{"quest":{"id":"d5926799-267","name":"UI","description":"UI/Infrastructure — consistent styling, responsive design, loading states","layer":"Cross-cutting","priority":66,"status":"active","created_at":"2026-04-02T10:00:57.209491+00:00","updated_at":"2026-04-10T14:44:10.355870+00:00"},"tasks":[{"id":"a0cc856c-b2a4-4ec1-97e7-fcffc54b4192","title":"[UI] D16.4: Add Mol* 3D Protein Viewer to Hypothesis Pages","description":"Embed interactive 3D protein structure viewer on hypothesis detail pages for target proteins.\n\nGoal: Provide rich molecular visualization for therapeutic targets, making hypotheses more compelling and scientifically rigorous.\n\nDeliverables:\n1. Integrate Mol* (molstar.org) JavaScript viewer into hypothesis detail pages\n2. For each hypothesis with target_gene, fetch PDB structure:\n - Query RCSB PDB API using gene name/protein name\n - Select best representative structure (highest resolution, relevant organism)\n - Load structure into Mol* viewer\n3. Add viewer controls: rotate, zoom, style (cartoon, surface, ball-stick)\n4. Highlight active sites, binding pockets, or disease-relevant regions if known\n5. Add caption with PDB ID, resolution, method (X-ray, cryo-EM, NMR)\n6. Test on top 10 hypotheses (LRP1, HCRTR1, SMPD1, CYP46A1, SST, ABCA1, etc.)\n\nImplementation:\n- Add
to hypothesis detail template in api.py\n- Include Mol* CDN scripts in page header\n- Fetch PDB data via RCSB REST API: https://data.rcsb.org/rest/v1/core/entry/{pdb_id}\n- Initialize viewer with structure on page load\n\nReference: Mol* documentation at molstar.org/viewer-docs/, PDB API at rcsb.org/docs/programmatic-access\n\nThis is Quest 16/17 priority - rich artifacts for demo showcase.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"running","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"1","started_at":"2026-04-17T22:14:36.310049+00:00","completed_at":"2026-04-17T17:33:00.022276+00:00","updated_at":"2026-04-17T22:14:50.888277+00:00","summary":"","completion_notes":"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\n\nChanged files:\n- .gitignore\n- .orchestra-slot.json\n- agent.py\n- api.py\n- api_shared/db.py\n- api_shared/nav.py\n- ci_route_health.py\n- ci_snapshot_prices.py\n- cli.py\n- docs/planning/specs/00739e13_fab_spec.md\n- docs/planning/specs/0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md\n- docs/planning/specs/051daf58_f92_spec.md\n- docs/planning/specs/05b6876b_61a_spec.md\n- docs/planning/specs/0850f78f_f00_spec.md\n- docs/planning/specs/0a4a42ea_f2c_spec.md\n- docs/planning/specs/0afd971e-686d-400b-98a4-f71293db1351_broken_links_in_entity_http_500_9746_links_spec.md\n- docs/planning/specs/0b5285ff-c077-455e-a4d6-f0dd3b538675_spec.md\n- docs/planning/specs/0d37548c_12f_spec.md\n- docs/planning/specs/0de12ae3_ba9_spec.md\n- docs/planning/specs/13d17f9d_fc6_spec.md\n- docs/planning/specs/1668104c_69f_spec.md\n- docs/planning/specs/197efcaa_cc16_static_asset_template_issues_spec.md\n- docs/planning/specs/19d7e4f1_87c_spec.md\n- docs/planning/specs/1a33a296_e05_spec.md\n- docs/planning/specs/1d21e01d-0d3_template_link_generation_spec.md\n- docs/planning/specs/1e337153-1ae0-4a95-a573-bc5f1cdddc58_spec.md\n- docs/planning/specs/1f62e277_c72_spec.md\n- docs/planning/specs/1fe0f02e-fcc9-4d27-b836-84d337b8acec_spec.md\n- docs/planning/specs/22ef73fa-7c9e-4b0c-9bdc-187bdbb8e888_broken_links_in_target_http_500_spec.md\n- docs/planning/specs/2310c378_ea0_spec.md\n- docs/planning/specs/245a4f77_da9_spec.md\n- docs/planning/specs/25dc2ab9-6d9e-4e1d-a415-eb8af9628b2c_broken_links_in_entity_http_500_34_links_spec.md\n- docs/planning/specs/2679e2c9_852_spec.md\n- docs/planning/specs/2f33adfc-814c-42cc-838a-e1d8f080e4e8_spec.md\n- docs/planning/specs/2fba3f5b_3e7_spec.md\n- docs/planning/specs/355a0e0b_92d_spec.md\n- docs/planning/specs/39d76f99-75b5-4451-83d0-01e462b9aca5_broken_links_in_entity_http_404_10_links_spec.md\n- docs/planning/specs/39f47701_938_spec.md\n- docs/planning/specs/3d5cb5ea-broken-links-in-image-http-0-141-links_spec.md\n- docs/planning/specs/3df7390a_4cd6_spec.md\n\nDiff stat:\n.gitignore | 2 -\n .orchestra-slot.json | 2 +-\n agent.py | 54 +-\n api.py | 3130 ++----\n api_shared/db.py | 30 +-\n api_shared/nav.py | 8 +-\n ci_route_health.py | 204 -\n ci_snapshot_prices.py | 104 -\n cli.py | 61 -\n docs/planning/specs/00739e13_fab_spec.md | 22 +-\n .../0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md | 24 -\n docs/planning/specs/051daf58_f92_spec.md | 63 -\n docs/planning/specs/05b6876b_61a_spec.md | 11 -\n docs/planning/specs/0850f78f_f00_spec.md | 57 -\n do","last_error":"Review gate REVISE attempt 2/10: Auto-deploy blocked: Merge failed (conflicts?):","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a0cc856c_b2a_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 9}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 11:53:30\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"4b779b36-8c03-4606-82ae-128432e78405\", \"_watchdog_repair_created_at\": \"2026-04-17T09:07:06.627194+00:00\", \"_gate_retry_count\": 2, \"_gate_last_decision\": \"REVISE\", \"_gate_last_reason\": 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\"docs/planning/specs/c0eee311_f09_spec.md\", \"docs/planning/specs/c0f32d2c-d759-47a8-8cca-04e28aa3c1d2_missing_analysis_html_spec.md\", \"docs/planning/specs/c1227e9b_0ef_spec.md\", \"docs/planning/specs/c172e5fc-48f8-42b3-9284-8e30aa787ba2_spec.md\", \"docs/planning/specs/c2d40207_a69_spec.md\", \"docs/planning/specs/c461cbaa-879e-45c6-b47d-0ae33f34b63f_spec.md\"], \"_gate_diff_stat\": \".gitignore | 2 -\\n .orchestra-slot.json | 2 +-\\n agent.py | 54 +-\\n api.py | 3130 ++----\\n api_shared/db.py | 30 +-\\n api_shared/nav.py | 8 +-\\n ci_route_health.py | 204 -\\n ci_snapshot_prices.py | 104 -\\n cli.py | 61 -\\n docs/planning/specs/00739e13_fab_spec.md | 22 +-\\n .../0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md | 24 -\\n docs/planning/specs/051daf58_f92_spec.md | 63 -\\n docs/planning/specs/05b6876b_61a_spec.md | 11 -\\n docs/planning/specs/0850f78f_f00_spec.md | 57 -\\n docs/planning/specs/0a4a42ea_f2c_spec.md | 36 -\\n ...ken_links_in_entity_http_500_9746_links_spec.md | 32 -\\n .../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 ...roken_links_in_entity_http_500_34_links_spec.md | 57 -\\n docs\", \"_gate_history\": [{\"ts\": \"2026-04-17 18:17:56\", \"decision\": \"REJECT\", \"reason\": \"ci_route_health.py is deleted in the task branch but scidex-route-health.service ExecStart still points to it \\u2014 the systemd service will fail to start after merge.\", \"instructions\": \"Either restore ci_route_health.py in the task branch, OR update scidex-route-health.service ExecStart to point to wherever route-health logic now lives, OR delete scidex-route-health.service entirely if route-health monitoring is no longer needed.\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"sonnet-4.6:1\", \"retry_count\": 8}, {\"ts\": \"2026-04-17 18:24:37\", \"decision\": \"REJECT\", \"reason\": \"ci_route_health.py is deleted in the diff but scidex-route-health.service ExecStart still points to it (line 9) \\u2014 the systemd service will fail to start after merge; this is the same unresolved issue from all four prior reviews.\", \"instructions\": \"Either restore ci_route_health.py, update scidex-route-health.service ExecStart to point to wherever route-health logic now lives, or delete scidex-route-health.service entirely if route-health monitoring is no longer needed.\\nVerify that all 20+ call sites for _encode_site_url_path, _figure_url_from_filepath, _figure_url_from_prefix_and_name, _fetch_ai_portrait_url, and _fetch_hypothesis_visual_url (currently at api.py lines 183, 213, 244, 6429, 6580, 23046, 23126, 23484, 23653, 23877, 23891, 23894, 33235, 34748, 35453, 35467, 35482, 39210, 52409, 63127, 65917) are also removed in the task branch, or restore the function definitions.\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"sonnet-4.6:1\", \"retry_count\": 9}, {\"ts\": \"2026-04-17 18:33:28\", \"decision\": \"REJECT\", \"reason\": \"ci_route_health.py is deleted in the diff (stat shows -204 lines) but scidex-route-health.service ExecStart still points to it \\u2014 the systemd service will fail to start after merge; additionally api.py deletes _encode_site_url_path, _figure_url_from_filepath, _figure_url_from_prefix_and_name, _fetch_ai_portrait_url, and _fetch_hypothesis_visual_url functions while 20+ active call sites remain (confirmed by prior reviews), causing NameError at runtime on any route touching figures or portraits.