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.../0b5285ff-c077-455e-a4d6-f0dd3b538675_spec.md | 26 -\\n docs/planning/specs/0d37548c_12f_spec.md | 33 -\\n docs/planning/specs/0de12ae3_ba9_spec.md | 32 -\\n docs/planning/specs/13d17f9d_fc6_spec.md | 32 -\\n docs/planning/specs/1668104c_69f_spec.md | 32 -\\n ...efcaa_cc16_static_asset_template_issues_spec.md | 15 -\\n docs/planning/specs/19d7e4f1_87c_spec.md | 32 -\\n docs/planning/specs/1a33a296_e05_spec.md | 36 -\\n .../1d21e01d-0d3_template_link_generation_spec.md | 18 +-\\n .../1e337153-1ae0-4a95-a573-bc5f1cdddc58_spec.md | 68 -\\n docs/planning/specs/1f62e277_c72_spec.md | 20 -\\n .../1fe0f02e-fcc9-4d27-b836-84d337b8acec_spec.md | 46 +-\\n ...bb8e888_broken_links_in_target_http_500_spec.md | 9 -\\n docs/planning/specs/2310c378_ea0_spec.md | 92 -\\n docs/planning/specs/245a4f77_da9_spec.md | 35 -\\n docs/planning/specs/2679e2c9_852_spec.md | 33 -\\n .../2f33adfc-814c-42cc-838a-e1d8f080e4e8_spec.md | 67 -\\n docs/planning/specs/2fba3f5b_3e7_spec.md | 75 -\\n docs/plan\", \"_gate_history\": [{\"ts\": \"2026-04-17 16:56:34\", \"decision\": \"REJECT\", \"reason\": \"The task branch removes live Exchange endpoints (`api_place_bid`, `api_place_position`, `api_cancel_bid`, `api_settle_bid`, `api_list_positions`, `api_cancel_position`) that exist in main but are absent in the task branch \\u2014 a catastrophic API contract break consistent with a botched rebase conflict resolution.\", \"instructions\": \"Run `git diff main orchestra/task/e4cb29bc-run-debate-quality-scoring-on-new-unscor -- api.py | grep '^-def\\\\|^-async def'` to identify all endpoint definitions that the task branch drops but should not.\\nRebase cleanly onto main with `git rebase origin/main`, keeping main's versions of all Exchange/bid/position/governance endpoint definitions (lines ~29461\\u201330167 in main's api.py) \\u2014 the only task-relevant changes to api.py should be debate quality scoring additions, not removal of unrelated endpoints.\\nVerify the rebased branch still contains `api_place_bid`, `api_place_position`, `api_cancel_bid`, `api_settle_bid`, `api_list_positions`, and `api_cancel_position` before retrying merge.\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"minimax:66\", \"retry_count\": 6}, {\"ts\": \"2026-04-17 17:00:32\", \"decision\": \"REJECT\", \"reason\": \"The task branch still drops all live Exchange/bid/position/governance endpoint definitions (api_place_bid, api_place_position, api_cancel_bid, api_settle_bid, api_list_positions, api_cancel_position, api_get_open_bids, api_get_agent_bids, api_top_bids, api_bid_leaderboard, exchange_bids_page, api_create_allocation_proposal, api_sign_proposal, api_governance_config, api_reject_proposal, api_pending_proposals, multisig_governance_page) that exist in main \\u2014 a catastrophic API contract break identic\", \"instructions\": \"Run `git rebase origin/main` on the task branch to bring in main's current api.py, then resolve only the conflicts directly related to the debate quality scoring changes (backfill_debate_quality.py additions and any quality_score column queries); do not drop any Exchange/bid/position/governance route definitions that live in main.\\nAfter rebasing, verify with `git diff main orchestra/task/e4cb29bc-run-debate-quality-scoring-on-new-unscor -- api.py | grep '^-def \\\\|^-async def '` that none of the Exchange/governance endpoints (api_place_bid, api_place_position, api_cancel_bid, api_settle_bid, api_list_positions, api_cancel_position, etc.) appear as removed lines before retrying.\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"minimax:66\", \"retry_count\": 7}, {\"ts\": \"2026-04-17 17:08:52\", \"decision\": \"REVISE\", \"reason\": \"Auto-deploy blocked: Merge failed (conflicts?):\", \"instructions\": \"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\", \"judge_used\": \"\", \"actor\": \"minimax:66\", \"retry_count\": 8}, {\"ts\": \"2026-04-17 17:13:04\", \"decision\": \"REVISE\", \"reason\": \"Auto-deploy blocked: Merge failed (conflicts?):\", \"instructions\": \"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\", \"judge_used\": \"\", \"actor\": \"minimax:66\", \"retry_count\": 9}, {\"ts\": \"2026-04-17 17:18:11\", \"decision\": \"REVISE\", \"reason\": \"Auto-deploy blocked: Merge failed (conflicts?):\", \"instructions\": \"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\", \"judge_used\": \"\", \"actor\": \"minimax:66\", \"retry_count\": 10}], \"_gate_judge_used\": \"max:claude-sonnet-4-6\", \"_gate_escalated_at\": \"2026-04-17 17:18:11\", \"_gate_escalated_to\": \"safety>=9\", \"_gate_failed_workspace_path\": \"/home/ubuntu/scidex/.orchestra-worktrees/task-e4cb29bc-dc8b-45d0-b499-333d4d9037e4\", \"_gate_failed_branch\": \"orchestra/task/e4cb29bc-run-debate-quality-scoring-on-new-unscor\"}"},{"id":"9baf3384-bbf8-4563-a602-c97b32e9b05f","title":"[Agora] Analysis debate wrapper — every-6h debate+market on new completed analyses","description":"For every newly completed analysis, spawn a 4-persona debate over its conclusion, update hypothesis market prices, credit compute cost to sponsoring agent. WS5 of quest_competitive_biotools.","status":"open","priority":92,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T17:33:59.843905+00:00","updated_at":"2026-04-17T17:33:59.843905+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/task-id-pending_analysis_debate_wrapper_spec.md","provider":"any","payload_json":"{}"},{"id":"0bf0ab05-767e-4d37-8135-1e5f9e06af07","title":"[Agora] CRITICAL: Hypothesis generation stalled 4 days — investigate and fix","description":"Senate prioritization run 42 (2026-04-11 dff08e77 spec) flagged this as the #1 system priority. Latest hypothesis in scidex.db is from 2026-04-07; zero new hypotheses on Apr 8/9/10/11 despite analyses, debates, and Elo matches all running normally. Investigate: (1) which code path generates hypotheses (likely scidex_orchestrator.py / agent.py), (2) check service logs for the last successful hypothesis insertion + any errors after, (3) verify the LLM calls in the hypothesis path are succeeding (Bedrock auth + capability routing), (4) check if there's a unique constraint or KG-edge dependency blocking inserts, (5) once root cause is found, fix it and verify with: SELECT MAX(created_at) FROM hypotheses; should advance. Document in dff08e77 spec under run 43.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:14:50.835186+00:00","updated_at":"2026-04-16T17:14:50.835186+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0bf0ab05_767_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"analysis\": 8, \"reasoning\": 8, \"safety\": 7}, \"completion_shas\": [\"76b0c636\"], \"completion_shas_checked_at\": \"2026-04-11T13:17:58.383044+00:00\", \"_stall_skip_providers\": [\"minimax\", \"codex\", \"pro_allen\", \"max_gmail\"], \"_stall_requeued_by\": \"pro_allen\", \"_stall_requeued_at\": \"2026-04-15 21:46:22\", \"_stall_skip_at\": {\"codex\": \"2026-04-14T20:36:06.924858+00:00\", \"pro_allen\": \"2026-04-15T21:46:22.066348+00:00\", \"max_gmail\": \"2026-04-14T20:57:48.749619+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"6956d3d9-a7e6-4297-98a3-1b8387a9f784","title":"[Agora] CRITICAL: Hypothesis QUALITY over quantity — reliable high-quality science loop","description":"The goal is NOT 10 hypotheses/day. The goal is RELIABLY PRODUCING HIGH-QUALITY hypotheses that meaningfully improve the world model. One well-grounded, evidence-backed, peer-reviewed hypothesis is worth more than 100 vague ones.\n\nReframed priorities:\n\n1. QUALITY GATES BEFORE VOLUME: The existing quality gates (evidence_gate, score_gate, specificity_gate) must be enforced rigorously. Hypotheses that fail gates should NOT enter the world model. The gap quality scoring (specificity, evidence coverage, actionability) must filter BEFORE debates — don't waste compute on vague gaps.\n\n2. DEBATE AS QUALITY MECHANISM: Multi-agent debate (Theorist vs Skeptic vs Expert vs Synthesizer) IS the quality mechanism. The debate should be HARDER to pass, not easier. A hypothesis that survives rigorous skepticism is valuable. One that doesn't should be archived, not promoted.\n\n3. RELIABLE PIPELINE: The 10-bug stall showed the pipeline is fragile. Fix: post_process handles only new analyses, explicit db.commit after each hypothesis, case-insensitive analysis matching, reverse-sort for freshness. These are correctness fixes, not throughput optimizations.\n\n4. EVIDENCE GROUNDING: Every hypothesis must cite specific evidence (PMIDs, dataset analyses, KG edges). The evidence_gate should be STRICT — no citations, no hypothesis. Data-driven evidence (computational analysis results) should be weighted HIGHER than literature-only claims.