bb99f8bfa1c49bc932b2ed97\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"9d82cf53-fac8-449d-b5fd-5cd505960a84","title":"[Exchange] CI: Update hypothesis scores from new debate rounds","description":"Check for debate rounds completed since last score update. Recalculate composite scores incorporating new evidence.\n\n[2026-04-05 update] [Exchange] CI: Update hypothesis scores — consider Elo ratings alongside composite scores","status":"blocked","priority":96,"task_type":"recurring","frequency":"every-2h","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T23:22:43.338383+00:00","updated_at":"2026-04-24T13:13:26.176812+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":"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:42:54.558650+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:45:19.728019+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:42:31.869898+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":"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":"blocked","priority":95,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T19:37:04.048403+00:00","updated_at":"2026-04-24T13:13:27.448877+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":"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T14:11:36.376552+00:00","updated_at":"2026-04-18T14:11:36.376552+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/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\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T21:38:40.240704+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T20:09:36.342424+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:21:13.687352+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:02:49.938381+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":"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":"blocked","priority":94,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T23:23:16.868215+00:00","updated_at":"2026-04-24T13:13:26.205312+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":"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:21:07.109134+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:28:41.614221+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":"011ff204-20eb-4d42-9345-515f8a336084","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-25T01:28:28.740301+00:00","updated_at":"2026-04-25T01:28:28.740301+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"4a1ea213-01c4-436b-a77e-7f36a8896b34","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-25T00:07:42.048100+00:00","updated_at":"2026-04-25T00:07:42.048100+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"27c386cf-4290-426d-812e-21a1c16e31bb","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-25T00:01:26.915760+00:00","updated_at":"2026-04-25T00:01:26.915760+00:00","summary":"","completion_notes":"Verified all 1039 hypotheses already have 1000+ char descriptions. The prior runs of this task (and related bulk-enrich tasks on other slots) successfully expanded all thin hypotheses. No further enrichment needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"bcce699e-c80e-405e-8fb1-17237a3e0b54","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:48:09.965607+00:00","updated_at":"2026-04-24T23:48:09.965607+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","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":null,"updated_at":"2026-04-24T23:41:59.427378+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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. 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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":null,"updated_at":"2026-04-24T23:41:59.356095+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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. 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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":null,"updated_at":"2026-04-24T23:41:59.316492+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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. 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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":null,"updated_at":"2026-04-24T23:41:59.266812+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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. 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Target: all hypotheses >1000 words.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:05:11.978349+00:00","updated_at":"2026-04-24T23:05:11.978349+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"42dd2eac-562d-41da-a6ac-240376230119","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"11 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:04:39.258894+00:00","updated_at":"2026-04-24T23:04:39.258894+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":"e18e10a2-0958-48f9-805d-dadad8d95c65","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:03:48.866236+00:00","updated_at":"2026-04-24T23:03:48.866236+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"cde8080f-3a31-4cf8-ae82-16ec69a88c4e","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:03:39.165361+00:00","updated_at":"2026-04-24T23:03:39.165361+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"bc651ff5-b4bc-4b94-9817-20c0be2e7df4","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:00:45.752414+00:00","updated_at":"2026-04-24T23:00:45.752414+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"7e4d23d1-7096-4000-a929-b5d698c76941","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"1 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. Target: all hypotheses >1000 words.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:00:25.272310+00:00","updated_at":"2026-04-24T23:00:25.272310+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"d07ed3a3-116c-4b58-ba43-b0036e18c640","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T22:59:44.113602+00:00","updated_at":"2026-04-24T22:59:44.113602+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"eabfda2c-1a9a-4031-93d0-32a8e126b037","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T22:58:20.820737+00:00","updated_at":"2026-04-24T22:58:20.820737+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"004561cc-5497-4b75-8b76-a496ae1567f5","title":"[Exchange] Bulk enrich hypotheses — expand thin descriptions to 1000+ words","description":"36 hypotheses have 100-500 char descriptions. Expand each with mechanism details, evidence, clinical relevance. 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Target: all hypotheses >1000 words.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T22:56:59.502013+00:00","updated_at":"2026-04-24T22:56:59.502013+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"f976db23-0500-4a51-87dc-5bd8aa641952","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T22:55:48.214478+00:00","updated_at":"2026-04-24T22:55:48.214478+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"1015abd8-19cd-47ed-8c29-ec405f2868ad","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:42:20.893944+00:00","updated_at":"2026-04-24T16:42:20.893944+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":"3c9f2590-6814-4a84-9fc4-ad2b2b1e024f","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:39:58.063417+00:00","updated_at":"2026-04-24T16:39:58.063417+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"fac29023-79b8-43f3-a4ef-146dcd24fb9c","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:37:28.009367+00:00","updated_at":"2026-04-24T16:37:28.009367+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"8c4655a4-88bf-4751-adef-5ec8ad29493a","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:34:13.934069+00:00","updated_at":"2026-04-24T16:34:13.934069+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":"4f4d6221-6db3-4dcf-a2db-ea7684312b08","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:34:11.404687+00:00","updated_at":"2026-04-24T16:34:11.404687+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"025d4633-7549-4fb4-bc97-1dcf080a3fe9","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:33:49.292711+00:00","updated_at":"2026-04-24T16:33:49.292711+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"7376aa04-d394-45c1-9753-b4dca9072b08","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:33:37.752881+00:00","updated_at":"2026-04-24T16:33:37.752881+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"ccd0dadb-6099-42b5-87b1-daa1b42314d6","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:32:03.523018+00:00","updated_at":"2026-04-24T16:32:03.523018+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"55b79d5a-8290-47a9-8789-76b96e565c65","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:31:38.309520+00:00","updated_at":"2026-04-24T16:31:38.309520+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"9cbac2bb-54c8-40a9-a87a-f9e40b7887fa","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:31:19.594122+00:00","updated_at":"2026-04-24T16:31:19.594122+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":"b5f62acd-4fcb-4132-9739-02c2b4dcff21","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:30:16.427390+00:00","updated_at":"2026-04-24T16:30:16.427390+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":"1dc5187c-0570-476f-9299-90ed98c66e77","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:29:15.201197+00:00","updated_at":"2026-04-24T16:29:15.201197+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"4f1c745c-809c-4184-9c4b-c3e1aa9b9078","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:28:53.087705+00:00","updated_at":"2026-04-24T16:28:53.087705+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"d21e3681-6bdb-49b7-be30-baefddc3a82f","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:26:56.101576+00:00","updated_at":"2026-04-24T16:26:56.101576+00:00","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:25:55.528323+00:00","updated_at":"2026-04-24T16:25:55.528323+00:00","summary":"","completion_notes":"Verification spec committed to task branch (9708a27a3). DB query confirmed 1071/1071 active hypotheses have >= 1000 char descriptions — task already satisfied on main via af6f31ed3.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"completion_shas\": [\"9708a27a3\"], \"completion_shas_checked_at\": \"\"}"},{"id":"5c2d6bbe-ef75-4857-96ab-6ce6de15cf27","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:25:51.124177+00:00","updated_at":"2026-04-24T16:25:51.124177+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c2c99550-c5c8-4387-8aec-ee78d6501173","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:24:06.933370+00:00","updated_at":"2026-04-24T16:24:06.933370+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"9426de2b-182f-4953-886e-bde0fdd63ccb","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:21:22.303331+00:00","updated_at":"2026-04-24T16:21:22.303331+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":"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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:21:11.306382+00:00","updated_at":"2026-04-24T16:21:11.306382+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":"e4878f92-fd91-4ea5-9ef1-579c5fe0aea6","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:20:58.441513+00:00","updated_at":"2026-04-24T16:20:58.441513+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"9c0b4de3-8008-4587-8019-e6aa04ec566e","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:20:11.902154+00:00","updated_at":"2026-04-24T16:20:11.902154+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":"b404e29c-4e72-4335-91d3-729d532a4180","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:19:24.125006+00:00","updated_at":"2026-04-24T16:19:24.125006+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":"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. Target: all hypotheses >1000 words.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:18:44.536775+00:00","updated_at":"2026-04-24T16:18:44.536775+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":"eab3f315-d64f-4983-9147-18a9fa01db3e","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:16:44.435933+00:00","updated_at":"2026-04-24T16:16:44.435933+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c4d3d1bb-d5d5-48eb-9ff0-9fd64026d7ae","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:16:18.479999+00:00","updated_at":"2026-04-24T16:16:18.479999+00:00","summary":"","completion_notes":"Verified: 1179 total hypotheses. 1071 have >1000 char descriptions. 0 have thin 100-500 char descriptions. Only 1 under-100 is h-11ba42d0 (archived test hypothesis — appropriately short). Already resolved by commits 60d6d6ae1, 7663a11df et al.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"5e765c78-0f7f-4c6c-91d0-02abd1638045","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:13:03.761495+00:00","updated_at":"2026-04-24T16:13:03.761495+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"b0f43ffb-9593-4f09-b713-ed27914d5a95","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:10:38.208526+00:00","updated_at":"2026-04-24T16:10:38.208526+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"7dad8ad8-af69-4243-9d33-eac04aaa658c","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:09:49.017039+00:00","updated_at":"2026-04-24T16:09:49.017039+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":"5dce8eeb-4c25-4379-889c-ed4aea510a41","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:06:00.037139+00:00","updated_at":"2026-04-24T16:06:00.037139+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:05:51.360849+00:00","updated_at":"2026-04-24T16:05:51.360849+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"1e9ebda1-b6dd-4646-9d5a-a888f6c42a41","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:05:11.503285+00:00","updated_at":"2026-04-24T16:05:11.503285+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:04:54.462261+00:00","updated_at":"2026-04-24T16:04:54.462261+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":"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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:04:24.341182+00:00","updated_at":"2026-04-24T16:04:24.341182+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":"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":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T15:50:03.089705+00:00","updated_at":"2026-04-24T15:50:03.089705+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":"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T01:07:07.009282+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T01:02:04.964218+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:45:15.449447+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:38:45.313200+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":"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:13:31.276823+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:54:25.400967+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:43:57.035088+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T07:26:43.703722+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T04:49:57.577405+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T03:52:23.064806+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T02:49:15.930566+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T02:34:14.568036+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":"0551b477-723c-44fb-9335-c480eb9dba75","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.","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-25T03:42:16.463858+00:00","updated_at":"2026-04-25T03:42:16.463858+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"32a569ef-3067-4bea-a1fd-0682d0e49b86","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:57.005444+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"5f0345e2-1ce9-468e-9bde-9d544e47e4d6","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:56.990950+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"f6671ddf-d6f6-4a96-bff4-d4942c8f2d23","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:56.976476+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"1d9870e2-ac85-4c6c-8dcd-778e43c35d99","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. 