\", \"instructions\": \"Either restore ci_route_health.py in the task branch, OR update scidex-route-health.service ExecStart to point to wherever route-health logic now lives, OR delete scidex-route-health.service entirely if route-health monitoring is no longer needed\\nRestore all five deleted helper functions from api.py (_encode_site_url_path, _figure_url_from_filepath, _figure_url_from_prefix_and_name, _fetch_ai_portrait_url, _fetch_hypothesis_visual_url) OR remove all 20+ call sites that use them \\u2014 deleting functions while callers remain causes runtime NameError\", \"judge_used\": \"glm:glm-4.5\", \"actor\": \"sonnet-4.6:1\", \"retry_count\": 10}, {\"ts\": \"2026-04-17 18:40:15\", \"decision\": \"REJECT\", \"reason\": \"ci_route_health.py is still deleted on the task branch while scidex-route-health.service ExecStart still points to it, AND all five api.py helper functions (_encode_site_url_path, _figure_url_from_filepath, _figure_url_from_prefix_and_name, _fetch_ai_portrait_url, _fetch_hypothesis_visual_url) are deleted while 23 call sites in api.py on main reference them \\u2014 merging will cause the systemd service to fail on start and NameError crashes at those 23 call sites.\", \"instructions\": \"Restore ci_route_health.py from main (git checkout main -- ci_route_health.py) OR delete scidex-route-health.service entirely if route-health monitoring is no longer needed\\nRestore all five helper functions from main into api.py on the task branch (git checkout main -- api.py is too broad; cherry-pick just those function definitions, lines ~127\\u2013257 on main) \\u2014 they have 23 active call sites that will throw NameError if merged without them\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"sonnet-4.6:1\", \"retry_count\": 1}, {\"ts\": \"2026-04-17 18:47:54\", \"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\": \"sonnet-4.6:1\", \"retry_count\": 2}], \"_gate_escalated_at\": \"2026-04-17 18:33:28\", \"_gate_escalated_to\": \"safety>=9\", \"_gate_failed_workspace_path\": \"/home/ubuntu/scidex/.orchestra-worktrees/task-a0cc856c-b2a4-4ec1-97e7-fcffc54b4192\", \"_gate_failed_branch\": \"orchestra/task/a0cc856c-d16-4-add-mol-3d-protein-viewer-to-hypot\"}"},{"id":"644bff75-6ed0-41e9-b983-a8a44f536a2b","title":"[UI] Fix tools import conflict - agent.py crashing","description":"Critical: agent.py cannot start due to import conflict. Both tools.py and tools/ directory exist. Python imports tools/ package instead of tools.py, breaking agent imports. Fix: rename tools/ to avoid conflict.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"running","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"0","started_at":"2026-04-17T22:13:04.983649+00:00","completed_at":"2026-04-17T13:11:31.904870+00:00","updated_at":"2026-04-17T22:13:39.115375+00:00","summary":"","completion_notes":"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\n\nChanged files:\n- .gitignore\n- .orchestra-slot.json\n- agent.py\n- api.py\n- api_shared/db.py\n- api_shared/nav.py\n- ci_route_health.py\n- ci_snapshot_prices.py\n- cli.py\n- docs/planning/specs/00739e13_fab_spec.md\n- docs/planning/specs/0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md\n- docs/planning/specs/051daf58_f92_spec.md\n- docs/planning/specs/05b6876b_61a_spec.md\n- docs/planning/specs/0850f78f_f00_spec.md\n- docs/planning/specs/0a4a42ea_f2c_spec.md\n- docs/planning/specs/0afd971e-686d-400b-98a4-f71293db1351_broken_links_in_entity_http_500_9746_links_spec.md\n- docs/planning/specs/0b5285ff-c077-455e-a4d6-f0dd3b538675_spec.md\n- docs/planning/specs/0d37548c_12f_spec.md\n- docs/planning/specs/0de12ae3_ba9_spec.md\n- docs/planning/specs/13d17f9d_fc6_spec.md\n- docs/planning/specs/1668104c_69f_spec.md\n- docs/planning/specs/197efcaa_cc16_static_asset_template_issues_spec.md\n- docs/planning/specs/19d7e4f1_87c_spec.md\n- docs/planning/specs/1a33a296_e05_spec.md\n- docs/planning/specs/1d21e01d-0d3_template_link_generation_spec.md\n- docs/planning/specs/1e337153-1ae0-4a95-a573-bc5f1cdddc58_spec.md\n- docs/planning/specs/1f62e277_c72_spec.md\n- docs/planning/specs/1fe0f02e-fcc9-4d27-b836-84d337b8acec_spec.md\n- docs/planning/specs/22ef73fa-7c9e-4b0c-9bdc-187bdbb8e888_broken_links_in_target_http_500_spec.md\n- docs/planning/specs/2310c378_ea0_spec.md\n- docs/planning/specs/245a4f77_da9_spec.md\n- docs/planning/specs/25dc2ab9-6d9e-4e1d-a415-eb8af9628b2c_broken_links_in_entity_http_500_34_links_spec.md\n- docs/planning/specs/2679e2c9_852_spec.md\n- docs/planning/specs/2f33adfc-814c-42cc-838a-e1d8f080e4e8_spec.md\n- docs/planning/specs/2fba3f5b_3e7_spec.md\n- docs/planning/specs/355a0e0b_92d_spec.md\n- docs/planning/specs/39d76f99-75b5-4451-83d0-01e462b9aca5_broken_links_in_entity_http_404_10_links_spec.md\n- docs/planning/specs/39f47701_938_spec.md\n- docs/planning/specs/3d5cb5ea-broken-links-in-image-http-0-141-links_spec.md\n- docs/planning/specs/3df7390a_4cd6_spec.md\n\nDiff stat:\n.gitignore | 2 -\n .orchestra-slot.json | 2 +-\n agent.py | 54 +-\n api.py | 3130 ++----\n api_shared/db.py | 30 +-\n api_shared/nav.py | 8 +-\n ci_route_health.py | 204 -\n ci_snapshot_prices.py | 104 -\n cli.py | 61 -\n docs/planning/specs/00739e13_fab_spec.md | 22 +-\n .../0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md | 24 -\n docs/planning/specs/051daf58_f92_spec.md | 63 -\n docs/planning/specs/05b6876b_61a_spec.md | 11 -\n docs/planning/specs/0850f78f_f00_spec.md | 57 -\n do","last_error":"Review gate REVISE attempt 7/10: Auto-deploy blocked: Merge failed (conflicts?):","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/644bff75_6ed_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 9}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 20:55:33\", \"_stall_skip_at\": {\"minimax\": \"2026-04-14T20:55:33.530103+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_gate_retry_count\": 7, \"_gate_last_decision\": \"REVISE\", \"_gate_last_reason\": \"Auto-deploy blocked: Merge failed (conflicts?):\", \"_gate_judge_used\": \"max:claude-sonnet-4-6\", \"_gate_last_instructions\": \"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\", \"_gate_branch\": \"orchestra/task/644bff75-tools-import-conflict-agent-py-crashing\", \"_gate_changed_files\": [\".gitignore\", \".orchestra-slot.json\", \"agent.py\", \"api.py\", \"api_shared/db.py\", \"api_shared/nav.py\", \"ci_route_health.py\", \"ci_snapshot_prices.py\", \"cli.py\", \"docs/planning/specs/00739e13_fab_spec.md\", \"docs/planning/specs/0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md\", \"docs/planning/specs/051daf58_f92_spec.md\", \"docs/planning/specs/05b6876b_61a_spec.md\", \"docs/planning/specs/0850f78f_f00_spec.md\", \"docs/planning/specs/0a4a42ea_f2c_spec.md\", \"docs/planning/specs/0afd971e-686d-400b-98a4-f71293db1351_broken_links_in_entity_http_500_9746_links_spec.md\", \"docs/planning/specs/0b5285ff-c077-455e-a4d6-f0dd3b538675_spec.md\", 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\"docs/planning/specs/9fcdbafb-78da_spec.md\", \"docs/planning/specs/9fef1c13_a80_spec.md\", \"docs/planning/specs/a18d6546_economics_dashboard_spec.md\", \"docs/planning/specs/a27b8c7a-1fa_economics_ci_snapshot_hypothesis_prices_spec.md\", \"docs/planning/specs/a3f12c37_8e0_spec.md\", \"docs/planning/specs/a449718f_532_spec.md\", \"docs/planning/specs/a572c16b_dd6_spec.md\", \"docs/planning/specs/a88f4944_cb09_forge_reduce_pubmed_metadata_backlog_spec.md\", \"docs/planning/specs/a9bbf4cf-0f86-4ed0-9c7b-0e951dc6393b_spec.md\", \"docs/planning/specs/aa561240_161_spec.md\", \"docs/planning/specs/ab99d47b-41e1-4b96-b27e-6b087a3ce107_spec.md\", \"docs/planning/specs/b13f71fa_465_spec.md\", \"docs/planning/specs/b5053347-091e-46e8-a9d1-f4521e633a91_spec.md\", \"docs/planning/specs/b68277b4_52c_spec.md\", \"docs/planning/specs/b920b7bc_556d_static_site_generation_spec.md\", \"docs/planning/specs/bebcf954_4716_4ef3_a173_47e8c1d414b7_spec.md\", \"docs/planning/specs/c0cfc918-a8f_spec.md\", \"docs/planning/specs/c0eee311_f09_spec.md\", \"docs/planning/specs/c0f32d2c-d759-47a8-8cca-04e28aa3c1d2_missing_analysis_html_spec.md\", \"docs/planning/specs/c1227e9b_0ef_spec.md\", \"docs/planning/specs/c172e5fc-48f8-42b3-9284-8e30aa787ba2_spec.md\", \"docs/planning/specs/c2d40207_a69_spec.md\", \"docs/planning/specs/c461cbaa-879e-45c6-b47d-0ae33f34b63f_spec.md\"], \"_gate_diff_stat\": \".gitignore | 2 -\\n .orchestra-slot.json | 2 +-\\n agent.py | 54 +-\\n api.py | 3130 ++----\\n api_shared/db.py | 30 +-\\n api_shared/nav.py | 8 +-\\n ci_route_health.py | 204 -\\n ci_snapshot_prices.py | 104 -\\n cli.py | 61 -\\n docs/planning/specs/00739e13_fab_spec.md | 22 +-\\n .../0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md | 24 -\\n docs/planning/specs/051daf58_f92_spec.md | 63 -\\n docs/planning/specs/05b6876b_61a_spec.md | 11 -\\n docs/planning/specs/0850f78f_f00_spec.md | 57 -\\n docs/planning/specs/0a4a42ea_f2c_spec.md | 36 -\\n ...ken_links_in_entity_http_500_9746_links_spec.md | 32 -\\n .../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 ...roken_links_in_entity_http_500_34_links_spec.md | 57 -\\n docs\", \"_gate_history\": [{\"ts\": \"2026-04-17 18:22:26\", \"decision\": \"REJECT\", \"reason\": \"ed every time. ```json { \\\"decision\\\": \\\"REJECT\\\", \\\"reason\\\": \\\"api.py on the task branch reverts two occurrences of the correct plural `/debates/{r['id']}` back to singular `/debate/{r['id']}`, breaking frontend navigation links \\u2014 a catastrophic API contract break flagged in every prior review and still not fixed.\\\", \\\"fixes\\\": [ \\\"In api.py, find both occurrences of `\\\\\\\"link\\\\\\\": f\\\\\\\"/debate/{r['id']}\\\\\\\"` (in the activity/recent-activity endpoints) and change them back to `\\\\\\\"link\\\\\\\": f\\\\\\\"/debates/{r['id']}\\\\\\\"` \", \"instructions\": \"\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"sonnet-4.6:0\", \"retry_count\": 3}, {\"ts\": \"2026-04-17 18:28:10\", \"decision\": \"REJECT\", \"reason\": \"ed in every prior review (Reviews 1, 2, and 5). ```json { \\\"decision\\\": \\\"REJECT\\\", \\\"reason\\\": \\\"api.py on the task branch reverts two occurrences of the correct plural `/debates/{r['id']}` back to singular `/debate/{r['id']}`, breaking frontend navigation links \\u2014 a catastrophic API contract break flagged and rejected in every prior review.\\\", \\\"fixes\\\": [ \\\"In api.py, replace both occurrences of `f\\\\\\\"/debate/{r['id']}\\\\\\\"` with `f\\\\\\\"/debates/{r['id']}\\\\\\\"` to restore the correct plural URL form that exists on \", \"instructions\": \"\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"sonnet-4.6:0\", \"retry_count\": 4}, {\"ts\": \"2026-04-17 18:33:53\", \"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\": \"sonnet-4.6:0\", \"retry_count\": 5}, {\"ts\": \"2026-04-17 18:39:43\", \"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\": \"sonnet-4.6:0\", \"retry_count\": 6}, {\"ts\": \"2026-04-17 18:45:25\", \"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\": \"sonnet-4.6:0\", \"retry_count\": 7}], \"_gate_escalated_at\": \"2026-04-17 18:05:25\", \"_gate_escalated_to\": \"safety>=9\", \"_gate_failed_workspace_path\": \"/home/ubuntu/scidex/.orchestra-worktrees/task-644bff75-6ed0-41e9-b983-a8a44f536a2b\", \"_gate_failed_branch\": \"orchestra/task/644bff75-tools-import-conflict-agent-py-crashing\"}"},{"id":"b3dafc56-7bf5-4ebf-a57d-acc77a7d478c","title":"[UI] Fix /notebooks 500 error — NoneType subscript at line 15678","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"open","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T12:10:40.493840+00:00","updated_at":"2026-04-17T20:30:01.202430+00:00","summary":"","completion_notes":"Switch to the correct task branch for task b3dafc56-7bf (the /notebooks 500 error fix) before submitting for review\nEnsure the diff contains a targeted fix near api.py line 15678 that guards against NoneType subscript in the /notebooks route handler (e.g., a None check before indexing the offending object)\n\nChanged files:\n- .gitignore\n- .orchestra-slot.json\n- agent.py\n- api.py\n- api_shared/db.py\n- api_shared/nav.py\n- ci_route_health.py\n- ci_snapshot_prices.py\n- cli.py\n- docs/planning/specs/00739e13_fab_spec.md\n- docs/planning/specs/0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md\n- docs/planning/specs/051daf58_f92_spec.md\n- docs/planning/specs/05b6876b_61a_spec.md\n- docs/planning/specs/0850f78f_f00_spec.md\n- docs/planning/specs/0a4a42ea_f2c_spec.md\n- docs/planning/specs/0afd971e-686d-400b-98a4-f71293db1351_broken_links_in_entity_http_500_9746_links_spec.md\n- docs/planning/specs/0b5285ff-c077-455e-a4d6-f0dd3b538675_spec.md\n- docs/planning/specs/0d37548c_12f_spec.md\n- docs/planning/specs/0de12ae3_ba9_spec.md\n- docs/planning/specs/13d17f9d_fc6_spec.md\n- docs/planning/specs/1668104c_69f_spec.md\n- docs/planning/specs/197efcaa_cc16_static_asset_template_issues_spec.md\n- docs/planning/specs/19d7e4f1_87c_spec.md\n- docs/planning/specs/1a33a296_e05_spec.md\n- docs/planning/specs/1d21e01d-0d3_template_link_generation_spec.md\n- docs/planning/specs/1e337153-1ae0-4a95-a573-bc5f1cdddc58_spec.md\n- docs/planning/specs/1f62e277_c72_spec.md\n- docs/planning/specs/1fe0f02e-fcc9-4d27-b836-84d337b8acec_spec.md\n- docs/planning/specs/22ef73fa-7c9e-4b0c-9bdc-187bdbb8e888_broken_links_in_target_http_500_spec.md\n- docs/planning/specs/2310c378_ea0_spec.md\n- docs/planning/specs/245a4f77_da9_spec.md\n- docs/planning/specs/25dc2ab9-6d9e-4e1d-a415-eb8af9628b2c_broken_links_in_entity_http_500_34_links_spec.md\n- docs/planning/specs/2679e2c9_852_spec.md\n- docs/planning/specs/2f33adfc-814c-42cc-838a-e1d8f080e4e8_spec.md\n- docs/planning/specs/2fba3f5b_3e7_spec.md\n- docs/planning/specs/355a0e0b_92d_spec.md\n- docs/planning/specs/39d76f99-75b5-4451-83d0-01e462b9aca5_broken_links_in_entity_http_404_10_links_spec.md\n- docs/planning/specs/39f47701_938_spec.md\n- docs/planning/specs/3d5cb5ea-broken-links-in-image-http-0-141-links_spec.md\n- docs/planning/specs/3df7390a_4cd6_spec.md\n\nDiff stat:\n.gitignore | 2 -\n .orchestra-slot.json | 2 +-\n agent.py | 54 +-\n api.py | 3130 ++----\n api_shared/db.py | 30 +-\n api_shared/nav.py | 8 +-\n ci_route_health.py | 204 -\n ci_snapshot_prices.py | 104 -\n cli.py | 61 -\n docs/planning/specs/00739e13_fab_spec.md | 22 +-\n .../0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md | 24 -\n docs/planning/specs/051daf","last_error":"zombie_sweeper: no live slot (assigned='70'), stale heartbeat 2026-04-17 20:04:35.877463+00:00","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b3dafc56_7bf_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 9}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-15 21:41:49\", \"_stall_skip_at\": {\"minimax\": \"2026-04-15T21:41:49.474776+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_gate_retry_count\": 7, \"_gate_last_decision\": \"REJECT\", \"_gate_last_reason\": \"The diff is on the wrong branch (orchestra/task/9b4b1e14-review-top-10-hypothesis-pages-for-demo as shown in .orchestra-slot.json) and contains no fix for the /notebooks 500 error or the NoneType subscript at line 15678 \\u2014 this is the eleventh consecutive rejection for exactly the same problem.\", \"_gate_judge_used\": \"max:claude-sonnet-4-6\", \"_gate_last_instructions\": \"Switch to the correct task branch for task b3dafc56-7bf (the /notebooks 500 error fix) before submitting for review\\nEnsure the diff contains a targeted fix near api.py line 15678 that guards against NoneType subscript in the /notebooks route handler (e.g., a None check before indexing the offending object)\", \"_gate_branch\": \"orchestra/task/b3dafc56-notebooks-500-error-nonetype-subscript-a\", \"_gate_changed_files\": [\".gitignore\", \".orchestra-slot.json\", \"agent.py\", \"api.py\", \"api_shared/db.py\", \"api_shared/nav.py\", \"ci_route_health.py\", \"ci_snapshot_prices.py\", \"cli.py\", \"docs/planning/specs/00739e13_fab_spec.md\", \"docs/planning/specs/0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md\", 