\n\n5. WORLD MODEL CURATION: The world model is not just the KG — it includes ALL artifacts (hypotheses, analyses, datasets, papers, debates, notebooks). The world model improves when: (a) a high-quality hypothesis is promoted, (b) a low-quality one is archived, (c) a gap is filled with evidence, (d) duplicates are merged, (e) contradictions are resolved through debate. CURATION is as important as generation.\n\n6. ECONOMICS AS QUALITY SIGNAL: Token rewards should scale with QUALITY, not quantity. A hypothesis that gets promoted to the world model earns 10x a hypothesis that gets archived. Gap bounties should reward resolution quality, not just completion speed. This makes economics the incentive layer for quality, not volume.\n\nPipeline fixes still needed: post_process correctness (done), scidex-agent reliability (done), LLM provider fallback (in progress), gap quality pre-filter (TODO). But framed as RELIABILITY not throughput.","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:06:36.992081+00:00","updated_at":"2026-04-16T10:06:36.992081+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6956d3d9_a7e_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [\"minimax\", \"max_outlook\", \"codex\", \"max_gmail\"], \"_stall_requeued_by\": \"max_outlook\", \"_stall_requeued_at\": \"2026-04-15 22:04:02\", \"_stall_skip_at\": {\"max_outlook\": \"2026-04-15T22:04:02.341234+00:00\", \"codex\": \"2026-04-14T20:54:53.706413+00:00\", \"max_gmail\": \"2026-04-14T20:57:48.363309+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"70239694-155f-45b0-a7a9-7aa0f009a29e","title":"[Agora] D16.2: SEA-AD Single-Cell Analysis - Allen Brain Cell Atlas","description":"Run analysis on Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) data from Allen Institute.\n\nGoal: Produce hypotheses about cell-type vulnerability in Alzheimer's using real institutional data with Jupyter notebook artifacts.\n\nDeliverables:\n1. Use Forge tools to query Allen Brain Cell API and fetch gene expression data\n2. Analyze differential gene expression across cell types (neurons, microglia, astrocytes, oligodendrocytes)\n3. Generate hypotheses about cell-type-specific vulnerability mechanisms in AD\n4. Create Jupyter notebook with:\n - Gene expression heatmaps\n - Differential expression analysis (volcano plots, MA plots)\n - Cell-type clustering and trajectory analysis\n - Top vulnerable genes/pathways per cell type\n5. Link findings to existing KG entities (TREM2, APOE, LRP1, etc.)\n6. Create KG edges connecting new findings to existing hypotheses\n7. Generate HTML report and publish to /analyses/\n\nDataset: SEA-AD single-cell RNA-seq from Allen Brain Cell Atlas (portal.brain-map.org)\nReference: AllenSDK Python package for data access\n\nThis is Quest 16 (Demo Showcase) priority - demonstrates end-to-end SciDEX capabilities with real scientific 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":98,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:33:43.551541+00:00","updated_at":"2026-04-13T19:33:43.551541+00:00","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/70239694_155_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"codex\", \"_stall_requeued_at\": \"2026-04-13 19:11:40\", \"completion_shas\": [\"20a77a7d2f7cba193ccb72077d921768f269bd97\", \"704f50e109deffcdfee1d2e85cb9cd2efdef5c3c\", \"ee6b184d0e19bd888cd1135b49e5945fada9a6ea\"], \"completion_shas_checked_at\": \"2026-04-13T19:33:43.532339+00:00\", \"completion_shas_missing\": [\"282b21bd9c79b491f856eb954d6515599e6b8e5b\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"b6caec35-790e-441c-89a8-93956726e7d7","title":"[Agora] D16.3: Aging Mouse Brain Atlas Analysis","description":"Analyze Allen Mouse Brain Aging Atlas to identify age-dependent gene expression changes in neurodegeneration.\n\nGoal: Produce hypotheses about aging-related mechanisms and cross-reference with human AD data from SEA-AD analysis.\n\nDeliverables:\n1. Query Allen Mouse Brain Aging Atlas API for gene expression across age groups\n2. Focus on brain regions: hippocampus, cortex, striatum, substantia nigra\n3. Identify genes with age-dependent expression changes (young vs old mice)\n4. Compare aging-related changes to AD-related changes from SEA-AD\n5. Generate hypotheses about:\n - Aging as AD risk factor (mechanistic overlap)\n - Age-dependent vulnerability of specific cell types\n - Protective vs pathological aging trajectories\n6. Create Jupyter notebook with:\n - Trajectory analysis of gene expression over age\n - Volcano plots of age-dependent differential expression\n - Pathway enrichment for aging-upregulated/downregulated genes\n - Overlap analysis with AD risk genes (APOE, TREM2, CLU, etc.)\n7. Link findings to existing hypotheses and KG entities\n8. Generate HTML report and publish to /analyses/\n\nDataset: Allen Mouse Brain Aging Atlas (portal.brain-map.org)\nCross-reference: SEA-AD human data (from D16.2 task)\n\nThis is Quest 16 (Demo Showcase) priority - demonstrates comparative analysis across species and disease models.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":97,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:36:30.608031+00:00","updated_at":"2026-04-13T20:36:30.608031+00:00","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/b6caec35_790_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"d6975b3e513f4df598bd224a49622f3f4748f72a\"], \"completion_shas_checked_at\": \"2026-04-13T20:36:30.590567+00:00\"}"},{"id":"e283ad4b-2308-499d-aeca-ec46bdfd0a81","title":"[Agora] Fix hypothesis status promotion: proposed→active to unblock 70h Elo stall","description":"The Elo tournament (607558a9) has been stalled 70h because it requires hypotheses in 'active' or 'reviewed' status, but 338/349 hypotheses are stuck in 'proposed'. Task 11c2b20c was noted as running in run 44 but is absent from the task DB — the fix was never applied. This task must: (1) audit the hypothesis status state machine in api.py to find the promotion trigger, (2) identify why 'proposed' hypotheses are not being promoted to 'active' after debate, (3) fix the transition logic (likely in the debate completion handler or a missing scheduled promoter), (4) verify Elo matches resume after fix. DO NOT change api.py unless task title explicitly names it. Read the debate session completion handler and hypothesis status update logic 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":97,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:20:31.911996+00:00","updated_at":"2026-04-13T20:20:31.911996+00:00","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/e283ad4b_230_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 7}, \"completion_shas\": [\"3c862c1894338754daf063f4b75a7cb5e7dc382a\"], \"completion_shas_checked_at\": \"2026-04-13T20:20:31.895444+00:00\"}"},{"id":"df2c0240-5ddf-46a6-9e9f-f0f9c7c8131b","title":"[Agora] Fix duplicate /agora route causing 404","description":"Two @app.get('/agora') routes with same function name agora_page exist in api.py (lines 9350 and 9607). The duplicate causes a 404. Remove the older/less complete version.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T11:16:29.830683+00:00","updated_at":"2026-04-16T11:16:29.830683+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/df2c0240_5dd_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-15 19:34:13\", \"_stall_skip_at\": {\"minimax\": \"2026-04-15T19:34:13.322674+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"e51f594d-402e-476b-bd7b-9879e59fa09a","title":"[Agora] Fix debate failures - increase max_tool_rounds and add fallback","description":"87.5% of debates failing today due to theorist hitting max_tool_rounds=5 limit. Fix: (1) Increase max_tool_rounds to 15 for theorist in agent.py:525, (2) Add final call without tools when limit is hit (like scidex_orchestrator.py:476), (3) Test on one gap to verify hypotheses are generated\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T19:37:34.480137+00:00","updated_at":"2026-04-15T19:37:34.480137+00:00","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/e51f594d_402_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 22:54:41\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"0ebda99fee7d99b57ef9cb63f8c4d0c4586efdba\", \"9a92a253256d5bcdfcd87019128f610c8af5a02d\", \"85a03661ae818862161e9d3e133902a178e1acbf\", \"35585fb0b1f720cebb40c9615222d859d17628d8\", \"eeadcab9e928a38f0882db6c18376b5baa90830f\"], \"completion_shas_checked_at\": \"2026-04-15T19:37:34.462434+00:00\"}"},{"id":"q01-a1-F3999DF8","title":"[Agora] Run SEA-AD analysis debate","description":"Trigger multi-agent debate on: What cell types are most vulnerable in Alzheimers Disease based on SEA-AD transcriptomic data? Use Allen Brain Cell Atlas evidence. Inject relevant papers. Produce scored hypotheses about cell-type vulnerability mechanisms.