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Target: all 142 hypotheses should have at least 3 evidence items each.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:54.141514+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c4675031-a71b-4930-8da2-d34a3092e7d4","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:54.126151+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"00c1c7a3-597b-47d4-86dd-25d8e6d2a520","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:54.111596+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"5e42735a-07e5-4ce5-8da4-0e737ce93906","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:54.096811+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"1a55faae-b17e-4bc6-b33b-8b6ca690750f","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:54.080800+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"cb79339e-4a3d-4448-a147-caa90dcedfc6","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:54.065330+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"255ae412-e064-4fc3-8484-1bcf35207e2a","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:54.049331+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"f1812e0c-8fdc-4783-ab0a-a335e542cc06","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:54.029173+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"9d5ca495-9aa5-4aa4-8c17-9e185bf2c5e9","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:54.008078+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"06dac8aa-0cc2-49df-9d0b-4a0263d475b5","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:53.992204+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c9529038-af3c-468e-b741-0a4e65dc6253","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:53.967273+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"5ec5b1f5-f12c-4b34-90fc-caae4aba2159","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:53.950394+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"ff74f4dc-7ebd-4f92-8495-a37245d3dddb","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.","status":"archived","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:53.930515+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"7397319a-8700-4e21-b2fc-b82911138c53","title":"[Exchange] Backfill PubMed evidence for 3 very-low-score hypotheses","description":"## Goal\nBackfill `evidence_for` and `evidence_against` JSONB fields for 3 hypotheses that have long descriptions but very low composite scores (0.105), suggesting they lack structured PubMed evidence citations.\n\n## Target hypotheses (by ID)\n- `h-9e51501a`: \"TYROBP Causal Network Inhibition for Microglial Repolarization\" (score=0.105, desc=7965 chars)\n- `h-5e0c4ddf`: \"IL-33/ST2 Axis Augmentation for Synaptic Protection\" (score=0.105, desc=7666 chars)\n- `h-f886036d`: \"P2RX7-PANX1 Channel Blockade for Neuroinflammatory Cascade\" (score=0.105, desc=6954 chars)\n\n## Steps\n1. For each hypothesis, run PubMed search for relevant papers\n2. Structure results as JSONB: `{\"pmid\": \"...\", \"citation\": \"...\", \"relevance\": \"high/medium/low\", \"findings\": \"...\"}`\n3. Update `evidence_for` (supporting papers) and `evidence_against` (contradicting papers) via DB write\n4. Verify composite_score changed after evidence update\n\n## Verification\n- Before: check composite_score for each hypothesis\n- After: re-check composite_score — verify it increased from 0.105\n- Also check that `evidence_for` and `evidence_against` columns are no longer NULL/empty\n\n## Constraints\n- Only update these 3 specific hypotheses (do not cascade to other hypotheses)\n- Use PubMed as primary evidence source\n- Document search terms used per hypothesis\n- If a hypothesis already has well-structured evidence (>3 entries in each field), skip it and note why","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T03:33:02.564003+00:00","updated_at":"2026-04-23T03:33:02.564003+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":"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":"2026-04-18T14:31:53.330058+00:00","updated_at":"2026-04-18T14:31:53.330058+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"2fef6ee66\"], \"completion_shas_checked_at\": \"2026-04-18T14:31:39.708164+00:00\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:54:28.395814+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:51:47.286116+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:47:19.685785+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:36:13.436289+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:33:59.947950+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:27:39.539611+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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:20:43.394942+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. Work Log shows hypotheses h-de579caf, h-5dbfd3aa, h-cb833ed8, h-ec731b7a, h-82922df8, h-f99ce4ca, h-1fe4ba9b enriched with 3,012-5,901 char descriptions, 6 evidence_for and 4 evidence_against citations each.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/97230db6_678_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"eeca3a31-d6f9-4d3f-b011-0866b4a36cd4","title":"[Exchange] Enrich top 5 thin 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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:19:44.507003+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":"1b911c77-4c4e-4dbe-a320-0cb129f1c38b","title":"[Exchange] CI: Enrich thin hypotheses — expand next 5 descriptions","description":"Rebuild theme AG1 (thin-content enrichment) as a polymorphic continuous process. SPEC: docs/planning/specs/rebuild_theme_AG1_thin_content_enrichment_spec.md. Follow docs/planning/specs/rebuild_theme_template_spec.md. Read docs/design/retired_scripts_patterns.md — especially the Design principles for continuous processes section — first. NO hardcoded entity lists, LLM rubric for semantic judgment, gap-predicate query (not calendar sweep), idempotent version-stamped writes, three surfaces (FastAPI+orchestra+MCP), outcome-feedback loop for progressive improvement, batch size cap 50.","status":"blocked","priority":90,"task_type":"recurring","frequency":"every-2h","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T15:13:40.332585+00:00","updated_at":"2026-04-24T13:13:26.150923+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/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":"1a0972d7-1170-44bd-b581-2e2d517faa1f","title":"[Exchange] Audit contribution credit gaps: 30 recent agent actions missing reward rows","description":"The agent contribution credit pipeline (driver #11) may have gaps where agent commits, debate rounds, and wiki edits were performed but no agent_contributions row was written.\n\n## Steps\n1. Query recent commits (last 7 days) from git log that have [task:ID] tags: `git log --since=\"7 days ago\" --format=\"%H %s\" | grep -E '\\[task:[a-f0-9-]+\\]'`\n2. For each commit, check if a corresponding agent_contributions row exists: `SELECT * FROM agent_contributions WHERE commit_sha LIKE '%%' AND created_at > NOW() - INTERVAL '7 days'`\n3. For any commits without credit rows, insert agent_contributions rows via the standard write path (credit_type='commit', base_reward=10)\n4. Log count of credits awarded\n\n## Acceptance Criteria\n- [ ] 30+ recent commits checked for credit coverage\n- [ ] Missing agent_contributions rows created for uncredited commits\n- [ ] Changes committed and pushed","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T05:06:21.433207+00:00","updated_at":"2026-04-23T05:06:21.433207+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_contribution_credit_audit_spec.md","provider":"any","payload_json":"{}"},{"id":"0bdaae5b-e1df-4740-814f-8d5f72f57432","title":"[Exchange] Implement funding allocation — Venture Funder + Grant Allocator agents fund challenges","description":"Use capital_pools.py and token_ledger.py to let Venture Funder and Grant Allocator agents evaluate open challenges, allocate tokens proportional to potential, and increase challenge bounties. Record transactions in ledger. Update /challenges page to show funded-by agents. 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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:32:01.970799+00:00","updated_at":"2026-04-18T16:32:01.970799+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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"f22b3c90f\"], \"completion_shas_checked_at\": \"2026-04-18T16:32:01.945985+00:00\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:50:27.838201+00:00","updated_at":"2026-04-18T15:50:27.838201+00:00","summary":"","completion_notes":"","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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:39:09.270029+00:00","updated_at":"2026-04-18T15:39:09.270029+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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:38:48.596166+00:00","updated_at":"2026-04-18T15:38:48.596166+00:00","summary":"","completion_notes":"Task reopened due to audit. Verified: hypothesis h-61196ade has 36 papers in evidence_for (target 10+), pathway_diagram=2695 chars showing TREM2 signaling cascade + microglial senescence + therapeutic intervention points, composite_score=0.904672. Prior commits eeac537ef/1cc2280e5 exist in repo but not on main (orphan branch). Data confirmed live in DB at /home/ubuntu/scidex/scidex.db. All acceptance criteria met.","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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:34:52.648857+00:00","updated_at":"2026-04-18T15:34:52.648857+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/2ee3753f_d47_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"df38f108d\"], \"completion_shas_checked_at\": \"2026-04-18T15:34:38.075553+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:31:27.266773+00:00","updated_at":"2026-04-18T15:31:27.266773+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/0aa736f8_ac1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:28:39.909282+00:00","updated_at":"2026-04-18T15:28:39.909282+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/850e3b86_690_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"ce442b72c\"], \"completion_shas_checked_at\": \"2026-04-18T15:28:16.040226+00:00\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:22:24.109294+00:00","updated_at":"2026-04-18T15:22:24.109294+00:00","summary":"","completion_notes":"","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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:20:12.805826+00:00","updated_at":"2026-04-18T15:20:12.805826+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1a4a55ae_53a_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:10:57.941506+00:00","updated_at":"2026-04-18T15:10:57.941506+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/408c42ab_98d_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:09:42.871485+00:00","updated_at":"2026-04-18T15:09:42.871485+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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:08:46.911540+00:00","updated_at":"2026-04-18T15:08:46.911540+00:00","summary":"","completion_notes":"Work verified in local DB: h-66078909 (2K ct, 604pd), h-7d24e096 (2.6K ct, 702pd), h-2ca830cd (2K ct, 708pd), h-5b35f7a5 (1.9K ct, 685pd), h-e14a97bf (2.9K ct, 803pd). Commit 751a22530 (enrich_hypotheses_batch3.py + spec) not ancestor of current main (50a6028fd); squash merge appears to have been lost in a rebase. Cannot push due to git auth failure.","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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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. 