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\"docs/planning/specs/22ef73fa-7c9e-4b0c-9bdc-187bdbb8e888_broken_links_in_target_http_500_spec.md\", \"docs/planning/specs/2310c378_ea0_spec.md\", \"docs/planning/specs/245a4f77_da9_spec.md\", \"docs/planning/specs/25dc2ab9-6d9e-4e1d-a415-eb8af9628b2c_broken_links_in_entity_http_500_34_links_spec.md\", \"docs/planning/specs/2679e2c9_852_spec.md\", \"docs/planning/specs/2f33adfc-814c-42cc-838a-e1d8f080e4e8_spec.md\", \"docs/planning/specs/2fba3f5b_3e7_spec.md\", \"docs/planning/specs/355a0e0b_92d_spec.md\", \"docs/planning/specs/39d76f99-75b5-4451-83d0-01e462b9aca5_broken_links_in_entity_http_404_10_links_spec.md\", \"docs/planning/specs/39f47701_938_spec.md\", \"docs/planning/specs/3d5cb5ea-broken-links-in-image-http-0-141-links_spec.md\", \"docs/planning/specs/3df7390a_4cd6_spec.md\", \"docs/planning/specs/3eb45ac3_complete_application_server_failure_spec.md\", \"docs/planning/specs/3fea4720-77a6-4a98-999b-0b54c81cae2e_broken_links_in_analysis_http_404_10_links_spec.md\", \"docs/planning/specs/42320e63_d82_spec.md\", \"docs/planning/specs/43abc1dc_631_spec.md\", \"docs/planning/specs/4a789ba1_bd0_spec.md\", \"docs/planning/specs/4e5c9924_11bc_4268_spec.md\", \"docs/planning/specs/4e76d954-e253-441a-af7b-b28d18059f59_spec.md\", \"docs/planning/specs/4ea61e17-0b95-445c-aa1b-961696f16126_broken_links_in_figures_http_0_1252_spec.md\", \"docs/planning/specs/50fd9c87-f086-4576-9d61-fa249719cb44_spec.md\", \"docs/planning/specs/51bbc267-83b1-41e6-bef4-ff90a3a91e0e_spec.md\", \"docs/planning/specs/53b098aba384_exchange_design_capital_allocation_mode_spec.md\", \"docs/planning/specs/53c618dd_a199_4fcb_9356_d43fbc922f59_spec.md\", \"docs/planning/specs/55888d47-5c2c-4a80-b007-2bbdc83a81ff_service_down_connection_failure_spec.md\", \"docs/planning/specs/55e3ea08_76c2_atlas_reduce_wiki_kg_link_backlog_spec.md\", \"docs/planning/specs/5a10152f_8bd_spec.md\", \"docs/planning/specs/5faca020_wiki_quality_review_spec.md\", \"docs/planning/specs/692f13b8_876_spec.md\", \"docs/planning/specs/6d5f040f-b3e2-431d-8345-d780f32e3ccb_spec.md\", \"docs/planning/specs/6db7722d_16b_spec.md\", \"docs/planning/specs/6e7d8631_63f_spec.md\", \"docs/planning/specs/7221a2c1-99dc-4f7a-aa92-56dd0a697a7e_broken_links_in_experiment_http_404_197_spec.md\", \"docs/planning/specs/77718e75-4f3d-4d2b-afdb-c5cf4152d9b9_spec.md\", \"docs/planning/specs/7c483e0e_5d1_spec.md\", \"docs/planning/specs/7ffcac76_07a_spec.md\", \"docs/planning/specs/85f207f0_aa7_spec.md\", \"docs/planning/specs/86c48eaa_senate_db_fk_integrity_spec.md\", \"docs/planning/specs/88da08c1_3d6_spec.md\", \"docs/planning/specs/8b0d3be0_0e7_spec.md\", \"docs/planning/specs/8b68a328_f55_spec.md\", \"docs/planning/specs/8ba1aa28-6d6e-42a1-810e-65dc17dee42f_spec.md\", \"docs/planning/specs/8f732eff_6f6_spec.md\", \"docs/planning/specs/93e4775f_690_spec.md\", \"docs/planning/specs/9401eb58-32bd-4a83-8823-c562758ca0eb_spec.md\", \"docs/planning/specs/9455e56c_3e3_spec.md\", \"docs/planning/specs/9b2fabdb_60f_spec.md\", \"docs/planning/specs/9f0f0742_7c6_spec.md\", \"docs/planning/specs/9fcdbafb-78da_spec.md\", \"docs/planning/specs/9fef1c13_a80_spec.md\", \"docs/planning/specs/a18d6546_economics_dashboard_spec.md\", \"docs/planning/specs/a27b8c7a-1fa_economics_ci_snapshot_hypothesis_prices_spec.md\", \"docs/planning/specs/a3f12c37_8e0_spec.md\", \"docs/planning/specs/a449718f_532_spec.md\", \"docs/planning/specs/a572c16b_dd6_spec.md\", \"docs/planning/specs/a88f4944_cb09_forge_reduce_pubmed_metadata_backlog_spec.md\", \"docs/planning/specs/a9bbf4cf-0f86-4ed0-9c7b-0e951dc6393b_spec.md\", \"docs/planning/specs/aa561240_161_spec.md\", \"docs/planning/specs/ab99d47b-41e1-4b96-b27e-6b087a3ce107_spec.md\", \"docs/planning/specs/b13f71fa_465_spec.md\", \"docs/planning/specs/b5053347-091e-46e8-a9d1-f4521e633a91_spec.md\", \"docs/planning/specs/b68277b4_52c_spec.md\", \"docs/planning/specs/b920b7bc_556d_static_site_generation_spec.md\", \"docs/planning/specs/bebcf954_4716_4ef3_a173_47e8c1d414b7_spec.md\", \"docs/planning/specs/c0cfc918-a8f_spec.md\", \"docs/planning/specs/c0eee311_f09_spec.md\", \"docs/planning/specs/c0f32d2c-d759-47a8-8cca-04e28aa3c1d2_missing_analysis_html_spec.md\", \"docs/planning/specs/c1227e9b_0ef_spec.md\", \"docs/planning/specs/c172e5fc-48f8-42b3-9284-8e30aa787ba2_spec.md\", \"docs/planning/specs/c2d40207_a69_spec.md\", \"docs/planning/specs/c461cbaa-879e-45c6-b47d-0ae33f34b63f_spec.md\", \"docs/planning/specs/c4a9a7ae-4d9_wiki_ci_add_mermaid_diagrams_to_next_5_spec.md\"], \"_gate_diff_stat\": \".gitignore | 2 -\\n .orchestra-slot.json | 2 +-\\n agent.py | 54 +-\\n api.py | 3130 ++----\\n api_shared/db.py | 30 +-\\n api_shared/nav.py | 8 +-\\n ci_route_health.py | 204 -\\n ci_snapshot_prices.py | 104 -\\n cli.py | 61 -\\n docs/planning/specs/00739e13_fab_spec.md | 22 +-\\n .../0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md | 24 -\\n docs/planning/specs/051daf58_f92_spec.md | 63 -\\n docs/planning/specs/05b6876b_61a_spec.md | 11 -\\n docs/planning/specs/0850f78f_f00_spec.md | 57 -\\n docs/planning/specs/0a4a42ea_f2c_spec.md | 36 -\\n ...ken_links_in_entity_http_500_9746_links_spec.md | 32 -\\n .../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 ...roken_links_in_entity_http_500_34_links_spec.md | 57 -\\n docs\", \"_gate_history\": [{\"ts\": \"2026-04-17 18:00:09\", \"decision\": \"REJECT\", \"reason\": \"The diff is on the wrong branch (orchestra/task/9b4b1e14-review-top-10-hypothesis-pages-for-demo as shown in .orchestra-slot.json) and contains no fix for the /notebooks 500 error or the NoneType subscript at line 15678 \\u2014 this is the seventh consecutive rejection for exactly the same problem.\", \"instructions\": \"Switch to the correct task branch for task b3dafc56-7bf (the /notebooks 500 error fix) before submitting for review\\nEnsure the diff contains a targeted fix near api.py line 15678 that guards against NoneType subscript in the /notebooks route handler (e.g., a None check before indexing the offending object)\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"openai:72\", \"retry_count\": 3}, {\"ts\": \"2026-04-17 18:15:49\", \"decision\": \"REJECT\", \"reason\": \"The diff is on the wrong branch (orchestra/task/9b4b1e14-review-top-10-hypothesis-pages-for-demo as shown in .orchestra-slot.json) and contains no fix for the /notebooks 500 error or the NoneType subscript at line 15678 \\u2014 this is the eighth consecutive rejection for exactly the same problem.\", \"instructions\": \"Switch to the correct task branch for task b3dafc56-7bf (the /notebooks 500 error fix) before submitting for review\\nEnsure the diff contains a targeted fix near api.py line 15678 that guards against NoneType subscript in the /notebooks route handler (e.g., a None check before indexing the offending object)\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"openai:71\", \"retry_count\": 4}, {\"ts\": \"2026-04-17 18:27:03\", \"decision\": \"REJECT\", \"reason\": \"The diff is on the wrong branch (orchestra/task/9b4b1e14-review-top-10-hypothesis-pages-for-demo as shown in .orchestra-slot.json) and contains no fix for the /notebooks 500 error or the NoneType subscript at line 15678 \\u2014 this is the ninth consecutive rejection for exactly the same problem.\", \"instructions\": \"Switch to the correct task branch for task b3dafc56-7bf (the /notebooks 500 error fix) before submitting for review\\nEnsure the diff contains a targeted fix near api.py line 15678 that guards against NoneType subscript in the /notebooks route handler (e.g., a None check before indexing the offending object)\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"openai:72\", \"retry_count\": 5}, {\"ts\": \"2026-04-17 18:37:41\", \"decision\": \"REJECT\", \"reason\": \"The diff is on the wrong branch (orchestra/task/9b4b1e14-review-top-10-hypothesis-pages-for-demo as shown in .orchestra-slot.json) and contains no fix for the /notebooks 500 error or the NoneType subscript at line 15678 \\u2014 this is the tenth consecutive rejection for exactly the same problem.\", \"instructions\": \"Switch to the correct task branch for task b3dafc56-7bf (the /notebooks 500 error fix) before submitting for review\\nEnsure the diff contains a targeted fix near api.py line 15678 that guards against NoneType subscript in the /notebooks route handler (e.g., a None check before indexing the offending object)\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"openai:71\", \"retry_count\": 6}, {\"ts\": \"2026-04-17 18:48:12\", \"decision\": \"REJECT\", \"reason\": \"The diff is on the wrong branch (orchestra/task/9b4b1e14-review-top-10-hypothesis-pages-for-demo as shown in .orchestra-slot.json) and contains no fix for the /notebooks 500 error or the NoneType subscript at line 15678 \\u2014 this is the eleventh consecutive rejection for exactly the same problem.