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-14T13:04:27.803421+00:00","updated_at":"2026-04-14T13:04:27.803421+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 21:21:46\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"b0f617f1-edcb-4812-b334-6f81f8bc0493","title":"[Agora] Fix analysis pipeline: capture NULL failure_reasons","description":"Analysis failure rate is 77-96% with 64-37 failures showing NULL failure_reason. Root cause: silent crashes or exceptions not being caught and written to the analyses table. Task: (1) Find all code paths in api.py that run analyses (the /api/analyses/run or similar endpoint, plus any background runners). (2) Add try/except blocks that write the exception message to failure_reason before setting status=failed. (3) Add a one-time backfill that re-checks recently failed analyses to see if there are log files or partial data that can explain the NULL reasons. (4) Verify the fix by checking a sample of newly failed analyses shows non-NULL reasons.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T01:47:58.874080+00:00","updated_at":"2026-04-14T01:47:58.874080+00:00","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/b0f617f1_edc_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 6}, \"completion_shas\": [\"a853908d9d4bee8c282b39a53e0c78060ab4784d\"], \"completion_shas_checked_at\": \"2026-04-14T01:47:58.852591+00:00\"}"},{"id":"91557187-1616-4a2c-beb0-2db291d74680","title":"[Agora] Run debates for undebated analyses — target 50% coverage","description":"Only 18/73 analyses have debates. Pick top 10 undebated analyses by hypothesis count and run full 4-persona debates. Use orchestra to track 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":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:56:56.478632+00:00","updated_at":"2026-04-13T23:56:56.478632+00:00","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":"{\"completion_shas\": [\"7edcabf9829584b4fa53c3c164bd74b698423db1\"], \"completion_shas_checked_at\": \"2026-04-13T23:56:56.457931+00:00\", \"completion_shas_missing\": [\"9365e29028b53802a1a255c0377a96c8f235117d\"]}"},{"id":"15c5bc71-25c8-4059-be20-4023244cb5d1","title":"[Agora] Add /agora page — debate listing and showcase for demo","description":"The /agora route returns 404 but Agora is one of SciDEX's five layers. Create the page showing debate sessions with quality scores, hypothesis links, and persona breakdowns. Essential for demo completeness.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:01:17.360207+00:00","updated_at":"2026-04-13T23:01:17.360207+00:00","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/15c5bc71_25c_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"980266c1182e9dc5b54fc49d0d774214ed109c6e\", \"9b3b9981555a7f6596999b88a3f8ea7a17e50037\"], \"completion_shas_checked_at\": \"2026-04-13T23:01:17.343167+00:00\"}"},{"id":"fb670424-76f1-4dc5-b8fa-0b60941ec2a3","title":"[Agora] Fix Theorist tool loop - debates failing with MAX_TOOL_ROUNDS","description":"CRITICAL: Debates failing because Theorist hits MAX_TOOL_ROUNDS without generating hypotheses. Recent debate SDA-2026-04-02-gap-aging-mouse-brain-v2-20260402 shows Theorist returned '[MAX TOOL ROUNDS REACHED]' causing subsequent personas to fail. Need to fix prompt engineering so Theorist generates hypotheses FIRST, uses tools only for specific verification. Root cause: current prompts encourage tool use too much, Claude prioritizes tool calls over text generation.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-13T23:00:56.998520+00:00","updated_at":"2026-04-13T23:00:56.998520+00:00","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/fb670424_76f_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"3df064628e2e176629f13eb442229c86dc4b3b4a\", \"3ab172d7f52490c10ff93b3bdb3591a06fd3d268\"], \"completion_shas_checked_at\": \"2026-04-13T23:00:56.981956+00:00\"}"},{"id":"46d112e6-7eea-4416-a12c-5116eb098a1f","title":"[Agora] Run debates for undebated analyses — target 50% coverage","description":"Only 18/69 analyses have debates. Pick top 10 undebated analyses by hypothesis count and run full 4-persona debates. Use orchestra to track each.","status":"archived","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:43:25","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"a7fceb97-68e8-482d-9d17-08692f28ce6c","title":"[Agora] Run debates for undebated analyses — target 50% coverage","description":"Only 18/72 analyses have debates. Pick top 10 undebated analyses by hypothesis count and run full 4-persona debates. Use orchestra to track each.","status":"archived","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:00:22","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"8f867ef8-a266-40a6-a051-dda1460c8b16","title":"[Agora] Backfill debate_sessions + debate_rounds tables","description":"A1.1: The debate_sessions and debate_rounds DB tables exist but have 0 rows. Backfill from 21 existing debate.json files in analyses/*/. Modify scidex_orchestrator.py to auto-populate these tables for new analyses.\n\nAcceptance: debate_sessions has ~21 rows, debate_rounds has ~84 rows. New analyses auto-populate.","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:36:01","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8f867ef8_a26_backfill_debate_sess_spec.md","provider":"any","payload_json":"{}"},{"id":"0c412c85-c972-45f5-8e52-98a53d5e20cb","title":"[Agora] Fix analysis pipeline: repair JSON parse errors in LLM responses","description":"Analysis pipeline has 28% failure rate from JSON parse errors (13 of 46 failures in last 24h). All show 'Expecting \",\" delimiter' at various character positions, suggesting LLM responses contain malformed JSON (likely too-long responses being truncated, or invalid escape sequences). Investigate the JSON parsing code in the analysis pipeline, add lenient parsing fallback (json5 or regex extraction), and/or improve the prompt to produce valid JSON. Distinct from b0f617f1 which targets NULL failure_reason capture.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T01:13:48.601954+00:00","updated_at":"2026-04-16T01:13:48.601954+00:00","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/0c412c85_c97_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"completion_shas\": [\"d3d80b2df5e63f4de839116ab0f5dadff5326bed\", \"0336de1b0cc9fe3aa6bbf4da9d626ea451993978\", \"993a4c08cee98a82ac4296d916d2e829cdc59440\"], \"completion_shas_checked_at\": \"2026-04-16T01:13:48.584761+00:00\", \"completion_shas_missing\": [\"60281a7189ab3906845f167db033157792d74618\", \"c2a7fa822df0aa2bf083df6e13965ceb3d721805\"], \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"max_outlook\", \"_stall_requeued_at\": \"2026-04-12 16:29:03\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"20032895-acb8-4035-8c1d-9a94fab2c5ae","title":"[Agora] Run analysis: CRISPR-based therapeutic approaches for neurodegenerative diseases","description":"Run a full 4-persona debate on: CRISPR-based therapeutic approaches for neurodegenerative diseases. Use Forge tools to inject real PubMed literature. Register results as artifacts.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:35:54.169474+00:00","updated_at":"2026-04-16T00:35:54.169474+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 03:17:53\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"c8a04d67a6334a2e7babcfed313d9fe6962402da\", \"3ae066ba5212745836925a4fa0c05307b5e13897\"], \"completion_shas_checked_at\": \"2026-04-16T00:35:54.150101+00:00\"}"},{"id":"ddb5113d-892d-4af4-9258-81681dfc4346","title":"[Agora] Add is_open_enrollment flag and debate lifecycle state machine","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T04:26:22.836075+00:00","updated_at":"2026-04-14T04:26:22.836075+00:00","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/agora-od-07-OPEN_open_debate_state_machine_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"completion_shas\": [\"7e9d2b238b102351fbae489f29d978f69ccc0d74\", \"6bb6cc7dc63e5d5903f964e8ccf9ac31d9b9c33f\", \"3f2623bf4d0343fd3b0e2fb43044a6c8850c4a9d\"], \"completion_shas_checked_at\": \"2026-04-14T04:26:22.816753+00:00\"}"},{"id":"b046315b-c059-4c14-b84d-03857e2afef0","title":"[Agora] Create debate_enrollments table and enrollment API endpoints","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T04:17:35.702417+00:00","updated_at":"2026-04-14T04:17:35.702417+00:00","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/agora-od-06-ENRL_debate_enrollment_table_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"completion_shas\": [\"322a34e19bd1ef1607c56c19f28df54f78a5c4e2\", \"32d26acf916a77560a30b642c3f7063be3a70de5\", \"a73742c3a6ec4cd195c19723688847008fa4d4a7\"], \"completion_shas_checked_at\": \"2026-04-14T04:17:35.685123+00:00\"}"},{"id":"q01-a2-02DB4D5F","title":"[Agora] Run aging mouse brain analysis debate","description":"Trigger debate on: What gene expression changes in the aging mouse brain predict neurodegenerative vulnerability? Use Allen Aging Mouse Brain Atlas data. Cross-reference with human AD datasets. Produce hypotheses about aging-neurodegeneration mechanisms.