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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":null,"updated_at":"2026-04-24T23:41:59.619264+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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":null,"updated_at":"2026-04-24T23:41:59.603211+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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":null,"updated_at":"2026-04-24T23:41:59.584329+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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":null,"updated_at":"2026-04-24T23:41:59.554706+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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":null,"updated_at":"2026-04-24T23:41:59.537387+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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":null,"updated_at":"2026-04-24T23:41:59.519065+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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":null,"updated_at":"2026-04-24T23:41:59.493633+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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":null,"updated_at":"2026-04-24T23:41:59.474224+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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":null,"updated_at":"2026-04-24T23:41:59.455912+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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":null,"updated_at":"2026-04-24T23:41:59.441557+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T09:54:00.221225+00:00","updated_at":"2026-04-21T09:54:00.221225+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/a5406a19_8a1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T04:30:47.655083+00:00","updated_at":"2026-04-21T04:30:47.655083+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":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"e2429cb0915f858301fb71eaf53fe86c920fa7da\"], \"completion_shas_checked_at\": \"2026-04-21T04:30:47.627796+00:00\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T04:00:22.955085+00:00","updated_at":"2026-04-21T04:00:22.955085+00:00","summary":"","completion_notes":"","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, \"safety\": 9}, \"completion_shas\": [\"ec0ffccaa4015713a09618906ae525ffb1cf2cfa\"], \"completion_shas_checked_at\": \"2026-04-21T04:00:22.923216+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T03:46:54.150019+00:00","updated_at":"2026-04-21T03:46:54.150019+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":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T01:17:53.225831+00:00","updated_at":"2026-04-21T01:17:53.225831+00:00","summary":"","completion_notes":"Verification commit pushed to branch. All 5 hypotheses already enriched beyond spec thresholds by other agents' work. Commit 84a75f32d adds verification evidence to spec.","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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"84a75f32d\"], \"completion_shas_checked_at\": \"2026-04-21T01:17:53.196416+00:00\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T00:35:23.617588+00:00","updated_at":"2026-04-21T00:35:23.617588+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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T00:31:32.123818+00:00","updated_at":"2026-04-21T00:31:32.123818+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":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-20T23:10:11.759887+00:00","updated_at":"2026-04-20T23:10:11.759887+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/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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-20T23:04:08.069109+00:00","updated_at":"2026-04-20T23:04:08.069109+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/88e25c11_8f6_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"aa4f29536\"], \"completion_shas_checked_at\": \"2026-04-20T23:03:52.378064+00:00\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T06:09:18.027042+00:00","updated_at":"2026-04-19T06:09:18.027042+00:00","summary":"","completion_notes":"","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":"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":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:22:52.672340+00:00","updated_at":"2026-04-19T02:22:52.672340+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{}"},{"id":"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:30:11.376061+00:00","updated_at":"2026-04-19T01:30:11.376061+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\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T17:24:03.386298+00:00","updated_at":"2026-04-18T17:24:03.386298+00:00","summary":"","completion_notes":"","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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"f3e5ee87a\"], \"completion_shas_checked_at\": \"2026-04-18T17:24:03.359109+00:00\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T17:14:31.503089+00:00","updated_at":"2026-04-18T17:14:31.503089+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":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-18T17:01:54.399095+00:00","updated_at":"2026-04-18T17:01:54.399095+00:00","summary":"","completion_notes":"Verified: Database query confirms target hypotheses h-e3e8407c and h-58e655ee have gene_expression_context populated (1260 and 1778 chars respectively). All 15 original target hypotheses from the spec have gene_expression_context. Commit 23110c721 at HEAD 83be098d6 confirms the work landed. Added verification block to spec.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c89ba1df_e51_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. 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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":null,"updated_at":"2026-04-24T23:42:02.873903+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c2d2f544-ec93-4dd3-bdd2-36703904df2d","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":null,"updated_at":"2026-04-24T23:42:02.858655+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"cfda7fc9-a27d-46b8-8627-0008dbec8f67","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":null,"updated_at":"2026-04-24T23:42:02.845420+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"7b04eaa5-4bf1-459b-9d29-61f86b33b8c4","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":null,"updated_at":"2026-04-24T23:42:02.830393+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"6517ba09-1412-4372-afa3-fcb2182ee310","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":null,"updated_at":"2026-04-24T23:42:02.815069+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"38a7ff20-2dfc-40bc-8fec-3e1a6394ed47","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":null,"updated_at":"2026-04-24T23:42:02.799148+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"a61e0f8b-4ff0-425b-8c07-3a548cbad99a","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":null,"updated_at":"2026-04-24T23:42:02.784161+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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. 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":null,"updated_at":"2026-04-24T23:42:02.769909+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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":null,"updated_at":"2026-04-24T23:42:02.755076+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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":null,"updated_at":"2026-04-24T23:42:02.740289+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"aaf0810e-274a-4796-a3f4-3faa2cd8b78d","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":null,"updated_at":"2026-04-24T23:42:02.726620+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"14c89945-6318-40d1-910b-52c0fde06e39","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":null,"updated_at":"2026-04-24T23:42:02.713265+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"5d4f707e-ee46-4b3d-8eec-2f361f9a58cc","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":null,"updated_at":"2026-04-24T23:42:02.698621+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","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. 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":null,"updated_at":"2026-04-24T23:42:02.684747+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c44f17b0-cf26-4cb2-a2c2-b35559afbcb8","title":"[Exchange] Calibrate liquidity bands for 20 low-liquidity active hypothesis markets","description":"Active markets have liquidity below threshold, which weakens price discovery and capital-allocation signals.\n\nVerification:\n- 20 low-liquidity active markets are reviewed and either calibrated or explicitly deferred\n- Each updated market has a rationale tied to artifact quality, volume, and confidence\n- Remaining low-liquidity active market count is reduced\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T06:56:28.092574+00:00","updated_at":"2026-04-24T06:56:28.092574+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_market_liquidity_calibration_spec.md","provider":"any","payload_json":"{}"},{"id":"62cee498-e805-406f-8404-5e27270c4b56","title":"[Exchange] Create prediction markets for 10 high-priority knowledge gaps with no markets","description":"Knowledge gaps with high priority_score but no prediction market miss out on price signal feedback. Creating markets allows agents to stake on gap resolution and signal research value.\n\n## Steps\n1. Query gaps without markets: `SELECT kg.id, kg.title, kg.priority_score FROM knowledge_gaps kg WHERE kg.status = 'open' AND NOT EXISTS (SELECT 1 FROM market_transactions mt WHERE mt.gap_id = kg.id) ORDER BY kg.priority_score DESC LIMIT 10`\n2. For each gap: create a prediction market with initial price = priority_score/2, market_type='gap_resolution'\n3. Log to market_transactions with action='market_created', and price_history\n4. Verify each market is accessible via /exchange\n\n## Acceptance Criteria\n- [ ] 10 gaps now have prediction markets\n- [ ] Each market has initial price set proportional to priority_score\n- [ ] market_transactions rows created for each new market\n- [ ] Changes committed and pushed","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T05:35:51.515178+00:00","updated_at":"2026-04-23T05:35:51.515178+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":"d0938cc7-3fd2-4bec-8318-7f0dfba19e92","title":"[Exchange] Calibrate liquidity bands for 25 low-liquidity active markets","description":"705 active markets have liquidity below 10, which weakens price discovery and capital-allocation signals.\n\nVerification:\n- 25 low-liquidity active markets are reviewed and either calibrated or explicitly deferred\n- Each updated market has a rationale tied to artifact quality, volume, and confidence\n- Remaining low-liquidity active market count is <= 680\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T21:15:42.496351+00:00","updated_at":"2026-04-21T21:15:42.496351+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_market_liquidity_calibration_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6}}"},{"id":"8853595f-030f-4de3-b6c9-8d2e9fc5ee02","title":"[Exchange] Calibrate liquidity bands for 25 low-liquidity active markets","description":"730 active markets have liquidity below 10, which weakens price discovery and capital-allocation signals.\n\nVerification:\n- 25 low-liquidity active markets are reviewed and either calibrated or explicitly deferred\n- Each updated market has a rationale tied to artifact quality, volume, and confidence\n- Remaining low-liquidity active market count is <= 705\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T20:58:51.928701+00:00","updated_at":"2026-04-21T20:58:51.928701+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_market_liquidity_calibration_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6}}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T03:25:10.323409+00:00","updated_at":"2026-04-19T03:25:10.323409+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/44c29e33-4ef_exchange_enrich_experiment_descriptions_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 5}}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T03:03:02.297372+00:00","updated_at":"2026-04-19T03:03:02.297372+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/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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:45:04.593194+00:00","updated_at":"2026-04-19T02:45:04.593194+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":"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":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:40:51.208916+00:00","updated_at":"2026-04-19T02:40:51.208916+00:00","summary":"","completion_notes":"","last_error":"","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":"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:37:10.963419+00:00","updated_at":"2026-04-19T02:37:10.963419+00:00","summary":"","completion_notes":"Verified on origin/main (HEAD 69a6249c2):\n- 8/10 original targets have detailed protocols (3000+ chars) from prior commit aab3e56f8\n- `enrich_top10_protocols.py` exists at origin/main:enrichment/enrich_top10_protocols.py (236 lines)\n- Script finds experiments with protocol < 300 chars, ordered by composite_score\n- 314 experiments still have short protocols (<300 chars) available for future enrichment\n- 286 experiments already have rich protocols (>1000 chars)\n\nPrior commit 68ffe9a13 added the script; aab3e56f8 enriched 10 experiments. The script and enriched data are confirmed on origin/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":"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:33:59.791873+00:00","updated_at":"2026-04-19T02:33:59.791873+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":"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:32:14.503302+00:00","updated_at":"2026-04-19T02:32:14.503302+00:00","summary":"","completion_notes":"Verified complete via database inspection and code review. Implementation exists inline in api.py _init_db() function (lines 1864+) and migration file migrations/051_create_actor_reputation_token_ledger.py. All acceptance criteria met. Could not push due to credential issues - verification spec committed locally.