\", \"instructions\": \"Switch to the correct task branch for task b3dafc56-7bf (the /notebooks 500 error fix) before submitting for review\\nEnsure the diff contains a targeted fix near api.py line 15678 that guards against NoneType subscript in the /notebooks route handler (e.g., a None check before indexing the offending object)\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"openai:70\", \"retry_count\": 7}], \"_gate_escalated_at\": \"2026-04-17 17:20:13\", \"_gate_escalated_to\": \"safety>=9\", \"_gate_failed_workspace_path\": \"/home/ubuntu/scidex/.orchestra-worktrees/task-b3dafc56-7bf5-4ebf-a57d-acc77a7d478c\", \"_gate_failed_branch\": \"orchestra/task/b3dafc56-notebooks-500-error-nonetype-subscript-a\"}"},{"id":"58e83560-3321-4ac1-931b-2e18d31c1d86","title":"[UI] Fix path traversal vulnerability in bridge.py","description":"SECURITY FIX: Bridge service has path traversal vulnerability. Line 32-33 checks if path starts with BASE before resolving symlinks/relative paths, allowing attackers to write to arbitrary locations via ../../ sequences. Service crashed attempting to write to /etc. Fix: use os.path.realpath() before validation. Add tests for common bypass techniques.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"open","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 10:55:15","updated_at":"2026-04-13T10:16:03.984606+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: ORPHAN_BRANCH — 2 commit(s) found but none on main; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/58e83560_332_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 9, \"safety\": 10}}"},{"id":"e2ca9a2e-6f00-448f-93c3-6d5e488fbc95","title":"[UI] Fix None-subscript vulnerabilities in api.py templates","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"open","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 01:11:24","updated_at":"2026-04-13T10:16:03.537792+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: ORPHAN_BRANCH — 1 commit(s) found but none on main; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e2ca9a2e_6f0_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 9, \"safety\": 10}}"},{"id":"2077201c-c23e-458e-bce9-1bdbdb94f658","title":"[UI] Add /experiments to navigation menu","description":"The experiments page exists but is not linked from navigation. Add it to the top bar nav (Main group) and sidebar nav (Explore group).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"open","priority":89,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 18:45:29","updated_at":"2026-04-13T10:16:01.888856+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: NO_COMMITS — No commits found referencing task ID; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/2077201c_c23_spec.md","provider":"any","payload_json":"{}"},{"id":"860e536b-4b93-46ee-9630-a2110cb8b5f5","title":"[UI] Add /targets to navigation menu","description":"Add /targets link to main nav and sidebar, similar to /experiments\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"open","priority":89,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 18:51:02","updated_at":"2026-04-13T10:16:01.850301+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: NO_COMMITS — No commits found referencing task ID; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/860e536b_4b9_spec.md","provider":"any","payload_json":"{}"},{"id":"bd5a6663-adb7-4eef-a792-76152c20f6d3","title":"[UI] Fix 500 errors on /entity/ and /target/ pages — null field handling","description":"Entity pages like /entity/CASP1 and target pages like /target/t-2a37aa51 crash with TypeError: NoneType object is not subscriptable. Need to add null-safe access to fields that may be None in the entity_detail and target_detail functions.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"open","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 19:10:36","updated_at":"2026-04-13T10:16:01.820169+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: NO_COMMITS — No commits found referencing task ID; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/bd5a6663_adb_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"50c9497b-381d-48cc-8917-914ff78a054a","title":"[UI] Fix search API 500 and compare page 500 — sqlite3.Row.get() and wrong column name","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"open","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 20:56:29","updated_at":"2026-04-13T10:16:00.649842+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: NO_COMMITS — No commits found referencing task ID; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/50c9497b_381_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"6d500cfd-b2c2-4b43-a0b7-8d0fb67d5a60","title":"[UI] Orphan work detection and linking system","description":"Build orphan_checker.py scanning for unlinked work: analyses without HTML, hypotheses not shown, KG edges not visualized, papers unreferenced. /api/coverage endpoint. Acceptance: zero orphaned work; >95% linkage; runs with linkcheck service; visible on Senate dashboard.","status":"open","priority":80,"task_type":"recurring","frequency":"every-12h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T11:42:19.800490+00:00","updated_at":"2026-04-17T11:42:19.800490+00:00","summary":"Closed: caused by temporary 502 outage, now resolved","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/6d500cfd-b2c_ui_orphan_work_detection__spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"auto_tagged_at\": \"2026-04-03T22:29:52.509594\", \"completion_shas\": [\"2eba2d9ea3fbf899712372ecbc03f2e78294f7c9\", \"ae9a04c93cbde1ecb803a354bdfc89c625dd8518\"], \"completion_shas_checked_at\": \"2026-04-12T23:15:52.847027+00:00\", \"completion_shas_missing\": [\"8048eef29154425e5f1f2c2b8d931d00820068d2\", 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check","description":"","status":"open","priority":80,"task_type":"recurring","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T00:15:13.356689+00:00","updated_at":"2026-04-17T00:15:13.356689+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/5616905a_812_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"50d8d0e2587bf4718fdc6138ffb2fe07bbf0c677\"], \"completion_shas_checked_at\": \"2026-04-12T23:20:04.630990+00:00\", \"completion_shas_missing\": [\"9992c89e98be0a7c3f290f93c3d48f63095f452f\", \"0c8f14ac3e6c0df9ef0c1ebf77c32508593024b1\", \"6b9cc44ea1287216f04e3cca8010446ffce345e0\", \"54465120182f03914bc1cf0dbdd224b71402947e\", \"678d3ca59aa379ebf318bee10dc4f4c2d8f4e39b\", \"6b617a08188fbe1e872a9018b78dde5e6e546995\", \"7d7075031ef2a86b5528013b602a5f4e99aa23e0\", \"b13a7e38e932c711103ee0262ee0533e482c11cf\", \"fdaf635147f665c4f701472407f0abc513a8c85b\", \"af76e647e9a7c849dcb02bedae70978c6a654752\", \"cbe2e04b6550f17c9446015503c27eb01d328611\", \"2cf6c59456d136412569fa3dfc62c252b2b0077b\", \"2da9547329f6a49208537f03aa3930c4b16da776\", \"c0903fb723952bae1c9e2188c7f6c0448a64cbeb\", \"0d959e5cd96b715e916d6cf95f7f8a6bfd192ca9\", \"d6da63393bca1d7ca2b5d7dcc23fcd88d815a803\", \"824675e796f8b926f414acf1a8dd01484d579bfc\", \"bd752c56394fd31c717136cc3e1514b7df1f1a8e\", \"7442f9da2175786ded460b8e2181a54d87b19a96\", \"ebd3d37ee2a8442cadd2ea511fb94f645abbbc37\", \"8ef6a067a3e355af3748e88746c5f75929014466\", \"df57e637fa5f839cc300e646cadf0cf3b0838f25\"], \"requirements\": {\"coding\": 5}}"},{"id":"3d7b4ecd-208c-4b20-98ac-e8980762e663","title":"[UI] CI: Verify all main pages render without errors","description":"Curl /, /analyses, /exchange, /gaps, /graph, /wiki, /atlas, /senate, /forge, /quests. Check 200 status. Report any failures.","status":"open","priority":80,"task_type":"recurring","frequency":"every-12h","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:48:16.489961+00:00","updated_at":"2026-04-16T23:48:16.489961+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/3d7b4ecd-208_ui_ci_verify_all_main_pages_render_with_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6, \"safety\": 8}, \"completion_shas\": [\"f019106f7d4876ef078b5ec9dccf021aa2bb6069\", \"e9382ed7c975e5aced01f249950c9f30685122cd\", \"8ddc1236bb90d602d74979be048ef9ca58ddfd53\", \"df7a0d9fecd2b9e2e0c879f4b110257d09596e3b\"], \"completion_shas_checked_at\": \"2026-04-12T22:03:10.411898+00:00\", \"completion_shas_missing\": [\"4ed3867f82ef316a41f6c8cddc61def9f64ec459\", \"9655e8a381ce3043674d95ca0a801690e91fcef9\", \"fbb6d784071565b93251e8223ee71a8cee9dc525\", \"d2ba7079441395a0de32b95db7c226894d2d1373\", \"3fd98512e17e60bf9c2223fe384f16e58d677dbe\", \"e7039d3c6283357df1aa9292497ff54f5a82cda9\", \"ec3ff9776bcc669555ea9b91b62b5c643e4a3a03\", \"69118d67130b4133c9b62ceeb49702521e0a9206\", \"b962efbc35257b5d15c2edfa881ac0aabbb50101\", \"38a43b0dde5f498478eff14f411ed8522902b34b\", \"b72975b4a7a6a89fa6b0ac8182ba28cd41a3eadf\", \"1c8d7682c9d9cdba8127664e192a08298651718f\", \"81ea3fc698df69a7c2fae271072cc1f3e60c03bf\", \"3a3eb056e75c7b34f4084ebc8fd86c923dc627b5\", \"d194b69382454f59a7bc6b62fe32e9f0479fcb67\", \"0615dca156becc048cff86c794756e8435a33974\", \"957149e1e9022ff265021f827d92995ba614a72d\", \"9dd67b94c246112a596ec2e33c6872d3fbd7dbc2\", \"c7658c0df2fbae08f9bb99f777a9c8e8e783e6dc\", \"daca7c49f57ac4f730e2002d50a652d17c6c3dad\", \"5e57c7d11ff65045de51ae082db104588bc980b3\", \"0ea283ac2ae1815a6c0c8984667e7b7ddcbf80b2\", \"6673ae3c817c570dca2dafe2a3afe2a656b0b022\"]}"},{"id":"a57248fd-cdce-4c58-b715-3c98632edf9a","title":"[UI] Fix UnboundLocalError in walkthrough_detail for WALKTHROUGH_IDS analyses","description":"Fix indentation bug at api.py:30601 causing UnboundLocalError when accessing walkthrough pages for analyses in WALKTHROUGH_IDS. Variable 'a' was only assigned in the else branch.