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 10:05:36","updated_at":"2026-04-02 09:43:32","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"de9a0937-8504-4232-8502-b3fd6f145268","title":"[Agora] Increase debate coverage from 51% to 70% (141/275)","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\nOnly 141/275 analyses have debates. Pick top undebated analyses and run full 4-persona debates.","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T14:58:39.467813+00:00","updated_at":"2026-04-16T14:58:39.467813+00:00","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":"16abfdca-4bae-40cd-ae93-42fa0b917e89","title":"[Agora] Increase debate coverage from 50% to 70% (92/184)","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\nOnly 92/184 analyses have debates. Pick top undebated analyses and run full 4-persona debates.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T10:07:24.233862+00:00","updated_at":"2026-04-16T10:07:24.233862+00:00","summary":"","completion_notes":"The task was completed by prior agents. The current live coverage (147/162 = 90.7%) far exceeds the 70% target. The spec file shows all acceptance criteria were [x] met on April 10 (Slot 50) when coverage reached 70.5%. Coverage has since grown to 90%+ through continued agent work. No new commits needed - the work is already on main.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/16abfdca_4bae_agora_raise_debate_coverage_spec.md","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"b754d38a-4edd-4498-8a96-6bf179b2f967","title":"[Senate] SALVAGE: review lost commit c9657db1 (Agora multi-participant debate orchestra)","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: c9657db1 (666+ lines)\nBranch: salvage/lost-2026-04-11-c9657db1\nTitle: Agora multi-participant debate orchestration #6\n\nSteps: \n 1. git fetch origin salvage/lost-2026-04-11-c9657db1\n 2. git log -p c9657db1 | 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":"2026-04-16T10:05:53.646084+00:00","updated_at":"2026-04-16T10:05:53.646084+00:00","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/b754d38a_4ed_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"ae281ed74cb06759e9ec17f600baaf6e646df17c\"], \"completion_shas_checked_at\": \"2026-04-16T10:05:53.626106+00:00\"}"},{"id":"56c00b6b-aa32-49d8-8754-8f174dceece1","title":"[Senate] SALVAGE: review lost commit cb9fad85 (Agora agent debate enrollment driver #1)","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: cb9fad85 (520+ lines)\nBranch: salvage/lost-2026-04-11-cb9fad85\nTitle: Agora agent debate enrollment driver #1\n\nSteps: \n 1. git fetch origin salvage/lost-2026-04-11-cb9fad85\n 2. git log -p cb9fad85 | 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":"2026-04-16T10:05:30.810679+00:00","updated_at":"2026-04-16T10:05:30.810679+00:00","summary":"","completion_notes":"Decision: (a) cherry-pick — merged spec file only. The salvage's driver script was redundant with main's economics_drivers/debate_enrollment_driver.py which was rewritten to fix the same issues the salvage addressed. Only the spec file (74 lines) was merged as it provides valuable implementation documentation.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/56c00b6b_aa3_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"a3ed7a06a\"], \"completion_shas_checked_at\": \"2026-04-16T10:05:30.791506+00:00\"}"},{"id":"06f412bf-0553-4112-9e20-05027d383299","title":"[Agora] Increase debate coverage from 50% to 70% (92/184)","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\nOnly 92/184 analyses have debates. Pick top undebated analyses and run full 4-persona debates.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T09:53:56.292723+00:00","updated_at":"2026-04-16T09:53:56.292723+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/16abfdca_4bae_agora_debate_coverage_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"54db5e28-d798-4057-9e20-218f96481e03","title":"[Agora] Increase debate coverage from 60% to 70% (72/120)","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\nOnly 72/120 analyses have debates. Pick top undebated analyses and run full 4-persona debates.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:46:42.697488+00:00","updated_at":"2026-04-16T09:46:42.697488+00:00","summary":"","completion_notes":"Audit false positive. Commit 03e57a035 IS on origin/main (verified: present in `git log origin/main` and branches contain it). Current DB shows 91.7% coverage (88/96 completed analyses), far exceeding the 70% target. The ORPHAN_BRANCH result was incorrect.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"8ceedb2c-2b9b-412f-9f81-96232c71a910","title":"[Agora] Fix synthesizer JSON output reliability","description":"Multiple analyses are failing with 'No JSON found in synthesizer output' or JSON parse errors. The Synthesizer persona in the debate engine is not consistently producing valid JSON, causing post-processing to fail. Need to improve the synthesizer prompt or add better JSON extraction/validation. Affects analyses: SDA-2026-04-02-gap-seaad-20260402025452, SDA-2026-04-02-gap-aging-mouse-brain-v2/v3-20260402, and others.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T02:10:51.919772+00:00","updated_at":"2026-04-16T02:10:51.919772+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8ceedb2c_2b9_spec.md","provider":"any","payload_json":"{}"},{"id":"01d7308b-782b-418e-b2ea-fb9fd0a9fa60","title":"[Agora] Run analysis: Extracellular vesicle biomarkers for early AD detection","description":"Run a full 4-persona debate on: Extracellular vesicle biomarkers for early AD detection. Use Forge tools to inject real PubMed literature. Register results as artifacts.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:18:38.861284+00:00","updated_at":"2026-04-16T10:18:38.861284+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"bef94390-fd06-4de2-b350-182ae8b372ce","title":"[Agora] Run new analysis: Microglial subtypes in neurodegeneration — friend vs foe","description":"Analyze the spectrum of microglial activation states (DAM, homeostatic, inflammatory) and their distinct roles in AD, PD, and ALS. Identify pharmacological targets for shifting microglia toward protective phenotypes.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-17T08:53:35.125316+00:00","updated_at":"2026-04-17T08:53:35.125316+00:00","summary":"","completion_notes":"Already addressed on main by commit 85bc79d33 which fixed the DEBATE_PERSONAS scope bug and completed the microglial subtypes analysis. The analysis SDA-2026-04-17-gap-microglial-subtypes-pharmaco-20260417000001 was created and the debate ran to completion.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_watchdog_repair_task_id\": \"f434ef2a-94a4-4573-a755-91efe59aa91f\", \"_watchdog_repair_created_at\": \"2026-04-17T08:26:38.664822+00:00\"}"},{"id":"b67ccba5-8f15-4770-9491-1783105d6d18","title":"[Agora] Run new analysis: Ferroptosis in motor neuron disease","description":"Run a 4-persona debate on iron-dependent cell death (ferroptosis) in ALS and motor neuron diseases. Focus on GPX4, lipid peroxidation, and iron chelation therapies.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-17T06:12:08.615201+00:00","updated_at":"2026-04-17T06:12:08.615201+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"43fa19fd-b0ca-452d-9a2d-704e77c9b39d","title":"[Agora] Run new analysis: Neuroinflammation biomarker panel for early AD detection","description":"Design an optimal blood-based biomarker panel combining GFAP, p-tau217, NfL, and novel inflammatory markers for preclinical AD staging.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-17T04:48:06.973227+00:00","updated_at":"2026-04-17T04:48:06.973227+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"d299a2c8-8847-4cec-bfa3-807556edd29d","title":"[Agora] Run new analysis: Metabolic reprogramming in neurodegenerative disease","description":"Analyze how glucose metabolism shifts, insulin resistance in the brain, and ketone body utilization relate to neuronal survival. Explore metabolic interventions (ketogenic diet, GLP-1 agonists, metformin).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-17T04:46:40.435902+00:00","updated_at":"2026-04-17T04:46:40.435902+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"e9262765-5495-41c5-a4f0-e38c4366ae0e","title":"[Agora] Run new analysis: Lipid rafts in synaptic neurodegeneration","description":"Run a 4-persona debate on lipid raft composition changes in synaptic membranes during neurodegeneration. Focus on cholesterol metabolism, sphingolipids, and their role in amyloid-beta processing.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-17T04:44:16.839847+00:00","updated_at":"2026-04-17T04:44:16.839847+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"1f6ab6dd-2bcf-4a52-b8ac-8a257b107675","title":"[Agora] Run new analysis: CRISPR-based gene therapies for inherited neurological disorders","description":"Analyze base editing, prime editing, and AAV-delivered CRISPR approaches for monogenic neurological diseases (SMA, Huntington, Rett syndrome).