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/da5b7995_f00_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:28:05.725169+00:00","updated_at":"2026-04-19T02:28:05.725169+00:00","summary":"","completion_notes":"","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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:20:20.239594+00:00","updated_at":"2026-04-19T02:20:20.239594+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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:17:22.572853+00:00","updated_at":"2026-04-19T02:17:22.572853+00:00","summary":"","completion_notes":"Verified all acceptance criteria after NO_COMMITS audit flag. The implementation was done under task 1f62e277-c72c-48f3-95f6-49f02b72cca7 but criteria apply to this task as well. Committed verification note to spec. Work includes: migration 050 (markets + market_trades tables), api.py endpoints with filters/sparklines, /exchange multi-asset view, /market/{market_id} detail page, compute_price_adjustment_market() generalized function.","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\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:09:17.735543+00:00","updated_at":"2026-04-19T02:09:17.735543+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/bdce957a_6b7_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:06:03.359440+00:00","updated_at":"2026-04-19T02:06:03.359440+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/68f868ec_c0a_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"c0825bd0-a0b0-4f79-8c33-f061066b7cbe","title":"[Exchange] Enrich target profiles — add druggability analysis and clinical context","description":"155 targets exist. Enrich with druggability scores, known drugs, clinical trial status, structural biology 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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:02:37.890678+00:00","updated_at":"2026-04-19T02:02:37.890678+00:00","summary":"","completion_notes":"Verification commit 29f50c767 pushed to branch but push rejected due to branch divergence (remote has f2ee1e24e as tip, local is based on main bb2ad4d7b). The actual work (enrich_targets_api_driven.py 839-line script + DB enrichment for 185 targets) was verified present in main HEAD via git show and DB queries. Task is done per f2ee1e24e.","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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"f2ee1e24ebcec4e3ecd99b61197bdff9f880e18a\"], \"completion_shas_checked_at\": \"2026-04-19T02:02:37.867654+00:00\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:00:14.340061+00:00","updated_at":"2026-04-19T02:00:14.340061+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":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:57:19.972264+00:00","updated_at":"2026-04-19T01:57:19.972264+00:00","summary":"","completion_notes":"","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\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:55:42.005321+00:00","updated_at":"2026-04-19T01:55:42.005321+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9d6a9404_a85_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:53:13.215472+00:00","updated_at":"2026-04-19T01:53:13.215472+00:00","summary":"","completion_notes":"DB corruption prevents task execution. sqlite3 integrity_check shows multiple errors including \"Tree 344 page 964411 cell 360: Rowid 17495 out of order\" and \"btreeInitPage() returns error code 11\". The update_kg_connectivity.py script exists in worktree and was designed to handle partial corruption via rowid iteration, but the DB is too corrupted for even basic SELECT queries. Escalating for DB restore before task can proceed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4de30635_b07_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:50:38.036011+00:00","updated_at":"2026-04-19T01:50:38.036011+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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:47:55.731441+00:00","updated_at":"2026-04-19T01:47:55.731441+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":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:47:47.934825+00:00","updated_at":"2026-04-19T01:47:47.934825+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:43:07.390777+00:00","updated_at":"2026-04-19T01:43:07.390777+00:00","summary":"","completion_notes":"File recalibrate_evidence_scores.py is on origin/main (commit c668ca13dc) identical to worktree. Task was already completed prior.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"id":"de093370-7c2b-4e62-aef9-abf38ac1d4b9","title":"[Exchange] Review and triage 15 pending market governance proposals","description":"Market governance proposals in 'proposed' or 'pending_review' status accumulate without decisions, blocking new markets from opening and stalling economic activity.\n\n## Steps\n1. Query: `SELECT id, title, proposal_type, proposed_by, created_at, current_status, rationale FROM market_proposals WHERE current_status IN ('proposed', 'pending_review') ORDER BY created_at ASC LIMIT 15`\n2. For each proposal:\n - Assess validity: is the proposed market on a real SciDEX hypothesis? Is the proposal well-specified?\n - Assess merit: would this market add price discovery value?\n - Recommend decision: approve (status='approved'), reject (status='rejected'), or request_revision (status='revision_needed')\n3. Update `market_proposals.current_status` and `market_proposals.review_notes` with decision\n4. For approved proposals: trigger market creation via `POST /api/markets/create` if API is available\n\n## Acceptance Criteria\n- [ ] 15 proposals reviewed\n- [ ] Each has a decision (approved/rejected/revision_needed) with review_notes\n- [ ] At least 3 proposals approved and market creation triggered\n- [ ] Changes committed and pushed\n\n## Constraints\n- Do NOT approve proposals for markets that already exist\n- Do NOT reject proposals without a stated reason","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T04:29:35.575072+00:00","updated_at":"2026-04-23T04:29:35.575072+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":"10644a9a-324e-4c2d-88d9-48fcafb0a1a6","title":"[Exchange] Review 5 pending market proposals","description":"Market proposals are awaiting review or voting. Proposal review keeps Exchange markets tied to useful scientific questions.\n\nVerification:\n- 5 market proposals are reviewed, advanced, rejected, or escalated\n- Review notes address pricing semantics, target artifact, and scientific utility\n- Remaining pending proposal count is reduced\n\nStart by reading this task's spec. Inspect pending market_proposals and their target entities or initial_entities. Evaluate whether each proposal is resolvable, useful, and non-duplicative. Advance status or create explicit follow-up with rationale.","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T01:23:10.618654+00:00","updated_at":"2026-04-23T01:23:10.618654+00:00","summary":"","completion_notes":"Bash EROFS blocker (same as prior 3 sessions on this recurring task) prevented git commit. Live API verified at scidex.ai. All proposals already decided by governance lifecycle. No reviews possible. See spec work log entry for 2026-04-22.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_market_proposal_review_spec.md","provider":"any","payload_json":"{}"},{"id":"d603660c-5100-4c50-94e5-1eeb02345c2d","title":"[Exchange] Review 5 pending market proposals","description":"Market proposals are awaiting review or voting. Proposal review keeps Exchange markets tied to useful scientific questions.\n\nVerification:\n- 5 market proposals are reviewed, advanced, rejected, or escalated\n- Review notes address pricing semantics, target artifact, and scientific utility\n- Remaining pending proposal count is recorded before and after\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T20:32:17.252149+00:00","updated_at":"2026-04-21T20:32:17.252149+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_market_proposal_review_spec.md","provider":"any","payload_json":"{}"},{"id":"b323c655-6a2b-4f5a-a90f-7c9e9abf7acd","title":"[Exchange] Review 2 pending market proposals","description":"2 market proposals are awaiting review or voting. Proposal review keeps Exchange markets tied to useful scientific questions.\n\nVerification:\n- 2 market proposals are reviewed, advanced, rejected, or escalated\n- Review notes address pricing semantics, target artifact, and scientific utility\n- Remaining pending proposal count is <= 0\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T19:08:41.310173+00:00","updated_at":"2026-04-21T19:08:41.310173+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_market_proposal_review_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6}}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:55:29.124317+00:00","updated_at":"2026-04-19T02:55:29.124317+00:00","summary":"","completion_notes":"","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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"id":"1d94dc96-8989-4c71-a911-9e8f32bdc15e","title":"[Exchange] Add hypothesis comparison radar charts to top hypothesis pages","description":"The /compare page has radar charts but individual hypothesis pages lack them. Add a radar chart showing the 10 scoring dimensions (confidence, novelty, feasibility, impact, mechanistic_plausibility, druggability, safety_profile, competitive_landscape, data_availability, reproducibility) to each hypothesis detail page. 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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:50:40.694699+00:00","updated_at":"2026-04-19T02:50:40.694699+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/1d94dc96_898_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:48:34.317606+00:00","updated_at":"2026-04-19T02:48:34.317606+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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:47:46.798714+00:00","updated_at":"2026-04-19T02:47:46.798714+00:00","summary":"","completion_notes":"","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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"40115777b\"], \"completion_shas_checked_at\": \"2026-04-19T02:47:46.777331+00:00\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T02:39:13.943316+00:00","updated_at":"2026-04-19T02:39:13.943316+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/9e96afa1_b9c_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"id":"7ad8fcaa-26c0-4414-bba8-df6665d2759c","title":"[Exchange] Resolve 20 zero-volume active hypothesis markets","description":"Active hypothesis markets with zero trading volume represent stale pricing. For 20 such markets, either: (a) trigger a price update by running composite scoring for the hypothesis, (b) create an initial trade to bootstrap price discovery, or (c) mark the market as low-priority if the hypothesis is archived.\\n\\nVerification:\\n- 20 markets reviewed and either updated with fresh pricing or flagged for archival\\n- Markets with active hypotheses have non-zero recent_volume or updated price_history","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T13:50:16.668522+00:00","updated_at":"2026-04-24T13:50:16.668522+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"fe401ade-ffd5-40ef-a98f-9c502cdaa7d6","title":"[Exchange] Review 10 pending allocation proposals","description":"Duplicate check probe","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T04:38:18.091750+00:00","updated_at":"2026-04-23T04:38:18.091750+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"3051fe55-353e-468a-8eee-d19faff0a5f2","title":"[Exchange] Create prediction markets for 10 high-confidence hypotheses without markets","description":"High-confidence hypotheses (composite_score > 0.6) that lack prediction markets are missing out on price discovery. Markets incentivize researchers to engage with the most promising hypotheses.\n\n## Steps\n1. Query: `SELECT h.id, h.title, h.composite_score, h.confidence FROM hypotheses h WHERE h.composite_score > 0.6 AND NOT EXISTS (SELECT 1 FROM prediction_markets pm WHERE pm.hypothesis_id = h.id) ORDER BY h.composite_score DESC LIMIT 10`\n2. For each hypothesis:\n - Set initial yes_prob based on confidence (clamp to 0.3–0.85 range)\n - Set initial liquidity = 100 tokens\n - Set resolution_date = 1 year from creation\n - Create market via `POST /api/markets/create` with hypothesis_id, initial probs, title\n3. Verify: `SELECT COUNT(*) FROM prediction_markets WHERE status = 'active'` increases by >= 8\n\n## Acceptance Criteria\n- [ ] 10 hypothesis markets created\n- [ ] Each market has: hypothesis_id, yes_prob, no_prob, liquidity, status='active'\n- [ ] yes_prob + no_prob = 1.0\n- [ ] Changes committed and pushed\n\n## Constraints\n- Do NOT create markets for hypotheses already in markets\n- Yes_prob must reflect composite_score, not be arbitrary","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T04:14:29.025606+00:00","updated_at":"2026-04-23T04:14:29.025606+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":"e0e21dda-1609-4a94-be59-62c155c3030c","title":"[Exchange] Calibrate confidence scores for 20 zero-confidence hypotheses","description":"Hypotheses with confidence=0.0 are excluded from Exchange markets and prediction mechanics. Many of these have substantive evidence but were never calibrated after initial creation.\n\n## Steps\n1. Query: `SELECT id, title, evidence_for, evidence_against, composite_score, debate_sessions FROM hypotheses WHERE confidence = 0.0 OR confidence IS NULL ORDER BY composite_score DESC NULLS LAST LIMIT 20`\n2. For each hypothesis with evidence_for or debate sessions, compute a calibrated confidence:\n - If has PubMed evidence (evidence_for non-empty): start at 0.3\n - If has completed debates (quality_score > 0.3): add 0.2 per debate\n - If composite_score > 0.5: add 0.1\n - Cap at 0.85 (reserve room for market discovery)\n3. Update `hypotheses.confidence` field in PostgreSQL\n4. Verify: `SELECT COUNT(*) FROM hypotheses WHERE confidence = 0.0 OR confidence IS NULL` decreases\n\n## Acceptance Criteria\n- [ ] 20 hypotheses have calibrated confidence > 0.0\n- [ ] Each calibrated value has a clear rationale based on evidence fields\n- [ ] No hypothesis gets confidence > 0.9 from this calibration\n- [ ] Changes committed and pushed\n\n## Constraints\n- Use `get_db()` for writes with explicit `conn.commit()`\n- Hypotheses with NO evidence should remain at 0.0 or be marked NULL — don't inflate\n- Log the rationale for each calibration in a brief commit message","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T03:47:18.124516+00:00","updated_at":"2026-04-23T03:47:18.124516+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":"db8eae7e-868e-4dee-a042-07d8f2f853d4","title":"[Exchange] Audit 50 open unclaimed token bounties for claimability","description":"Token bounties are open with no claimant. Bounties should either attract work, be clarified, be consolidated, or expire when no longer useful.\n\nVerification:\n- 50 open unclaimed bounties are reviewed for claimability, expiry, consolidation, or clarification\n- Each reviewed bounty has an action or rationale grounded in artifact state and bounty terms\n- Remaining open unclaimed bounty count is reduced\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T01:45:09.783452+00:00","updated_at":"2026-04-23T01:45:09.783452+00:00","summary":"","completion_notes":"Audited 50 oldest open unclaimed token bounties. Found 10 EXPIRING_SOON (Orchestra task bounties, past expiry) + 40 ORPHANED (gap-debate, wiki-edit, ai-tool artifact_ids not in artifacts table). Expired all 50 via PostgreSQL UPDATE. Open unclaimed reduced from 121 to 71. 5 counterargument bounties will expire tonight at 23:35 UTC-7.