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"open","priority":50,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 07:35:07","updated_at":"2026-04-13T10:14:01.179347+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: NO_COMMITS — No commits found referencing task ID; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a57248fd_cdc_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"99bf52d0-5cd8-4e82-9017-0f023ec92ecf","title":"[UI] Build documentation system and evolve SciDEX knowledge base","description":"Build /docs section reusing wiki_pages table (source_repo=SciDEX). System Inspirations page, Five Layers, Three Primitives, guides, architecture docs. Docs help agents evolve the system coherently. 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The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:34:36.186093+00:00","updated_at":"2026-04-13T19:34:36.186093+00:00","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/f5b03fad_a92_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"725a54e19b158771a410519912093f91e227be17\"], \"completion_shas_checked_at\": \"2026-04-13T19:34:36.165885+00:00\"}"},{"id":"c2519a02-1afe-48d8-a236-0357412fc2a1","title":"[UI] Fix hypothesis page timeout - critical demo blocker","description":"The /hypothesis/{id} endpoint is timing out (>15s). This is a critical blocker for the demo since hypothesis pages are the core showcase. Investigate the hypothesis_detail route in api.py and fix performance issues.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:21:31.743960+00:00","updated_at":"2026-04-13T19:21:31.743960+00:00","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/c2519a02_1af_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"e1c38f18e7d16e80652a928f2e6821e5086bbd83\"], \"completion_shas_checked_at\": \"2026-04-13T19:21:31.724835+00:00\", \"completion_shas_missing\": [\"0b0e9dc38412b8285e207cf3947ee96b369e9be8\", \"1aa12f3b4a1151bac35edb5c51f7b022ec2172a4\", \"a0d7199416443590a2061daf4a2cd8665012b915\"]}"},{"id":"172e4e64-a243-4d3d-8ab0-b7cadee521e8","title":"[UI] Fix 500 errors on /notebooks and /atlas pages","description":"Both /notebooks and /atlas return 500 Internal Server Error. /notebooks has an f-string curly brace issue at line ~15678. /atlas also crashes. These are demo-critical pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:05:44.625106+00:00","updated_at":"2026-04-13T19:05:44.625106+00:00","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/172e4e64_a24_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"max_outlook\", \"_stall_requeued_at\": \"2026-04-13 19:03:53\", \"completion_shas\": [\"0c92a60fbb4cc3d74de168b13a457b0519c98a48\"], \"completion_shas_checked_at\": \"2026-04-13T19:05:44.606379+00:00\", \"completion_shas_missing\": [\"07f5f56e0711ab379c13cb188488f1bace7e25fe\", \"ebb732cb40ce8ab2b832700476205883283329f2\", \"afb4e4a40e8f52dba860b6379b599e1f79738302\", \"08c99a181a13fbb6f716adbb3a3cca062bf88aef\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"12777691-adc7-4498-9a7e-b6ea13b1fe13","title":"[UI] Fix NameError in hypothesis page: undefined _get_cached_page","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:05:15.538178+00:00","updated_at":"2026-04-13T19:05:15.538178+00:00","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/12777691_adc_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"max_outlook\", \"_stall_requeued_at\": \"2026-04-13 19:02:28\", \"completion_shas\": [\"a632aa02219750432763fbfd0cd6155b7b7c084e\"], \"completion_shas_checked_at\": \"2026-04-13T19:05:15.519538+00:00\", \"completion_shas_missing\": [\"90076d3c783c0a942d61e40dd1a7641d09c83512\", \"1dbc0850468d8fadd2066fc915d9e80154fe4bf4\", \"c3ce675052165fd2263775bff095d792248be369\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"4bc7e5a2-30fd-4043-8b14-83d3cf5f432d","title":"[UI] Fix SQLite connection leaks causing API hangs","description":"API is hung with 464 open FDs. Root cause: ~40 endpoints open db connections via get_db() but never close them in finally blocks. WAL has 7600+ uncheckpointed frames. Fix: wrap all db operations in try/finally with db.close(), add context manager helper.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:05:12.176501+00:00","updated_at":"2026-04-13T19:05:12.176501+00:00","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/4bc7e5a2_30f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 19:00:54\", \"completion_shas\": [\"442f0a23a6ab2b5220c72eb8bfbe841ce70b826c\"], \"completion_shas_checked_at\": \"2026-04-13T19:05:12.154496+00:00\", \"completion_shas_missing\": [\"a863dcf7f87889c0d8c330499896dfc9ec48bbfb\", \"0defd65ffe9e8f87f3b4ea784ec9aab98c0deb20\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"a80556f8-e41e-478c-9497-81695c47afe2","title":"[UI] Fix 500 errors on /atlas and /notebooks pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":98,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:25:05.515611+00:00","updated_at":"2026-04-16T22:25:05.515611+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a80556f8_e41_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 11:23:27\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"ac596e54-a43a-4ba6-90a6-b7027e6dd0a0","title":"[UI] Fix hypothesis page 22s hang — wiki pages JOIN causes full scan","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":98,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:13:50.778076+00:00","updated_at":"2026-04-16T17:13:50.778076+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ac596e54_a43_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 11:14:23\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"8a478e5c-8e3e-49f0-894d-5e969c2fd97f","title":"[UI] Fix mermaid diagram rendering on hypothesis detail pages","description":"Hypothesis pages contain mermaid code blocks but the mermaid JS library is not loaded, so diagrams render as raw text. Need to: 1) Add mermaid CDN script to hypothesis pages, 2) Parse mermaid code blocks from description markdown, 3) Render them as actual diagrams. 141/149 hypotheses have mermaid diagrams that should be visible.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T10:22:45.937586+00:00","updated_at":"2026-04-16T10:22:45.937586+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8a478e5c_8e3_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_stall_skip_providers\": [\"minimax\", \"codex\"], \"_stall_requeued_by\": \"codex\", \"_stall_requeued_at\": \"2026-04-14 20:04:13\", \"_stall_skip_at\": {\"codex\": \"2026-04-14T20:04:13.029002+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"14ce2ee2-3313-4229-a2cf-506777305d8a","title":"[UI] Fix hypothesis/analysis wiki link timeout — reapply SUBSTR join fix","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":98,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:56:44.544038+00:00","updated_at":"2026-04-13T19:56:44.544038+00:00","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/14ce2ee2_331_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"codex\", \"_stall_requeued_at\": \"2026-04-13 19:43:16\", \"completion_shas\": [\"926b1e12678b05595e542e2321ffed4095ae9188\", \"4321e5a3c460d7ae7f005cca44315dc3bc3d0297\"], \"completion_shas_checked_at\": \"2026-04-13T19:56:44.523595+00:00\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"8e5186fe-55e2-4a4e-9bd7-76b0828a1426","title":"[UI] Fix hypothesis detail pages hanging/timeout (blocks demo)","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":97,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:22:42.953767+00:00","updated_at":"2026-04-13T20:22:42.953767+00:00","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/8e5186fe_55e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"a0c382042ca68015177a13b6c2e8a03fffff30ed\", \"1ceb41cc012dd566c29588a60e29889a1d55503f\"], \"completion_shas_checked_at\": \"2026-04-13T20:22:42.937820+00:00\"}"},{"id":"b40095a9-3798-42e0-8a26-0255bd48f1d5","title":"[UI] Fix hypothesis page 25s load time — remove blocking API call","description":"Hypothesis detail pages take 25+ seconds to load due to a blocking ClinicalTrials.gov API call in _hypothesis_detail_render. Fix: skip the external API call on page load (show cached data or placeholder), batch debate N+1 queries.