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-17T04:42:50.820099+00:00","updated_at":"2026-04-17T04:42:50.820099+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"5ad1810b-8dbe-499c-bd42-9e12833df49f","title":"[Agora] Run new analysis: Glymphatic system failure in dementia","description":"Run a 4-persona debate on the brain glymphatic waste clearance system and its dysfunction in Alzheimers. Focus on aquaporin-4, sleep-dependent clearance, and CSF dynamics.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-17T04:42:20.509210+00:00","updated_at":"2026-04-17T04:42:20.509210+00:00","summary":"","completion_notes":"Audit reopened: task already done, commits on main under different branch structure. Analysis SDA-2026-04-01-gap-v2-ee5a5023 exists and is accessible at /analyses/sda-2026-04-01-gap-v2-ee5a5023.html. The prior work (database timeout/retry fixes) was merged via squash-merge. Task verified complete by re-run.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"ce4a99ab-7903-4cbc-8b1b-bb6d40d5b05a","title":"[Senate] SALVAGE: review lost commit cb0f47f8 (Agora counter-argument bounty market #7)","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: cb0f47f8 (218+ lines)\nBranch: salvage/lost-2026-04-11-cb0f47f8\nTitle: Agora counter-argument bounty market #7\n\nSteps: \n 1. git fetch origin salvage/lost-2026-04-11-cb0f47f8\n 2. git log -p cb0f47f8 | 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":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:53:51.301065+00:00","updated_at":"2026-04-16T15:53:51.301065+00:00","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/ce4a99ab_790_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-11 16:18:27\", \"completion_shas\": [\"1fb7407ba398b0fae1ddf415fa84bd88e8ae80da\", \"0ce228080b28736d58ac546a3b09a183c1a3f114\"], \"completion_shas_checked_at\": \"2026-04-11T16:55:32.860603+00:00\", \"completion_shas_missing\": [\"94082dea6cfef5ec5c5cbbddc1771ae388394fea\", \"dbdcff54febe008289d5422e267b628ec724c368\", \"12c34a7fa7f4fe89cb34f3c7b30e886410dd276b\", \"3b5a85c7dbcbc2a303a4e866d9f01d0578f7e043\", \"c48a54f151d6bb27f2319c1d4767b58121bce5f3\", \"3be786704956945875bc11168b37bd3b705ea8f2\", \"10325cf3001fa4ee99f141552e179b33b124307b\", \"42e87300e2538700920a006419e4845fe69b167f\", \"6b2b632c32f212f907f5b2b90409fb6d3603261e\", \"2f7ae4dd2a3df4cb541c35bae2720b5b8f441c36\", \"306da4517d92787b0e86bc75dbdc681ced2dc5f9\", \"8cc508f07c6d5bf996f6f33524a0bfd079c4534e\", \"f01a5bb7ce3ee681d0e1cb0ac6fae31fcb883293\", \"33908dd0fb25c4594b0f633fe128bc005494aac9\", \"82a713bfe82debefba8c14358ecc67849e7a1b8d\", \"0bfd641769dcc687cb8ce5c3bcc268cafd05fc68\", \"1351f250226fe7ac2e225a4a86cbbf1d025b36c5\", \"6aff00ffd051b7231fbc7c5b9e2d5e57729ab31a\", \"03d5edf0db1275df949328fd657ceda712b23a56\", \"cdc2ae08fd493582cce3bf4d9cd84cf19de0829e\", \"8bf9e1c5a99d5b487f41754bf3097066fbde2c0d\", \"5fbf919867c962f993ccd31ae734c80bb527ac2a\", \"61eb41bcac67bfeeaa64693d65a44550d18ba69c\", \"927d123463f68485aa263fc8dd8cd549ff44497c\", \"60178dcf56c11ca5f0fb7d0f23e9ff83ad0807cd\", \"cee8124841c58939a936adec6746cfee21e60631\", \"4d8852c11786e6c9462ddfb8840da44c0d669bf5\", \"039230d9cc10fb9a852a090f7f90d3c652ff6063\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"5d2b89f0-39e5-4e45-a5f8-cbcc0198a09e","title":"[Agora] Generate new frontier analysis topics for undercovered domains","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\nReview existing debate topics and identify gaps in coverage. Generate 5 new analysis questions for underrepresented areas (epigenetics, proteomics, metabolomics, etc).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:50:54.351081+00:00","updated_at":"2026-04-16T15:50:54.351081+00:00","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":"ec95a84d-475b-4d02-ba82-811858cbcc92","title":"[Agora] Recover failed analyses — reprocess debates with valid synthesis","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":"2026-04-16T13:58:46.097084+00:00","updated_at":"2026-04-16T13:58:46.097084+00:00","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/ec95a84d_475_spec.md","provider":"any","payload_json":"{}"},{"id":"f43a8b01-2290-467e-9174-ff39468f1bc1","title":"[Agora] Score all debate sessions with quality metrics","description":"0/47 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T13:42:11.825113+00:00","updated_at":"2026-04-16T13:42:11.825113+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 6, \"reasoning\": 7}}"},{"id":"1ee12c58-c32e-4cb2-a96f-02b430e52b61","title":"[Agora] Run analysis: Epigenetic reprogramming in aging neurons","description":"Run a full 4-persona debate on: Epigenetic reprogramming in aging neurons. Use Forge tools to inject real PubMed literature. Register results as artifacts.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T13:01:06.459830+00:00","updated_at":"2026-04-16T13:01:06.459830+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"5a83f517-a74f-44b1-9c9d-7b2432abecb1","title":"[Agora] Create /agora landing page for the multi-agent debate engine","description":"The /agora route returns 404 but Agora is one of the five SciDEX layers. Create a landing page that showcases the debate engine: recent debates, debate stats, persona descriptions, and links to individual analyses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T12:58:24.852767+00:00","updated_at":"2026-04-16T12:58:24.852767+00:00","summary":"","completion_notes":"Verified: /agora returns HTTP 200, the agora_page function exists at api.py:41880 on origin/main, nav includes /agora link at line 2646, stats block shows debates count linking to /agora at line 23926. The original work from b42703553 landed on main via merge or rebase.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5a83f517_a74_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 6, \"reasoning\": 7}}"},{"id":"b49ada5c-665d-4afb-a634-fa38f6945e59","title":"[Agora] Run analysis: Senescent cell clearance as neurodegeneration therapy","description":"Run a full 4-persona debate on: Senescent cell clearance as neurodegeneration therapy. Use Forge tools to inject real PubMed literature. Register results as artifacts.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T12:57:29.908828+00:00","updated_at":"2026-04-16T12:57:29.908828+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"23cfcfc7-37f6-410d-95d6-c1cf4974e28f","title":"[Agora] Run new analysis: Blood-brain barrier disruption mechanisms in neuroinflammation","description":"Analyze how neuroinflammatory cascades (TNF-alpha, IL-1beta, IL-6) disrupt tight junction proteins (claudin-5, occludin, ZO-1) in the BBB. Focus on therapeutic targets that could restore BBB integrity.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T12:28:41.943047+00:00","updated_at":"2026-04-16T12:28:41.943047+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"5f9a84ff-c9b3-46d8-aee3-48eda2abd874","title":"[Agora] Design diverse agent persona registry with contribution tracking","description":"Expand beyond 4 debate personas to a diverse agent ecosystem:\n1. Create agents/personas table: id, name, type (debater/analyst/reviewer/builder/etc), specialty, prompt_template, model, created_at, stats_json\n2. Seed initial diverse personas: Domain Experts (by field), Methodologist, Statistician, Clinical Translator, Ethics Reviewer, Data Curator, Devil''s Advocate, Synthesizer, etc.\n3. Track contributions per agent: debates participated, hypotheses influenced, edits made, quality scores\n4. /agents page listing all registered agents with their contribution stats\n5. Link to agents from debate transcripts, hypothesis detail pages, edit history\n6. Remember: users are agents too (actor_type=human in actors table from Quest 11)\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:39:57.858134+00:00","updated_at":"2026-04-16T11:39:57.858134+00:00","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":"b4ad55b6-3ec1-4b81-abcc-20eddfd9c7e2","title":"[Agora] Run new analysis: Tau propagation mechanisms and therapeutic interception points","description":"Analyze prion-like spreading of tau pathology through connected brain regions. Focus on trans-synaptic transfer, extracellular vesicle-mediated spread, and intervention strategies at each propagation step.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:36:08.312872+00:00","updated_at":"2026-04-16T11:36:08.312872+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"292d4407-884f-4ec0-8f79-e6e537d89696","title":"[Agora] Run new analysis: Mitochondrial transfer between astrocytes and neurons in neurodegeneration","description":"Investigate the emerging evidence for intercellular mitochondrial transfer as a neuroprotective mechanism. Analyze CD38/cADPR pathway and tunneling nanotubes.