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_token_bounty_claim_audit_spec.md","provider":"any","payload_json":"{}"},{"id":"e9db1a26-67da-4406-8552-54aa3f929ba0","title":"[Exchange] Audit 30 open unclaimed token bounties for claimability","description":"Unclaimed token bounties represent unfulfilled incentive commitments that block the economics flywheel. For 30 oldest open bounties (SELECT id, title, amount, requirements FROM token_bounties WHERE status='open' ORDER BY created_at ASC LIMIT 30): (1) read bounty requirements; (2) check whether the requirements have been met by recent commits or contributions (search git log, agent_contributions, task completions); (3) if met: mark the bounty claimed and emit the payout event; (4) if expired: mark archived; (5) if still valid: add a structured comment with specific remaining criteria. Verification: 30 bounties reviewed; claimed/archived/updated count recorded.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-22T21:13:58.511750+00:00","updated_at":"2026-04-22T21:13:58.511750+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_token_bounty_claim_audit_spec.md","provider":"any","payload_json":"{}"},{"id":"2090d0af-9229-445a-8b98-78fec2c3c54b","title":"[Exchange] Audit 50 open unclaimed token bounties for claimability","description":"1077 token bounties are open with no claimant. Bounties should either attract work, be clarified, be consolidated, or expire when no longer useful.\n\nVerification:\n- 50 open unclaimed bounties are reviewed for claimability, expiry, consolidation, or clarification\n- Each reviewed bounty has an action or rationale grounded in artifact state and bounty terms\n- Remaining open unclaimed bounty count is <= 1027\n\nStart by reading this task spec and checking for duplicate recent work.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T22:10:04.769870+00:00","updated_at":"2026-04-21T22:10:04.769870+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_token_bounty_claim_audit_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6}}"},{"id":"0f9eee23-45b2-41fb-9c13-b3e3b14e1966","title":"[Exchange] Audit 50 open unclaimed token bounties for claimability","description":"1127 token bounties are open with no claimant. Bounties should either attract work, be clarified, be consolidated, or expire when no longer useful.\n\nVerification:\n- 50 open unclaimed bounties are reviewed for claimability, expiry, consolidation, or clarification\n- Each reviewed bounty has an action or rationale grounded in artifact state and bounty terms\n- Remaining open unclaimed bounty count is <= 1077\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T20:28:34.588894+00:00","updated_at":"2026-04-21T20:28:34.588894+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_token_bounty_claim_audit_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6}}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T05:30:27.236939+00:00","updated_at":"2026-04-19T05:30:27.236939+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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:50:23.774021+00:00","updated_at":"2026-04-19T04:50:23.774021+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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:49:54.492353+00:00","updated_at":"2026-04-19T04:49:54.492353+00:00","summary":"","completion_notes":"","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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:33:30.213177+00:00","updated_at":"2026-04-19T04:33:30.213177+00:00","summary":"","completion_notes":"Verified task 0c020210 is fully implemented on origin/main (commit e3519edc5). Evidence: git show origin/main:api.py confirms API endpoints at lines ~8151, ~8218, ~8290; migrations/049 confirms schema; sort algorithms at api.py:8099-8138. All acceptance criteria satisfied. Only deferred items (reputation updates + event bus) remain unchecked. Updated spec with ## Already Resolved block.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/threaded_comments_voting_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:31:17.496743+00:00","updated_at":"2026-04-19T04:31:17.496743+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/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\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:28:27.446586+00:00","updated_at":"2026-04-19T04:28:27.446586+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":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:26:50.518026+00:00","updated_at":"2026-04-19T04:26:50.518026+00:00","summary":"","completion_notes":"","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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:20:52.795298+00:00","updated_at":"2026-04-19T04:20:52.795298+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":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:12:26.649681+00:00","updated_at":"2026-04-19T04:12:26.649681+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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:11:11.684927+00:00","updated_at":"2026-04-19T04:11:11.684927+00:00","summary":"","completion_notes":"","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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T03:48:02.244776+00:00","updated_at":"2026-04-19T03:48:02.244776+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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T03:30:25.914450+00:00","updated_at":"2026-04-19T03:30:25.914450+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/0c378120_911_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T03:30:18.593333+00:00","updated_at":"2026-04-19T03:30:18.593333+00:00","summary":"","completion_notes":"Cannot verify or re-execute: local DB corrupted (database disk image is malformed), and batch2 script was migrated to deprecated/ by PG migration (aec879a68). Original work commits (1ed142fb5 etc.) never merged to main — only on orphan task branches. Task requires database access which is currently unavailable.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/fa89d516_0a7_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T03:27:33.217926+00:00","updated_at":"2026-04-19T03:27:33.217926+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}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"id":"8339375e-4ca2-476a-bae5-d9cf731530a9","title":"[Exchange] Audit 25 open unclaimed token bounties for claimability","description":"Token bounties that have been open for > 7 days without a claimant may be incorrectly scoped, missing claimability criteria, or stale.\n\n## Steps\n1. Query: `SELECT id, title, amount, created_at, status, claim_criteria FROM token_bounties WHERE status IN ('open', 'unclaimed') AND created_at < NOW() - INTERVAL '7 days' ORDER BY amount DESC LIMIT 25`\n2. For each bounty, assess:\n - Is the claim criteria clear and achievable? (yes/no)\n - Has anyone attempted to claim it? (check bounty_claims table)\n - Is the linked task or gap still relevant?\n3. For unclear criteria: update the claim_criteria field with specific, actionable requirements\n4. For stale/irrelevant bounties: mark as archived with reason\n5. For valid but unclaimed bounties: verify they're visible in the Exchange and properly linked\n\n## Acceptance Criteria\n- [ ] 25 bounties audited (status recorded for each)\n- [ ] >= 5 bounties have improved claim_criteria\n- [ ] Stale/impossible bounties marked archived (with reason)\n- [ ] Changes committed and pushed\n\n## Constraints\n- Do NOT mark bounties as claimed unless they meet their criteria\n- Do NOT archive bounties that are valid and just unclaimed","status":"done","priority":84,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T05:42:16.836631+00:00","updated_at":"2026-04-23T05:42:16.836631+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":"b3c9e0f5-fda2-4ee6-a763-0db0a7b6cd68","title":"[Exchange] Normalize prices for 20 hypotheses with stale market scores","description":"Many hypothesis markets have prices that haven't been updated in 7+ days despite new debate rounds or evidence accumulating. Stale prices misrepresent the current evidence state.\n\nVerification:\n- 20 hypotheses with stale market prices (no price update in 7+ days) have prices recalculated\n- New prices incorporate: current composite_score, recent debate outcomes, latest evidence\n- price_history rows created for each price update event\n- market_transactions table updated with recalibration events\n\nQuery: SELECT h.id, h.title, h.composite_score, MAX(ph.created_at) as last_price_update FROM hypotheses h LEFT JOIN price_history ph ON ph.hypothesis_id = h.id WHERE h.status = 'active' GROUP BY h.id HAVING last_price_update < NOW() - INTERVAL '7 days' OR last_price_update IS NULL ORDER BY h.composite_score DESC LIMIT 20. Recompute prices from current composite_score and debate data. Insert price_history rows and verify.","status":"done","priority":84,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T04:19:15.515174+00:00","updated_at":"2026-04-23T04:19:15.515174+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":"f6c281d3-b947-496c-bdcb-866a9955c831","title":"[Exchange] Review 10 pending allocation proposals","description":"Allocation proposals are pending or proposed. Capital allocation proposals need review so tokens flow toward high-evidence scientific work.\n\nVerification:\n- 10 pending allocation proposals are approved, rejected, or escalated with rationale\n- Each decision references evidence strength, requested tokens, and target artifact utility\n- Remaining pending allocation proposal count is reduced\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":84,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T01:03:29.214645+00:00","updated_at":"2026-04-23T01:03:29.214645+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_allocation_proposal_review_spec.md","provider":"any","payload_json":"{}"},{"id":"b5b3a5b2-abcb-496b-8f8b-9ae5cd91aa8e","title":"[Exchange] Review 10 pending allocation proposals","description":"Allocation proposals are pending or proposed. Capital allocation proposals need review so tokens flow toward high-evidence scientific work.\n\nVerification:\n- 10 pending allocation proposals are approved, rejected, or escalated with rationale\n- Each decision references evidence strength, requested tokens, and target artifact utility\n- Remaining pending allocation proposal count is reduced\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":84,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-22T21:07:49.971901+00:00","updated_at":"2026-04-22T21:07:49.971901+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_allocation_proposal_review_spec.md","provider":"any","payload_json":"{}"},{"id":"55730901-9a37-4f3e-a154-4d3b26483b6c","title":"[Exchange] Audit 25 stale active markets for update or resolution","description":"430 active markets have not been updated in at least 14 days. Stale markets should either ingest new evidence, stay active with rationale, or resolve.\n\nVerification:\n- 25 stale active markets have updated_at refreshed by a substantive review or are resolved/deferred\n- Each review records evidence considered and the reason for update, deferral, or resolution\n- Remaining stale active market count is <= 405\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":84,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T21:04:43.685016+00:00","updated_at":"2026-04-21T21:04:43.685016+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_market_stale_update_audit_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6}}"},{"id":"e6584b7b-4acc-4cbf-bce3-836c8d36f3ae","title":"[Exchange] Review 4 pending allocation proposals","description":"4 allocation proposals are pending or proposed. Capital allocation proposals need review so tokens flow toward high-evidence scientific work.\n\nVerification:\n- 4 pending allocation proposals are approved, rejected, or escalated with rationale\n- Each decision references evidence strength, requested tokens, and target artifact utility\n- Remaining pending allocation proposal count is <= 0\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":84,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T19:33:07.165939+00:00","updated_at":"2026-04-21T19:33:07.165939+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_allocation_proposal_review_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"1bb821a4-1c68-4484-86a1-dfd293d085a5","title":"[Exchange] Review 15 pending market allocation proposals for approval","description":"15 rows in `market_allocation_proposals` have status='pending' and have not been reviewed. For each proposal: evaluate the proposed capital allocation against current market depth, hypothesis quality score, and quest priority alignment. Approve proposals that increase liquidity for high-priority hypotheses (composite_score > 0.6 or quest_priority > 85). Reject proposals for low-quality or duplicate hypotheses. Update status via the market governance API. Acceptance: 15 proposals reviewed, each with an approved/rejected status and a written rationale in proposal_review_notes.","status":"done","priority":83,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T06:45:45.144484+00:00","updated_at":"2026-04-24T06:45:45.144484+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"b887f991-906c-4fa4-9eaf-f32ce43d996a","title":"[Exchange] Reconcile market prices with current hypothesis Elo ratings for 25 markets","description":"Market prices (composite_score) may have drifted from Elo ratings after tournament rounds. Reconciling them ensures the Exchange reflects the latest tournament outcomes.\n\n## Steps\n1. Query: `SELECT h.id, h.title, h.composite_score, h.elo_score, h.updated_at FROM hypotheses h WHERE h.elo_score IS NOT NULL AND ABS(h.composite_score - (h.elo_score / 3000.0)) > 0.1 ORDER BY ABS(h.composite_score - (h.elo_score / 3000.0)) DESC LIMIT 25`\n2. For each divergent hypothesis: normalize Elo to 0-1 scale and update composite_score to blend: new_score = 0.7 * old_composite + 0.3 * (elo/3000)\n3. Record price change in market_transactions: action='elo_reconciliation', old_score=old, new_score=new\n4. Log to price_history\n\n## Acceptance Criteria\n- [ ] 25 hypotheses with divergent Elo/market prices reconciled\n- [ ] composite_score updated to reflect Elo outcomes\n- [ ] market_transactions rows created for audit trail\n- [ ] Changes committed and pushed","status":"done","priority":83,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T05:21:26.366372+00:00","updated_at":"2026-04-23T05:21:26.366372+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":"89510902-84ad-45e6-819f-136688bfad47","title":"[Exchange] Reconcile hypothesis market prices with current Elo ratings","description":"When Elo ratings update after tournament rounds, prediction market probabilities should be recalculated to reflect the new relative ranking. Market prices that lag Elo ratings create arbitrage opportunities that distort the Exchange.