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-13T18:51:32.207781+00:00","updated_at":"2026-04-13T18:51:32.207781+00:00","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/b40095a9_379_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"cf78c101f55bcc17389c33fd2cdcf801322b5d41\"], \"completion_shas_checked_at\": \"2026-04-13T18:51:32.188136+00:00\"}"},{"id":"c1b5459f-d25a-4475-8da8-851dc413b864","title":"[UI] Add Mol* 3D protein viewer to hypothesis detail pages","description":"Embed Mol* 3D protein structure viewer on hypothesis detail pages for target proteins. When a hypothesis mentions specific proteins (e.g., TREM2, LRP1, APOE), show an interactive 3D viewer using PDB structures. Tasks D16.4 and A17.1 from Quests 16/17.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"71","started_at":"2026-04-17T08:18:47.339198+00:00","completed_at":"2026-04-17T02:25:03.996998+00:00","updated_at":"2026-04-17T08:38:29.022357+00:00","summary":"","completion_notes":"","last_error":"Watchdog bulk: 7 abandonments, queued for repair","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c1b5459f_d25_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:15:48\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"3fbd1ed0-de43-4cf1-9bca-b31449c372f5\", \"_watchdog_repair_created_at\": \"2026-04-17T08:26:37.386174+00:00\"}"},{"id":"d88e9dec-98bb-49fe-beef-466c8dfb2f95","title":"[UI] Fix /atlas 500 error — _cache_page undefined","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":"archived","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"72","started_at":"2026-04-17T07:02:10.273588+00:00","completed_at":"2026-04-17T07:02:09.480466+00:00","updated_at":"2026-04-17T07:03:06.611378+00:00","summary":"","completion_notes":"","last_error":"worker_exit_unclean exit_code=0","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d88e9dec_98b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:51:47\", \"_stall_skip_at\": {\"minimax\": \"2026-04-14T12:51:47.028221+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"997b8179-1a84-4480-b33c-c136c1914a3d","title":"[UI] Add Mol* 3D protein viewer component to hypothesis pages","description":"Embed Mol* (molstar) 3D protein viewer on hypothesis detail pages. For hypotheses with known target proteins/genes, show an interactive 3D structure viewer using PDB IDs. This addresses Quest 16 D16.4 and Quest 17 A17.1. Implementation: add a mol* viewer section to the hypothesis detail page in api.py that maps target_gene to PDB IDs and embeds the Mol* viewer.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T19:38:21.749983+00:00","updated_at":"2026-04-14T19:38:21.749983+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/997b8179_1a8_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 20:57:49\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"6ccc1c98-bd54-422c-a87a-bf4c2763f4b2","title":"[UI] Fix multiple NoneType and empty-sequence crashes in agent/senate performance pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:56:37.772706+00:00","updated_at":"2026-04-13T20:56:37.772706+00:00","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/6ccc1c98_bd5_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"b2661aa2b37b414babb40f748c435185a8088c0e\"], \"completion_shas_checked_at\": \"2026-04-13T20:56:37.756183+00:00\"}"},{"id":"d6623186-98e2-4b1e-855e-9ba3dbec375c","title":"[UI] Fix /atlas 500 error — undefined _cache_page function","description":"The /atlas route returns 500 due to NameError: name '_cache_page' is not defined at api.py:19442 in atlas_page. This is a key demo page (Layer 4 - Living Knowledge Graph) that must work for the end-to-end demo.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-17T13:19:29.917459+00:00","updated_at":"2026-04-17T13:43:15.299203+00:00","summary":"","completion_notes":"","last_error":"Paused after 12 exit-0 runs with no commits on branch=(none)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d6623186_98e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-15 21:41:11\", \"_stall_skip_at\": {\"minimax\": \"2026-04-15T21:41:11.615930+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"a76c7764-3845-40b1-9275-96b8b1289d86\", \"_watchdog_repair_created_at\": \"2026-04-17T13:40:25.977185+00:00\"}"},{"id":"c2d40207-a69a-490e-9e20-e61ad7adc611","title":"[UI] Fix /notebooks 500 error: NoneType not subscriptable in notebooks_page","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T13:35:32.882381+00:00","updated_at":"2026-04-17T13:35:32.882381+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c2d40207_a69_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-15 21:52:13\", \"_stall_skip_at\": {\"minimax\": \"2026-04-15T21:52:13.901769+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"498315b3-03e4-42ab-86b5-aeca11fa39c5\", \"_watchdog_repair_created_at\": \"2026-04-17T13:30:16.223906+00:00\"}"},{"id":"0f4d2691-88e2-4530-bca3-691f17dd7b84","title":"[UI] Fix /notebooks 500 error — stale code reference in running server","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T12:39:36.220222+00:00","updated_at":"2026-04-17T12:41:22.036374+00:00","summary":"","completion_notes":"","last_error":"Paused after 14 exit-0 runs with no commits on branch=(none)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0f4d2691_88e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-15 21:38:13\", \"_stall_skip_at\": {\"minimax\": \"2026-04-15T21:38:13.628830+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"7181120b-0162-4e72-9f05-40eb03f805b4\", \"_watchdog_repair_created_at\": \"2026-04-17T12:39:51.862033+00:00\"}"},{"id":"17bb1bfc-ea9c-4009-87f5-7066705da890","title":"[UI] Fix hypothesis_detail AttributeError in resource usage display","description":"api.py hypothesis_detail() crashes with AttributeError: 'float' object has no attribute 'get' when displaying resource usage. The bug is at lines 15301/15314/15326 where tokens_data/api_data/cpu_data (flat dicts with 'amount'/'cost_usd' keys) are incorrectly iterated via .values() then .get() called on individual floats. Fix: access .get('amount', 0) directly on the dict.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:47:17.257083+00:00","updated_at":"2026-04-15T23:47:17.257083+00:00","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/17bb1bfc_ea9_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:14:05\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"ba870a954630754c23c50e596ac44603f9be2ee3\", \"2df9f80fb48b89d403d8c686a52709a8d1cf2a6d\"], \"completion_shas_checked_at\": \"2026-04-15T23:47:17.239048+00:00\"}"},{"id":"eb11ca2a-6ff3-48db-b6ba-a92f85422ac9","title":"[UI] Add Mol* 3D protein structure viewer to hypothesis pages","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:11:30.225669+00:00","updated_at":"2026-04-15T23:11:30.225669+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/eb11ca2a_6ff_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 00:46:56\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"6e2f0e65-8371-4bfb-ac3f-cb88b7c31658","title":"[UI] Fix /api/graph/{analysis_id} case-sensitivity bug","description":"The /api/graph/{analysis_id} endpoint returns 404 for valid analysis IDs because it converts IDs to lowercase but the SQL query is case-sensitive. This affects 17+ broken links across the site. Fix: Make SQL query case-insensitive using LOWER() on both sides of comparison at api.py:1443.