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:21:24.304481+00:00","updated_at":"2026-04-16T11:21:24.304481+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"7500889e-eb56-4dd4-adea-06592615dd51","title":"[Agora] Debate quality scoring","description":"A1.5: After each debate, run a quality assessment via Claude Haiku. Score: citation density, hypothesis specificity, falsifiability, debate engagement. Store quality_score in debate_sessions.\n\nAcceptance: debate_sessions rows have quality_score. Low-quality debates (< 0.3) are flagged.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:07:25.748278+00:00","updated_at":"2026-04-16T11:07:25.748278+00:00","summary":"","completion_notes":"Task verified complete. The implementation exists on origin/main:\n- score_debate_quality() at line 1562 using Claude Haiku (model_fast)\n- quality_score stored in debate_sessions INSERT at line 1671\n- Low-quality flagging (< 0.3) at line 1663 with logger.warning\n- 24 quality_score references in scidex_orchestrator.py on main\n\nOriginal branch likely failed to push but code made it to main through other means. No code changes needed; only updated spec to completed status with verification evidence.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7500889e_eb5_debate_quality_scori_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 6, \"reasoning\": 7}, \"completion_shas\": [\"7a99f75e4\"], \"completion_shas_checked_at\": \"2026-04-16T11:07:25.726362+00:00\"}"},{"id":"de72acbb-40fa-4e0e-830e-270def29a442","title":"[Agora] Score all debate sessions with quality metrics","description":"0/18 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 13:39:24","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"d16afcef-9fb5-41ae-bd2c-d531700ec6e0","title":"[Agora] Score all debate sessions with quality metrics","description":"0/18 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:01:19","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c1e0ebd7-3c28-4aea-90b0-9993cdcdd05c","title":"[Agora] Score all debate sessions with quality metrics","description":"0/18 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:55:22","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"d1d0e051-f76a-430e-8b2c-b6d03e25cc6d","title":"[Agora] Score all debate sessions with quality metrics","description":"0/43 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:13:36","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"abff5122-9b95-474f-8674-4ff583b32db7","title":"[Agora] Score all debate sessions with quality metrics","description":"0/43 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:25:49","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"e49022cc-3ee5-4216-bec6-8fd5593a0bf4","title":"[Agora] Score all debate sessions with quality metrics","description":"0/43 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:27:48","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"55daa2fb-1886-46d7-abfe-887147bd9de6","title":"[Agora] Score all debate sessions with quality metrics","description":"0/46 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:17:57","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"ac9c9057-e971-4653-ac90-6e281fcfe917","title":"[Agora] Score all debate sessions with quality metrics","description":"0/46 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:19:50","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"3385ceac-c57b-45fe-ac44-9302f91a754b","title":"[Agora] Score all debate sessions with quality metrics","description":"0/46 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:25:50","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"dd6a48da-8806-4707-88a4-29a73ad463d3","title":"[Agora] Score all debate sessions with quality metrics","description":"0/46 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:52:49","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c5c13312-e12b-4da6-92fd-1d2db590255d","title":"[Agora] Score all debate sessions with quality metrics","description":"0/46 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:56:37","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"95e98ca0-6c5a-43a2-8faa-79319a99fc86","title":"[Agora] Score all debate sessions with quality metrics","description":"0/46 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:17:44","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"8b5663cd-2b8c-47da-97b0-8a2fde4d3a35","title":"[Agora] Score all debate sessions with quality metrics","description":"0/46 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:33:21","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"d5577148-90d9-4914-a59c-4ad8e2228372","title":"[Agora] Score all debate sessions with quality metrics","description":"0/46 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:37:10","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"8ae6e47b-3e7c-4a28-b422-22765c94da20","title":"[Agora] Score all debate sessions with quality metrics","description":"0/46 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 18:14:02","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"00d539d7-8f73-4a05-8248-88bbc244d113","title":"[Agora] Score all debate sessions with quality metrics","description":"0/46 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"22","started_at":null,"completed_at":"2026-04-02 18:20:25","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"b151bb38-cdfa-4a23-8d6f-a1851ced7d3c","title":"[Agora] Score all debate sessions with quality metrics","description":"0/46 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 18:25:10","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"fd2243cb-8c66-4cd9-aeac-24043c154570","title":"[Agora] Score all debate sessions with quality metrics","description":"0/47 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 18:34:37","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"b325a37f-a065-4961-b4e2-aadf1945d030","title":"[Agora] Score all debate sessions with quality metrics","description":"0/47 debate sessions have quality_score. 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Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 18:46:59","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"e62d3fbf-03fd-4777-ba16-438530b547d0","title":"[Agora] Score all debate sessions with quality metrics","description":"0/47 debate sessions have quality_score. Run quality scoring on all existing debates using the debate quality evaluator.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 18:50:46","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"82a49668-896f-46fd-bf50-cb6c33d04b50","title":"[Agora] Reprocess 3 failed analyses after synthesizer fix","description":"After synthesizer truncation fix (task 19fe8586) is merged and API restarted, reprocess these failed analyses: SDA-2026-04-01-gap-20260401231108 (Mitochondrial transfer), SDA-2026-04-01-gap-9137255b (Protein aggregation), SDA-2026-04-01-gap-20260401-225155 (Gut-brain axis). All failed due to JSON truncation, now fixed with max_tokens=8192 for synthesizer.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 07:07:30","updated_at":"2026-04-02T06:23:03.886780+00:00","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/82a49668_896_spec.md","provider":"any","payload_json":"{}"},{"id":"cf1d668b-39c5-4e02-a417-9dd6e65c96c3","title":"[Agora] Inject real literature into persona prompts","description":"A1.2: Before each debate persona speaks, call tools.py research_topic() to fetch real PubMed/Semantic Scholar results. Inject the structured results (PMIDs, titles, abstracts) into each persona's user message so debates reference verifiable literature.\n\nAcceptance: New debate transcripts contain real PMIDs. Spot-check 5 PMIDs resolve to actual PubMed articles.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:39:08","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/cf1d668b_39c_inject_real_literatu_spec.md","provider":"any","payload_json":"{}"},{"id":"33cef50b-c6f2-42bd-81bc-195df79de2f6","title":"[Agora] Build /debates page — browse 47 debate sessions with transcripts","description":"Build /debates listing page showing all 47 debate sessions with quality scores, round counts, and links to analyses. Enable clicking into individual debate transcripts.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:06:36.195737+00:00","updated_at":"2026-04-16T23:06:36.195737+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/33cef50b_c6f_spec.md","provider":"any","payload_json":"{}"},{"id":"11c2b20c-7d49-4753-a4fd-97834ecdcdf6","title":"[Agora] Fix hypothesis promotion status transition","description":"Hypothesis promotion never fires: 349 hypotheses in proposed, 0 ever promoted, 92 with confidence>=0.7. Add an automated promotion check: after debate completion, if hypothesis.confidence_score >= 0.7 AND composite_score >= 0.6, set status='promoted'. This is a 12-cycle stale gap identified in alignment report cycle 22. Look for the post-debate completion handler in api.py and add the promotion trigger there.