\n\n## Steps\n1. Query: `SELECT h.id, h.elo_rating, pm.id as market_id, pm.yes_prob FROM hypotheses h JOIN prediction_markets pm ON pm.hypothesis_id = h.id WHERE pm.status = 'active' AND ABS(pm.yes_prob - h.elo_rating / 3000.0) > 0.1 LIMIT 20`\n2. For each misaligned market:\n - Compute target_yes_prob = elo_rating / (elo_max + elo_min) where elo bounds define the [0.1, 0.9] probability range\n - Update `prediction_markets.yes_prob = target_yes_prob` and `no_prob = 1 - target_yes_prob`\n - Log the adjustment reason\n3. Verify: market prices cluster more tightly with Elo bands\n\n## Acceptance Criteria\n- [ ] 20 markets updated to reflect current Elo ratings\n- [ ] yes_prob + no_prob = 1.0 for all updated markets\n- [ ] Price change logged in market_price_history table if it exists\n- [ ] Changes committed and pushed","status":"done","priority":83,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T04:40:50.556061+00:00","updated_at":"2026-04-23T04:40:50.556061+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":"6402e872-e816-4cd3-9f0f-2db40750e442","title":"[Exchange] Review 5 zero-volume markets for resolution or archival","description":"Some hypothesis markets have had zero trading volume for 30+ days. Zero-volume markets waste resources and provide no price signal — they should be resolved, archived, or reset.\n\nVerification:\n- 5 zero-volume markets are reviewed with a documented decision: resolve/archive/reset/keep-active\n- Each decision cites the hypothesis quality, evidence state, and market design factors\n- Market status updated in PostgreSQL (resolved, archived, or flagged for redesign)\n- Remaining zero-volume active market count is reduced\n\nQuery: SELECT h.id, h.title, h.status, h.composite_score, COUNT(mt.id) as trades FROM hypotheses h LEFT JOIN market_transactions mt ON mt.hypothesis_id = h.id AND mt.created_at > NOW() - INTERVAL '30 days' WHERE h.status = 'active' GROUP BY h.id HAVING trades = 0 ORDER BY h.created_at ASC LIMIT 5. Evaluate and decide. Persist decisions and verify.","status":"done","priority":83,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T03:03:56.818513+00:00","updated_at":"2026-04-23T03:03:56.818513+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":"ad3641b2-bbe4-4b25-9a1e-acb24dba2aea","title":"[Exchange] Triage 15 stale market proposals for close or escalation","description":"Market proposals that are pending > 7 days without a vote decision are stale. For 15 oldest stale proposals: review the proposal content, check if the proposed market still makes sense given current hypothesis state, then either advance to voting, reject with reason, or escalate to Senate for governance review.\\n\\nVerification:\\n- 15 stale market proposals have been triaged with a documented decision\\n- Each decision has a rationale in the proposal's decision_reason field\\n- Proposals advanced to voting have clear acceptance criteria","status":"done","priority":83,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T01:46:33.354741+00:00","updated_at":"2026-04-23T01:46:33.354741+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"94f055c7-6cf8-4b50-b24d-0928722d323f","title":"[Exchange] Resolve 15 stale prediction markets with no activity in 30 days","description":"Prediction markets that have been open > 30 days with zero trades are consuming system resources and distorting the Exchange liquidity pool. They need resolution or archival.\n\n## Steps\n1. Query: `SELECT id, title, status, yes_prob, created_at, last_trade_at FROM prediction_markets WHERE status = 'active' AND (last_trade_at IS NULL OR last_trade_at < NOW() - INTERVAL '30 days') AND created_at < NOW() - INTERVAL '30 days' ORDER BY created_at ASC LIMIT 15`\n2. For each stale market:\n - Check if the underlying hypothesis has a clear resolution (composite_score > 0.7 = resolve YES, < 0.3 = resolve NO, middle = extend)\n - If resolvable: call `POST /api/markets/{id}/resolve` with outcome and resolution_note\n - If not resolvable: set status='suspended' with a suspension_reason\n3. Verify: `SELECT COUNT(*) FROM prediction_markets WHERE status = 'active' AND last_trade_at < NOW() - INTERVAL '30 days'` decreases\n\n## Acceptance Criteria\n- [ ] 15 stale markets have a decision (resolved or suspended)\n- [ ] Each decision has a resolution_note or suspension_reason\n- [ ] No market resolved arbitrarily — must have a basis\n- [ ] Changes committed and pushed","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T04:16:15.319088+00:00","updated_at":"2026-04-23T04:16:15.319088+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"completion_shas\": [\"534fb70d9\"], \"completion_shas_checked_at\": \"2026-04-23T04:16:15.288290+00:00\"}"},{"id":"38a651aa-dc74-4fa4-99d6-509673a4aaa6","title":"[Exchange] Seed liquidity review for 25 zero-volume active markets","description":"Many active markets have zero volume. Zero-volume markets do not provide useful confidence or prioritization signals.\n\nVerification:\n- 25 zero-volume markets are reviewed for seeding, closure, or consolidation\n- Each reviewed market has a rationale tied to entity, resolution, and scientific utility\n- Remaining zero-volume active markets is reduced\n\nStart by reading this task's spec. Select active zero-volume markets from PostgreSQL (dbname=scidex user=scidex_app) ordered by priority, age, or linked artifact utility. Determine whether to seed liquidity, consolidate with another market, or propose closure. Record actions and verify market volume/status changes or follow-up tasks.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T01:36:59.951955+00:00","updated_at":"2026-04-23T01:36:59.951955+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_zero_volume_market_liquidity_spec.md","provider":"any","payload_json":"{}"},{"id":"d29bfc51-8aaa-492d-8311-dd9097db28ea","title":"[Exchange] Add clinical-trial context to 20 hypotheses missing trial signals","description":"Many active hypotheses lack clinical_trials context. Trial context improves translational feasibility estimates, market pricing, and challenge design.\n\nVerification:\n- 20 active hypotheses gain clinical_trials context or documented no-trial rationale\n- Each trial signal includes NCT ID, PMID, registry URL, or explicit search provenance\n- Remaining active hypotheses missing clinical trial context is reduced\n\nStart by reading this task's spec. Select active hypotheses from PostgreSQL (dbname=scidex user=scidex_app) missing clinical_trials, prioritizing therapeutic targets and high market relevance. Search ClinicalTrials.gov, PubMed, and linked SciDEX papers for related trials or explicit absence. Persist concise trial context and verify updated translational fields.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T01:10:20.369619+00:00","updated_at":"2026-04-23T01:10:20.369619+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_hypothesis_clinical_context_backfill_spec.md","provider":"any","payload_json":"{}"},{"id":"0122f887-6b2c-4c01-baae-57b7bb07fae7","title":"[Exchange] Calibrate liquidity bands for 20 low-liquidity active markets","description":"Find 20 active hypothesis markets with fewer than 5 trades in the last 7 days (low liquidity). For each market, review the current bid/ask spread and price history. Adjust liquidity parameters to tighten spreads and encourage participation. Acceptance criteria: 20 markets have updated liquidity_band settings; each has a market_transactions audit entry recording the calibration; spread reduced by at least 20%.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T00:14:14.043136+00:00","updated_at":"2026-04-23T00:14:14.043136+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest-engine-ci.md","provider":"any","payload_json":"{}"},{"id":"9c8d3163-6727-40d4-a7a4-5d56fd6483ee","title":"[Exchange] Add clinical-trial context to 20 hypotheses missing trial signals","description":"Active hypotheses lack clinical_trials context. Trial context improves translational feasibility estimates, market pricing, and challenge design.\n\nVerification:\n- 20 active hypotheses gain clinical_trials context or documented no-trial rationale\n- Each trial signal includes NCT ID, PMID, registry URL, or explicit search provenance\n- Remaining active hypotheses missing clinical trial context is reduced\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-22T23:34:06.843328+00:00","updated_at":"2026-04-22T23:34:06.843328+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_hypothesis_clinical_context_backfill_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 7}}"},{"id":"62d01cc2-2ab1-40ba-ac73-0bccfa23e365","title":"[Exchange] Calibrate liquidity bands for 20 low-liquidity active markets","description":"Markets with near-zero trading volume have stale prices that don't reflect current evidence, reducing the prediction market's signal quality. For 20 active hypothesis markets with lowest trading volume (SELECT h.id, h.title, h.composite_score, COUNT(mt.id) as trade_count FROM hypotheses h LEFT JOIN market_transactions mt ON mt.hypothesis_id=h.id GROUP BY h.id ORDER BY trade_count ASC LIMIT 20): (1) check if current price reflects recent debate evidence and composite_score; (2) if price is stale (diverges from composite_score by >0.15): inject a calibration trade to bring price within 0.05 of composite_score; (3) log calibration with rationale; (4) INSERT INTO market_transactions. Verification: 20 markets reviewed; stale prices corrected.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-22T23:23:31.745654+00:00","updated_at":"2026-04-22T23:23:31.745654+00:00","summary":"","completion_notes":"Verified: 6 hypotheses calibrated (376dc00dd) all have market_price matching composite_score. Task already resolved by prior agent.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_market_liquidity_calibration_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 7}}"},{"id":"7d27298e-f49b-49ba-9fee-d7bd9710fe21","title":"[Exchange] Add clinical-trial context to 20 hypotheses missing trial signals","description":"416 active hypotheses lack clinical_trials context. Trial context improves translational feasibility estimates, market pricing, and challenge design.\n\nVerification:\n- 20 active hypotheses gain clinical_trials context or documented no-trial rationale\n- Each trial signal includes NCT ID, PMID, registry URL, or explicit search provenance\n- Remaining active hypotheses missing clinical trial context is <= 396\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T21:17:31.352717+00:00","updated_at":"2026-04-21T21:17:31.352717+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_hypothesis_clinical_context_backfill_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6}}"},{"id":"5b7ca0ed-5eac-4450-8474-d35b45f51f33","title":"[Exchange] Seed liquidity review for 25 zero-volume active markets","description":"535 active markets have zero volume. Zero-volume markets do not provide useful confidence or prioritization signals.\n\nVerification:\n- 25 zero-volume markets are reviewed for seeding, closure, or consolidation\n- Each reviewed market has a rationale tied to entity, resolution, and scientific utility\n- Remaining zero-volume active markets is <= 510\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T21:04:52.388704+00:00","updated_at":"2026-04-21T21:04:52.388704+00:00","summary":"","completion_notes":"Root cause: EROFS read-only filesystem on /home/ubuntu/Orchestra/data/claude_creds/max_outlook/session-env/. Every Bash call fails before executing. API server connection refused on port 8000. No PostgreSQL access possible. Files written to worktree but not committable. The review script encodes complete logic: prioritizes hypothesis markets, seeds those with confidence>=0.6 or debate_count>=3 or wiki coverage, closes markets older than 90d with quality<0.4 or older than 180d (stale), consolidates duplicates, defers recent/indeterminate ones. Before count from task description: 535. Expected after count when script runs: <=510.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_zero_volume_market_liquidity_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 5}}"},{"id":"87c2e6dc-e774-4ec9-a454-15f8baaeccda","title":"[Exchange] Add clinical-trial context to 20 hypotheses missing trial signals","description":"Many active hypotheses lack clinical_trials context. Trial context improves translational feasibility estimates, market pricing, and challenge design.\n\nVerification:\n- 20 active hypotheses gain clinical_trials context or documented no-trial rationale\n- Each trial signal includes NCT ID, PMID, registry URL, or explicit search provenance\n- Remaining active hypotheses missing clinical trial context is recorded before and after\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T20:29:27.866410+00:00","updated_at":"2026-04-21T20:29:27.866410+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_hypothesis_clinical_context_backfill_spec.md","provider":"any","payload_json":"{}"},{"id":"ce9eb8e2-fbac-48b1-a761-46b3c3159763","title":"[Exchange] Seed liquidity review for 25 zero-volume active markets","description":"There are active Exchange markets with zero volume. Zero-volume markets do not provide useful confidence or prioritization signals unless they are seeded, consolidated, closed, or given clearer resolution plans.\n\nVerification:\n- 25 zero-volume markets are reviewed for seeding, closure, or consolidation\n- Each reviewed market has a rationale tied to entity, resolution, and scientific utility\n- Remaining zero-volume active markets is recorded before and after\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T19:49:11.251372+00:00","updated_at":"2026-04-21T19:49:11.251372+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_zero_volume_market_liquidity_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 5}}"},{"id":"f6f5ec6d-af59-4a98-8486-bf8b10a8ad4a","title":"[Exchange] Seed liquidity review for 25 zero-volume active markets","description":"562 active markets have zero volume. Zero-volume markets do not provide useful confidence or prioritization signals.\n\nVerification:\n- 25 zero-volume markets are reviewed for seeding, closure, or consolidation\n- Each reviewed market has a rationale tied to entity, resolution, and scientific utility\n- Remaining zero-volume active markets is <= 537\n\nStart by reading this task's spec and checking for duplicate recent work.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-21T19:00:39.688333+00:00","updated_at":"2026-04-21T19:00:39.688333+00:00","summary":"","completion_notes":"Already resolved. Verified: 537 zero-volume active markets (target ≤ 537: PASS). The 25 markets documented in the spec work log were closed in a prior commit (8ced22b29). Before/after: 562 → 537.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_zero_volume_market_liquidity_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 5}}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T05:15:13.656523+00:00","updated_at":"2026-04-19T05:15:13.656523+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":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"id":"fa55a07f-587e-43a0-9d7b-21aa1c7d057f","title":"[Exchange] Review resolution readiness for 25 stale active markets","description":"Many active markets are older than seven days with no resolution. Stale markets need resolution criteria, renewed activity, or governance cleanup.\n\nVerification:\n- 25 stale active markets are reviewed for resolution readiness or cleanup\n- Each reviewed market has updated rationale, resolution plan, or follow-up task\n- Remaining stale unresolved active markets is reduced\n\nStart by reading this task's spec. Select stale active markets from PostgreSQL (dbname=scidex user=scidex_app) by age and low activity. Inspect resolution fields, linked artifacts, trades, and scientific status. Resolve, update criteria, or create cleanup tasks with explicit rationale.","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-24T14:49:43.936895+00:00","updated_at":"2026-04-24T14:49:43.936895+00:00","summary":"","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_stale_market_resolution_review_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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T05:34:44.713129+00:00","updated_at":"2026-04-19T05:34:44.713129+00:00","summary":"","completion_notes":"Verified /compare endpoint exists at api.py:31462 with full implementation: radar charts (10 dimensions), evidence lists, price history, verdict summary, score breakdown, shared evidence, KG comparison, pathway diagrams. All features from task description present on origin/main.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"4da0c83a2\"], \"completion_shas_checked_at\": \"2026-04-19T05:34:44.689807+00:00\"}"},{"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: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-19T05:33:49.877604+00:00","updated_at":"2026-04-19T05:33:49.877604+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}"},{"id":"53a7edd2-9e2e-4806-aa16-20055f6715b3","title":"[Exchange] Review and close 10 stale markets unresolved after 30 days","description":"Markets open more than 30 days without resolution lock capital and pollute the active market feed. For 10 markets (SELECT hypothesis_id, current_price, opened_at FROM market_state WHERE status='active' AND opened_at < NOW() - INTERVAL '30 days' LIMIT 10): (1) check hypothesis status — if hypothesis is archived/superseded, close the market as 'no_resolution'; (2) if hypothesis is active and composite_score is definitive (>0.7 or <0.3), settle the market based on score; (3) if neither: extend with a 14-day extension and add an evidence audit comment; (4) UPDATE market_state SET status=, resolved_at=NOW(), resolution_note= WHERE hypothesis_id=. Verification: 10 markets processed; status updated from 'active' for all rows.","status":"done","priority":79,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-22T23:31:23.967222+00:00","updated_at":"2026-04-22T23:31:23.967222+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_stale_market_resolution_review_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 7}}"},{"id":"5fdebad5-f1d8-4018-b61f-5eb534d6b17c","title":"[Exchange] Create prediction markets for 15 high-quality new hypotheses","description":"High-quality hypotheses without prediction markets cannot receive crowd-sourced probability assessments or trigger funding. For 15 hypotheses with composite_score > 0.5 and status IN ('promoted','debated') that have no market_state entry (SELECT h.id, h.title, h.composite_score FROM hypotheses h WHERE h.composite_score > 0.5 AND h.status IN ('promoted','debated') AND h.id NOT IN (SELECT hypothesis_id FROM market_state) LIMIT 15): (1) compute initial market price as composite_score × 100 (0-100 scale); (2) INSERT INTO market_state (hypothesis_id, current_price, status, opened_at, total_volume) VALUES (, , 'active', NOW(), 0); (3) emit market_created event; (4) record in market_transactions as initial seeding. Verification: 15 new market_state rows with status='active'; events emitted.","status":"done","priority":79,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-22T20:58:25.355515+00:00","updated_at":"2026-04-22T20:58:25.355515+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":"7de9e81d-d2f7-4af2-b784-81d1150d8bb8","title":"[Exchange] Review 10 pending market proposals for governance approval","description":"Market proposals waiting for governance approval block new prediction markets from opening and reduce Exchange participation. For 10 oldest market_proposals with status='pending' (SELECT id, hypothesis_id, proposed_by, rationale FROM market_proposals WHERE status='pending' ORDER BY created_at ASC LIMIT 10): (1) read the proposal rationale and the underlying hypothesis quality (composite_score, evidence count); (2) apply approval criteria: composite_score > 0.3, evidence_for non-empty, not a duplicate of an open market; (3) if approved: UPDATE market_proposals SET status='approved'; trigger market_state row creation; (4) if rejected: UPDATE status='rejected' with a rejection_reason. Verification: 10 proposals reviewed; status updated from 'pending' for all rows.","status":"done","priority":78,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-22T20:43:48.583920+00:00","updated_at":"2026-04-22T20:43:48.583920+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_market_proposal_review_spec.md","provider":"any","payload_json":"{}"},{"id":"7554689e-f5b0-449f-bef6-1f449f02ff10","title":"[Exchange] Review 10 Senate allocation proposals for research funding decisions","description":"Pending allocation proposals block research squads from receiving pool funding. For 10 allocation_proposals with status='pending' (SELECT id, squad_id, requested_amount, justification FROM allocation_proposals WHERE status='pending' ORDER BY created_at ASC LIMIT 10): (1) read justification and the squad's target importance_score; (2) check squad progress: log entries, findings posted, evidence quality; (3) approve if: importance_score > 0.5, squad has active members, at least 1 finding posted; (4) deny if: squad inactive >7 days or justification insufficient; (5) UPDATE allocation_proposals SET status=, decision_note=, decided_at=NOW(). Verification: 10 proposals processed; status changed from 'pending' for all; at least 5 approved for active squads.","status":"done","priority":76,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-22T23:19:01.975128+00:00","updated_at":"2026-04-22T23:19:01.975128+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_allocation_proposal_review_spec.md","provider":"any","payload_json":"{}"},{"id":"aaaf6bd6-bccf-426a-bc6b-4f82db2a19e2","title":"[Exchange] Seed liquidity for 10 zero-volume markets to activate price discovery","description":"Markets with zero trading volume produce no price signal and cannot inform hypothesis ranking. For 10 active markets with total_volume = 0 (SELECT hypothesis_id, current_price FROM market_state WHERE status='active' AND total_volume = 0 LIMIT 10): (1) read the associated hypothesis composite_score; (2) inject a seed transaction: create a market_transaction at price anchored to composite_score (e.g., composite_score × 100); (3) INSERT INTO market_transactions (hypothesis_id, action, price, agent_id, volume) with volume=10; (4) UPDATE market_state SET total_volume=10, last_price= WHERE hypothesis_id=; (5) emit a market_seeded event. Verification: 10 markets have total_volume > 0; current_price set to a reasonable value based on composite_score.","status":"done","priority":76,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-22T20:44:24.795317+00:00","updated_at":"2026-04-22T20:44:24.795317+00:00","summary":"","completion_notes":"Infrastructure blocker: every Bash command in this session fails with \"EROFS: read-only file system, mkdir '/home/ubuntu/Orchestra/data/claude_creds/max_outlook/session-env/3cbf1973-b886-44b2-9908-11330eaf3472'\". This blocks all execution including python3, psql, and git.\n\nWork completed (file created on disk, not committed due to git also being blocked):\n- /home/ubuntu/scidex/.orchestra-worktrees/task-aaaf6bd6-bccf-426a-bc6b-4f82db2a19e2/seed_zero_volume_markets.py\n\nKey schema discoveries from codebase analysis:\n1. Task description references 'market_state' table — this does NOT exist. Real table is 'markets' (id, market_type, entity_id, entity_name, current_price, volume, liquidity, status, created_at, updated_at).\n2. market_transactions action CHECK constraint allows only: buy, sell, score_update (NOT 'seed'). Script uses action='buy', agent_id='system'.\n3. composite_score is stored 0-1 range (not 0-10 as task says), so seed_price = composite_score directly, clamped to [0.01, 0.99].\n4. Event bus EVENT_TYPES does not include 'market_seeded'; script uses 'hypothesis_scored' with payload action='market_seeded'.\n5. quest_engine.py confirms real query: SELECT COUNT(*) FROM markets WHERE status='active' AND COALESCE(volume,0)=0.\n\nThe script: queries up to 10 zero-volume active markets, for each does UPDATE markets SET volume=10 current_price=seed_price + INSERT market_transactions(action='buy') + INSERT price_history(event_type='seed') + INSERT events(hypothesis_scored with market_seeded payload), then commits and verifies.\n\nTo execute once EROFS is resolved: cd /home/ubuntu/scidex/.orchestra-worktrees/task-aaaf6bd6-bccf-426a-bc6b-4f82db2a19e2 && python3 seed_zero_volume_markets.py","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_zero_volume_market_liquidity_spec.md","provider":"any","payload_json":"{}"},{"id":"6575a67d-33ab-4c35-a0b6-436bb4c32a6b","title":"[Exchange] Diagnose stalled economics driver cluster (drivers #1, #3, #6 all no-op)","description":"Resource audit found three core economics drivers all consistently no-op at every-2h: driver #1 Agent debate enrollment (73ff9962), driver #3 Multi-agent market order (e240778b), driver #6 Multi-participant debate orchestration (8a568010). Together 252 wasted runs/wk. Find the root blockage in the pipeline, fix or lower frequency to every-6h. See docs/planning/specs/exchange_economics_drivers_noop_fix_spec.md and resource audit docs/planning/specs/resource_intelligence_audit_2026_04_23.md","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T05:54:47.805889+00:00","updated_at":"2026-04-23T05:54:47.805889+00:00","summary":"","completion_notes":"Diagnosis complete. All 3 drivers are data-driven no-ops at equilibrium. Driver #1: all debates already enrolled (235 stale sessions cleaned per run); Driver #3: market order capacity exhausted per cycle (50 orders max, correctly idempotent); Driver #6: no sessions need more debate rounds. Frequencies updated to every-6h via orchestra task update CLI. Estimated savings: 168 runs/week.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"3a61e65c-d660-40a4-a505-739ea13c90e1","title":"[Exchange] Commit harvest.py PostgreSQL fix from task-3e1a8177 worktree","description":"The recurring squad harvest driver (task 3e1a8177) fixed harvest.py for PostgreSQL compatibility but could not commit/push because the Bash tool was unavailable (EROFS on session-env). The fix is already written to the worktree file.\n\n## What to do\n\n1. Check the worktree at `/home/ubuntu/scidex/.orchestra-worktrees/task-3e1a8177-4e47-4067-8ae1-62102de6528d` for uncommitted changes to `economics_drivers/squads/harvest.py`\n\n2. If the file has uncommitted changes matching the description below, verify and commit:\n ```\n cd /home/ubuntu/scidex/.orchestra-worktrees/task-3e1a8177-4e47-4067-8ae1-62102de6528d\n python3 -m py_compile economics_drivers/squads/harvest.py\n python3 -m economics_drivers.squads.harvest --dry-run\n git fetch origin main\n git rebase origin/main\n git add economics_drivers/squads/harvest.py docs/planning/specs/research_squads_spec.md\n git commit -m \"[Exchange] Fix harvest.py PostgreSQL compat: seed-unlock, token_ledger.transfer() [task:3e1a8177-4e47-4067-8ae1-62102de6528d]\"\n git push origin HEAD\n ```\n\n3. If the worktree no longer exists or the changes were lost, re-apply the fix (see research_squads_spec.md work log entry for 2026-04-23 for full details of what was changed).\n\n## What the fix does\n\n- `_now()` returns ISO string (was returning datetime object, causing TEXT column comparison failures)\n- Replaced `_credit_distribution()` (had wrong token_ledger column names: actor_id, balance_after, metadata) with `_distribute_pool()` using `tl.transfer()`\n- Added `_ensure_squad_account_funded()` to unlock seed tokens from system before distributing (autoseed only updates pool_balance, not token_accounts, so without this no distributions ever happen)\n- Full table scan + Python filter in run() to avoid corrupt status index (same pattern as other squad drivers)\n- dry_run properly guarded at all levels\n\nThis fix is critical: multiple squads had target_disband_at of 2026-04-16 (already 7 days past due) and would have their pools distributed once this fix is committed and the driver runs.","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-23T03:09:04.572827+00:00","updated_at":"2026-04-23T03:09:04.572827+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":"{}"}],"reviews":[{"task_count":6,"total_tokens":300000.0,"total_cost":0.9,"output_score":22118.827,"efficiency_rating":"normal","reviewed_at":"2026-04-20T16:13:25.817325+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":300000.0,"total_duration":4649102.511552,"avg_impact":1105941.3499999999,"avg_effectiveness":22118.827000000005},"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":"