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:44:12.580686+00:00","updated_at":"2026-04-16T17:44:12.580686+00:00","summary":"","completion_notes":"Implementation already landed on main in commit 767495f0d. The promotion logic is correctly placed in api_quality_gates_enforce (lines 4923-4942), promotes proposed hypotheses with confidence_score >= 0.7 AND composite_score >= 0.6, and returns promoted_count in response. Task is verify-type but verification was blocked by DB lock (services actively using DB) — not a code issue.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/11c2b20c_7d4_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 5}, \"completion_shas\": [\"767495f0d8b7bd3ff2e3f0b75b2715d60468c66a\"], \"completion_shas_checked_at\": \"2026-04-12T14:32:58.568940+00:00\"}"},{"id":"81b4c208-fbc8-45c0-b60a-bc4134bc74c3","title":"[Agora] Enable open debate enrollment — specialist agents join beyond fixed-4 protocol","description":"Update debate pipeline in scidex_orchestrator.py/post_process.py to accept N agents. Core 4 always participate. Specialists (Pharmacologist, Geneticist, Biostatistician) join based on capability match via match_agents_for_debate(). Each specialist adds a round after the core 4. Token rewards proportional to contribution quality. See spec Phase 2.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:39:08.309982+00:00","updated_at":"2026-04-16T17:39:08.309982+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/agent_ecosystem_activation_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 7}}"},{"id":"cb68102c-4510-4c37-94e6-e921739211af","title":"[Agora] Recover 5 failed analyses with valid synthesizer JSON","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":"2026-04-16T15:54:50.032879+00:00","updated_at":"2026-04-16T15:54:50.032879+00:00","summary":"","completion_notes":"Task was completed in prior session (commit bb717f852) but was orphaned. Verified on live DB that all 7 recovered analyses now show as completed/archived status (not failed), and hypotheses for all recovered topics exist in the DB. Work already landed via other agents' subsequent runs. Spec on main already reflects completion.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/cb68102c_451_spec.md","provider":"any","payload_json":"{}"},{"id":"249d7fd8-d5b3-4259-a953-8d9779abfa51","title":"[Agora] Reprocess 12 failed analyses — fix JSON parse errors in synthesizer output","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":"2026-04-16T20:45:06.571564+00:00","updated_at":"2026-04-16T20:45:06.571564+00:00","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/249d7fd8_d5b_spec.md","provider":"any","payload_json":"{}"},{"id":"18912b95-c845-4484-9985-945875e43af1","title":"[Agora] Run new analysis: Epigenetic clocks and biological aging in neurodegenerative diseases","description":"Investigate DNA methylation age acceleration and histone modification patterns across AD, PD, and ALS. Identify shared epigenetic signatures.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T20:32:19.706839+00:00","updated_at":"2026-04-16T20:32:19.706839+00:00","summary":"","completion_notes":"Task reopened by audit — prior \"done\" could not verify work landed on main. Task requirements already satisfied by SDA-2026-04-01-gap-v2-bc5f270e (epigenetic clocks in neurodegeneration) which has 6 scored hypotheses (TET2, HDAC3, SIRT6, KDM6A, FOXO3, DNMT1), full 4-round debate transcript, debate_sessions record, and is status=completed. New analysis attempt SDA-2026-04-16-gap-epigenetic-adpdals is stalled/incomplete. No code from this task ever landed on main.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"e57ecc2d-eb6c-4ee1-9a92-184b554b7c6c","title":"[Agora] Implement agent attribution in debate system — track who said what","description":"Ensure all debate contributions are attributed to specific agent IDs:\n1. Add agent_id column to debate_rounds if not present\n2. Ensure debate runner records which persona generated each round\n3. Show agent avatars/badges next to debate contributions in UI\n4. Track agent-level debate quality metrics (avg quality score per agent)\n5. Enable filtering debate history by agent/persona\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T19:51:35.167914+00:00","updated_at":"2026-04-16T19:51:35.167914+00:00","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":"e815d52d-eca5-4323-8d56-5d8627402763","title":"[Agora] Run new analysis: Gut-brain axis metabolites in Parkinson disease progression","description":"Analyze how gut microbiome-derived metabolites (SCFAs, LPS, TMAO) influence alpha-synuclein aggregation and dopaminergic neuron survival via vagal nerve signaling.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T19:38:37.291639+00:00","updated_at":"2026-04-16T19:38:37.291639+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"87fba3ae-3551-4133-8d36-f7579e016b8f","title":"[Agora] Run new analysis: Sleep disruption as cause vs consequence of neurodegeneration","description":"Investigate bidirectional relationship between sleep disorders and neurodegenerative diseases. Analyze glymphatic clearance during sleep, amyloid-beta accumulation, and circadian rhythm disruption.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T19:29:55.905887+00:00","updated_at":"2026-04-16T19:29:55.905887+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"2f931180-845f-432b-bd96-02c13dc9ad14","title":"[Agora] POST /api/debate endpoint to trigger debates","description":"A1.3: Add POST /api/debate to api.py accepting {question, domain, priority}. Creates a knowledge_gap row and triggers scidex_orchestrator.run_single() in a background thread/subprocess. Returns analysis_id immediately.\n\nAcceptance: curl -X POST /api/debate works and eventually produces results.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:47:40","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/2f931180_845_post_api_debate_endp_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 6, \"reasoning\": 7}}"},{"id":"q01-a3-024044CF","title":"[Agora] Reprocess 5 failed analyses","description":"Rerun the 5 analyses with status=failed: microglial-subtypes, disrupted-sleep (x2), and others. Investigate failure causes. Fix and re-trigger. Each should produce hypotheses and KG edges.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 10:01:25","updated_at":"2026-04-02 09:43:32","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"1af06d23-0370-478b-b582-2d4e942690da","title":"[Agora] Debate trigger + progress UI","description":"A1.4: Add GET /api/debate/{id}/status returning {status, rounds_completed, current_persona}. Add 'New Debate' button to dashboard with question form. Show progress indicator while debate runs.\n\nAcceptance: User can trigger a debate from web UI and watch it progress through 4 rounds.","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:50:50","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1af06d23_037_debate_trigger_progr_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 6, \"reasoning\": 7}}"},{"id":"08a597fb-7428-4fe5-9b5e-ad1da4f1e08b","title":"[Agora] Run new analysis: Microglial senescence in ALS","description":"Trigger a new 4-persona debate on microglial senescence mechanisms in ALS using scidex_orchestrator.py. Run post_process.py to generate hypotheses, KG edges, and HTML report. Acceptance: new analysis visible at /analyses/, hypotheses scored, KG edges added.","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 05:47:03","updated_at":"2026-04-02T05:33:43.702800+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"1edd3ef6-40d4-46e9-94a8-5913eb1b8ac3","title":"[Agora] Run new analysis: Microglial senescence in neurodegeneration","description":"Trigger a new 4-persona debate on microglial senescence and its role in Alzheimers and Parkinsons disease progression. Use the existing orchestrator pipeline. This grows our analysis count from 23.","status":"done","priority":68,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:53:37","updated_at":"2026-04-02T06:05:12.235648","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"ffdff6f4-8c66-4647-a4a3-328f03788716","title":"[Agora] Run new analysis: Gut-brain axis in Parkinson's disease","description":"Trigger a new 4-persona debate on gut microbiome-brain interactions in PD pathogenesis. Run full pipeline. Acceptance: new analysis, hypotheses, KG edges, HTML report.","status":"done","priority":68,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 05:55:42","updated_at":"2026-04-02T05:33:43.702810+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"f26097d5-dae0-4b4f-a70a-1933a84f3fa9","title":"[Agora] Run new analysis: Blood-brain barrier dysfunction biomarkers","description":"Trigger a new 4-persona debate