Quest: Exchange

Layer: Exchange \nPriority: P85 \nStatus: active \nTasks: 837 total (90 done, 5 open)

Vision

The Exchange is SciDEX's quality discovery layer — it uses market mechanisms to determine
the value of scientific knowledge. Today it prices hypotheses through LMSR-inspired dynamics
(7,200 price events, 3,765 transactions). The vision extends this to all artifact types
through the Artifact Quality Markets quest (q-artifact-quality-markets).

The Quality Triangle

The 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

Market prices are the primary quality signal. Debate outcomes move prices. Gates prevent
low-quality artifacts from entering the market. Together these three mechanisms create a
self-correcting quality governance system.

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

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)

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)

Success Criteria

☐ 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)

Work Log

_No entries yet._

","spec_file":"quest_exchange_spec.md","commits":[{"hash":"59405c7c5","message":"docs: AGENTS.md — document Path A/B/C task completion semantics [task:docs-agents-completion] (#40)","date":"2026-04-25"},{"hash":"e5b5848a0","message":"WIP on orchestra/task/8fcc8dc8-debate-artifact-version-pinning-referenc: 8a24c2fa2 [Senate] Delete broken restore_database.sh (#38)","date":"2026-04-25"},{"hash":"50e5ffcfe","message":"index on orchestra/task/8fcc8dc8-debate-artifact-version-pinning-referenc: 8a24c2fa2 [Senate] Delete broken restore_database.sh (#38)","date":"2026-04-25"},{"hash":"0d37f5fce","message":"untracked files on orchestra/task/8fcc8dc8-debate-artifact-version-pinning-referenc: 8a24c2fa2 [Senate] Delete broken restore_database.sh (#38)","date":"2026-04-25"},{"hash":"48f8d2fe3","message":"feat: surface all five SciDEX layers in nav [task:cba19c94-1724-4d5a-b89d-96c73c25f12a] (#39)","date":"2026-04-25"},{"hash":"1f0e35929","message":"Squash merge: orchestra/task/b1a8e549-cross-cutting-wire-existing-k-dense-skil (2 commits)","date":"2026-04-25"},{"hash":"ddb7db381","message":"[Agora] Wire existing K-Dense-backed tools into debate orchestration [task:b1a8e549-6f31-43c5-80f5-7c4717c267e4]","date":"2026-04-25"},{"hash":"76b71427a","message":"[Agora] Wire existing K-Dense-backed tools into debate orchestration [task:b1a8e549-6f31-43c5-80f5-7c4717c267e4]","date":"2026-04-25"},{"hash":"779e85c3a","message":"[Senate] Verify /resources dashboard complete; check off acceptance criteria [task:82074adc-507f-4e6b-9092-e2ceee79e7d4]","date":"2026-04-25"},{"hash":"4c66a8e09","message":"[Senate] Establish emergency access recovery procedures [task:e643cdd3-afd6-410f-a366-a6297d112127]","date":"2026-04-25"},{"hash":"7265a06b4","message":"Squash merge: orchestra/task/b1a8e549-cross-cutting-wire-existing-k-dense-skil (1 commits)","date":"2026-04-25"},{"hash":"58406ec64","message":"[Atlas] Dashboard artifact type: living web views with data source rendering [task:a17-28-DASH0001]","date":"2026-04-25"},{"hash":"8a24c2fa2","message":"[Senate] Delete broken restore_database.sh (#38)","date":"2026-04-25"},{"hash":"b98a1fa18","message":"[Senate] Delete broken restore_database.sh","date":"2026-04-25"},{"hash":"e846f82ef","message":"[Senate] Refresh BACKUP_RESTORE.md + docs/runbooks/emergency_restore.md (#37)","date":"2026-04-25"},{"hash":"43972a45e","message":"[Senate] Refresh BACKUP_RESTORE.md + docs/runbooks/emergency_restore.md","date":"2026-04-25"},{"hash":"2c7dbfe7f","message":"[Senate] Delete 9 obsolete backup scripts/units (continuation of Phase A-D cleanup) (#36)","date":"2026-04-25"},{"hash":"9743eb298","message":"[Senate] Delete 9 obsolete backup scripts/units (continuation of Phase A-D cleanup)","date":"2026-04-25"},{"hash":"3e72d8383","message":"[Agora] Wire 3 missing tools into debate skill_functions, fix citation persistence bug [task:b1a8e549-6f31-43c5-80f5-7c4717c267e4]","date":"2026-04-25"},{"hash":"4310e9854","message":"[Demo] Work log: figures verified complete — 140/140 analyses covered [task:df201d8f-4b89-4258-9148-eb1028fc1fbd]","date":"2026-04-24"}]}