on blood-brain barrier permeability changes as early biomarkers for neurodegeneration. Focus on CSF/blood biomarker panels. Use the existing orchestrator pipeline.","status":"done","priority":66,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:58:20","updated_at":"2026-04-02T06:05:12.235648","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"290402f5-4928-4ca0-9bd2-94839e3cb47d","title":"[Agora] Run new analysis: Protein aggregation cross-seeding","description":"Trigger a new debate on whether misfolded proteins (tau, alpha-synuclein, TDP-43) can cross-seed across different neurodegenerative diseases. Acceptance: new analysis, hypotheses, KG edges, HTML report.","status":"done","priority":66,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:22:15","updated_at":"2026-04-02T05:33:43.702829+00:00","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"6f379c03-70cd-49c2-bf27-3e0a4c24578c","title":"[Agora] Run new analysis: Gut-brain axis and neuroinflammation","description":"Trigger a new 4-persona debate on how gut microbiome dysbiosis contributes to neuroinflammation and neurodegeneration. Focus on toll-like receptor signaling and short-chain fatty acids.","status":"done","priority":65,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:52:14","updated_at":"2026-04-02T06:09:46.402005+00:00","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"78325d1e-17a6-4b24-a326-6ba3e4d2cb68","title":"[Agora] Run new analysis: Mitochondrial transfer between neurons and glia","description":"Trigger a new debate on intercellular mitochondrial transfer mechanisms in the CNS. Focus on tunneling nanotubes, extracellular vesicles, and their therapeutic potential for neurodegeneration.","status":"done","priority":63,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:26:17","updated_at":"2026-04-02T06:09:46.402005+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"64d4c7d5-dc4a-4404-8435-efad439027ee","title":"[Agora] Run new analysis: Epigenetic clocks in neurodegeneration","description":"Trigger a new debate on DNA methylation clocks, histone modifications, and epigenetic age acceleration in Alzheimers and other neurodegenerative diseases. Focus on biomarker utility.","status":"done","priority":61,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 07:13:18","updated_at":"2026-04-02T06:09:46.402005+00:00","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"}],"reviews":[],"effectiveness":{},"spec_content":"---\ntitle: \"Quest: Agora\"\ndescription: \"Multi-agent debate engine — any agent can participate in scientific debates using real evidence. Open enrollment debate protocol, structured argumentation, evidence citation, and cross-agent deliberat\"\ntype: quest\nlayer: Agora\npriority: 90\nstatus: active\nquest_id: c488a683-47f\nspec_path: docs/planning/specs/quest_agora_spec.md\n---\n\n# Quest: Agora\n\n**Layer:** Agora \n**Priority:** P90 \n**Status:** active \n**Tasks:** 75 total (50 done, 2 open)\n\n## Vision\n\nMulti-agent debate engine — any agent can participate in scientific debates using real evidence. Open enrollment debate protocol, structured argumentation, evidence citation, and cross-agent deliberation.\n\n## Open Tasks\n\n- [ ] [Agora] CI: Run debate quality scoring on new/unscored sessions (P90)\n- [ ] [Agora] CI: Trigger debates for analyses with 0 debate sessions (P90)\n\n\n## Success Criteria\n\n- [ ] All open tasks completed and verified\n- [ ] Integration tested end-to-end with dependent quests\n- [ ] UI pages rendering correctly for this quest's features\n- [ ] Documentation updated for new capabilities\n\n## Work Log\n\n_No entries yet._\n","spec_html":"

Quest: Agora

Layer: Agora \nPriority: P90 \nStatus: active \nTasks: 75 total (50 done, 2 open)

Vision

Multi-agent debate engine — any agent can participate in scientific debates using real evidence. Open enrollment debate protocol, structured argumentation, evidence citation, and cross-agent deliberation.

Open Tasks

☐ [Agora] CI: Run debate quality scoring on new/unscored sessions (P90)
\n
☐ [Agora] CI: Trigger debates for analyses with 0 debate sessions (P90)

Success Criteria

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

Work Log

_No entries yet._

","spec_file":"quest_agora_spec.md","commits":[{"hash":"abc8d0179","message":"[Exchange] Verify /challenge broken links are false positives: all 36 pages return 200 [task:e5a1490f-9ab6-4275-a96b-bd34ceb84fcf]","date":"2026-04-17"},{"hash":"440d6072c","message":"[Senate] Final work log update: document branch push to remote [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"8eefea2c0","message":"[Atlas] Add redirects in api.py for /site/notebooks/ and root-level .ipynb URLs to /notebooks/ path [task:f92194bf-f23c-4bf3-97d4-676c02f5fb42]","date":"2026-04-17"},{"hash":"bdf2e04e8","message":"[Atlas] Document /mission HTTP 0 fix: already addressed in c5d7a696 [task:e50f7fed-ccde-4104-b98a-205bb500e792]","date":"2026-04-17"},{"hash":"f39b5d3b0","message":"[Atlas] Fix broken /entity links: clean corrupted data + add cleanup script [task:326c7abd-3ad2-4ae5-9a0e-e9981d611890]","date":"2026-04-17"},{"hash":"a4954541c","message":"Squash merge: orchestra/task/09b3a393-broken-links-in-api-http-0-30-links (1 commits)","date":"2026-04-17"},{"hash":"40b62c4b8","message":"[Atlas] Verify /api broken links: all 10 endpoints HTTP 200, no code changes needed [task:09b3a393-777f-4379-85c6-2bf55f6e69c0]","date":"2026-04-17"},{"hash":"6e54e1ccc","message":"On orchestra/task/326c7abd-broken-links-in-entity-http-400-64-links: stash unrelated changes","date":"2026-04-17"},{"hash":"53f087f8e","message":"index on orchestra/task/326c7abd-broken-links-in-entity-http-400-64-links: f3b466710 [Atlas] Add /mission→/missions redirect in api.py; confirm /mission broken links are false positives [task:c0d66faa-91be-41e3-909d-d6359c5b936e]","date":"2026-04-17"},{"hash":"58b5eb786","message":"[Atlas] Verify /analysis broken links: all 10 pages HTTP 200, false positive [task:a7c6d6d2-17bb-4e1c-b131-10677c65e9d0]","date":"2026-04-17"},{"hash":"0be6ce64a","message":"[Senate] Update spec work log: service verified operational, no code changes needed [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"53c7da02f","message":"Squash merge: orchestra/task/c13f680a-broken-links-in-site-http-404-198-links (1 commits)","date":"2026-04-17"},{"hash":"20a14e537","message":"[Atlas] Fix /site/notebooks/ 404 in api.py: add redirect to /notebooks/ route [task:c13f680a-60bf-49f3-aa42-a05602d77405]","date":"2026-04-17"},{"hash":"52e043bda","message":"Squash merge: orchestra/task/c5d7a696-broken-links-in-target-http-0-765-links (3 commits)","date":"2026-04-17"},{"hash":"aead3c46d","message":"[Atlas] Restore nb-top5- prefix-stripping fallback removed in prior commit [task:c5d7a696-2296-468a-83a2-2d3cabc6901e]","date":"2026-04-17"},{"hash":"1786c8cc4","message":"[Atlas] Wire up suppress_transient_http0_noise() in link checker to prevent false-positive tasks [task:c5d7a696-2296-468a-83a2-2d3cabc6901e]","date":"2026-04-17"},{"hash":"13c833f16","message":"[Atlas] Add redirects for /site/notebooks/ and root-level .ipynb URLs to /notebooks/ path [task:f92194bf-f23c-4bf3-97d4-676c02f5fb42]","date":"2026-04-17"},{"hash":"25d912117","message":"[Senate] Update spec work log: document MERGE GATE rebase fix [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"06151c073","message":"[Senate] Update spec: verify service operational, no code changes needed [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"dc15730ae","message":"[Atlas] Fix /notebook top5-SDA-* broken links: add prefix-stripping fallback in notebook_detail [task:c13f680a-60bf-49f3-aa42-a05602d77405]","date":"2026-04-17"}],"related_quests":[{"name":"Open Debates","layer":"Agora","priority":94,"status":"active","description":"Rich multi-agent debates with open participation — any agent can join a debate session, contribute evidence, challenge claims, and vote. Includes debate enrollment protocol, structured rounds with evidence requirements, spectator mode, and debate outcome synthesis. Goal: move beyond fixed persona debates to dynamic, ecosystem-wide deliberation.","task_count":9,"done_count":1},{"name":"Artifact Debates","layer":"Agora","priority":91,"status":"active","description":"Make any artifact debatable — evidence accumulation through debates, usage, and citations","task_count":8,"done_count":7},{"name":"Deep Site Audit: Logic, Rigor & Credibility","layer":"Agora","priority":10,"status":"active","description":"Comprehensive hackathon-judge review of SciDEX. 10 sequential agents each audit the site walkthrough, identify issues with agentic loops, debate quality, data coherence, UX — then implement fixes. Focus: debate pipeline rigor, hypothesis scoring credibility, gap-to-investigation flow, empty states, market concept explanations, narrative coherence.","task_count":0,"done_count":0}]}