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-15T19:09:21.618005+00:00","updated_at":"2026-04-15T19:09:21.618005+00:00","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/6e2f0e65_837_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 22:32:19\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"40163e5dc4b9fe8398ad6bdef391c92ce08f6f1e\", \"7841e6dea1a18336f280b69d68007c7d2809c9f1\", \"1bef28af9a0421fdc6352b98fdcb24bc9bc67b54\"], \"completion_shas_checked_at\": \"2026-04-15T19:09:21.598103+00:00\"}"},{"id":"b8706bc7-222d-497b-bb39-c74633858345","title":"[UI] Fix /api/graph/{analysis_id} case-insensitive lookup","description":"The /api/graph/{analysis_id} endpoint converts analysis_id to lowercase but queries the database with exact match, causing 404s. Need to use LOWER(id) for case-insensitive matching. Affects 17 broken links across hypothesis and analysis pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T19:08:05.782797+00:00","updated_at":"2026-04-15T19:08:05.782797+00:00","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/b8706bc7_222_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 22:22:26\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"9c933ca3e5749622cd0228a1e2741aa764427add\"], \"completion_shas_checked_at\": \"2026-04-15T19:08:05.689488+00:00\"}"},{"id":"747735c9-3b92-4855-a518-5b92c601aa1d","title":"[UI] Fix case-insensitive analysis ID lookup in /api/graph/{analysis_id} endpoint","description":"The /api/graph/{analysis_id} endpoint (line 1383 in api.py) uses case-sensitive SQL query 'WHERE id=?' which fails for uppercase analysis IDs like 'SDA-2026-04-01-gap-013'. This causes 144 broken links. Fix: Change to 'WHERE LOWER(id)=LOWER(?)' to match pattern used at line 3575. Test: curl /api/graph/SDA-2026-04-01-gap-013 should return graph data instead of 404.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-14T21:09:49.084605+00:00","updated_at":"2026-04-14T21:09:49.084605+00:00","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/747735c9_3b9_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 22:07:05\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"4702c5e2bfe7cdaed2cea9abecd8c54078a57d62\"], \"completion_shas_checked_at\": \"2026-04-14T21:09:49.064905+00:00\"}"},{"id":"84f45f68-44e4-4b5a-b176-dccb68b61e9a","title":"[UI] Fix agent ImportError - tools module conflict","description":"CRITICAL: Agent service failing to start due to tools/ package conflicting with tools.py module. When MethBase was added, a tools/ directory was created, causing Python to import tools/__init__.py instead of tools.py. This breaks all tool imports in agent.py (research_topic, pubmed_search, etc). Impact: No analyses can run. Fix: Either (1) rename tools/ to tools_methbase/ or (2) update tools/__init__.py to re-export all functions from parent tools.py\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T20:51:42.690801+00:00","updated_at":"2026-04-14T20:51:42.690801+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/84f45f68_44e_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 22:17:15\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"3c578c96-0429-4fad-9982-209926aa9bdf","title":"[UI] Fix Python import conflict: tools/ directory shadowing tools.py","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T20:50:41.792704+00:00","updated_at":"2026-04-14T20:50:41.792704+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3c578c96_042_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 22:16:48\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"bd7a7fc1-bcc4-4248-a3f4-ca0c1c5cdd95","title":"[UI] Fix artifacts gallery 500 error and target detail TypeError","description":"Fix UnboundLocalError in artifacts_gallery (line 7201, caption variable) and TypeError in target_detail (line 15141, str vs int comparison)\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-14T01:20:51.242396+00:00","updated_at":"2026-04-14T01:20:51.242396+00:00","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/bd7a7fc1_bcc_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"ce9050f1d47b8485c2cd0e436ed474c76dbb02f5\", \"3f0c0fd0015a75af316813df29d3b11571a60b89\", \"50e4a38d9349fba95ead818fbe9093fedbe3d1f9\", \"ee9380dc7c7f22a2ace80e0de66a4ac4aae6df69\", \"d943ed4192e81f55510f29a85867d8dc33b7271d\"], \"completion_shas_checked_at\": \"2026-04-14T01:20:51.222366+00:00\"}"},{"id":"fe943db4-2d3d-4364-b083-3f1da78f9c55","title":"[UI] Fix /atlas 500 error — _cache_page NameError","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:55:54.802876+00:00","updated_at":"2026-04-13T23:55:54.802876+00:00","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/fe943db4_2d3_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"c1f8945cd177a70ed43fef5265557f56d4ee600c\"], \"completion_shas_checked_at\": \"2026-04-13T23:55:54.785463+00:00\"}"},{"id":"29f3dddc-9c22-432e-9db1-f351b95166f1","title":"[UI] Fix /notebooks page returning HTTP 500","description":"The /notebooks page returns a 500 Internal Server Error. This is a critical demo bug since notebooks are key artifacts. Need to debug and fix.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-13T23:48:59.785121+00:00","updated_at":"2026-04-13T23:48:59.785121+00:00","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/29f3dddc_9c2_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"5b1dec0b4262172f03e4aba224d7a1da1cdcc388\"], \"completion_shas_checked_at\": \"2026-04-13T23:48:59.768594+00:00\", \"completion_shas_missing\": [\"d8ea08c1c4cccfc2149f561e579a7b0314a4b116\", \"85649cdf6c806c88a71b92aa85fc2a1b0be159e4\"]}"},{"id":"20673928-ba1b-442a-81b5-e4c9d2402f52","title":"[UI] Fix broken /atlas.html links in navigation — should be /atlas","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:48:28.165301+00:00","updated_at":"2026-04-13T23:48:28.165301+00:00","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/20673928_ba1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"477593e7e88f29d980c3da12de6c8937db40bfcb\", \"4deca3c1d57c47af429afd4405d57674dd69497e\"], \"completion_shas_checked_at\": \"2026-04-13T23:48:28.146781+00:00\"}"},{"id":"5ed01f64-9a78-465b-9090-9495c312adf9","title":"[UI] Fix Unicode Greek characters in hypothesis mermaid diagrams","description":"70+ hypotheses have Unicode Greek characters (α, β, γ, κ, etc.) in their mermaid diagram blocks, which breaks client-side rendering. Includes top-3 hypotheses (h-61196ade score 0.85, h-de0d4364 0.83, h-9e9fee95 0.82). Replace Greek chars with ASCII equivalents (alpha, beta, gamma, kappa) in mermaid blocks only, preserving them in regular text. Uses regex to find mermaid blocks and substitute characters.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-13T23:47:52.353279+00:00","updated_at":"2026-04-13T23:47:52.353279+00:00","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/5ed01f64_9a7_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"a0986ecdff6180a7732839976f018b48e1543ec3\", \"cacf5a9bdc3037ee75ef9e29a460ff567ecb8966\", \"fab41223fc256cd02dc98e2004a728d6fcd48038\"], \"completion_shas_checked_at\": \"2026-04-13T23:47:52.334784+00:00\", \"completion_shas_missing\": [\"0cafc1e72931ceb4f100b47023e81996be3f857d\"]}"},{"id":"f259e7f0-9efd-458d-8eff-01ce21c81eaf","title":"[UI] Harden senate_performance_page against empty/null data and fix HTML escaping in notebooks_page","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:46:48.183596+00:00","updated_at":"2026-04-13T23:46:48.183596+00:00","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/f259e7f0_9ef_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"b70152701d33df091c1ae2b09bcb10664bcf6ecb\", \"ae6ef9de182e9f49654513426f8d3c2212a0c497\"], \"completion_shas_checked_at\": \"2026-04-13T23:46:48.163816+00:00\"}"},{"id":"eb0e09ed-9d37-42a8-8524-74463d079354","title":"[UI] Fix NoneType error in entity_detail route","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:15:30.811655+00:00","updated_at":"2026-04-13T23:15:30.811655+00:00","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/eb0e09ed_9d3_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"9ec03067c5a16119d40cc685f1e1ccee7bc07030\", \"285585e62b625b442ed709bc05d483bb5a7e7b22\"], \"completion_shas_checked_at\": \"2026-04-13T23:15:30.794144+00:00\"}"},{"id":"936fae01-e371-454b-8ff6-b71aac05ce96","title":"[UI] Optimize API response times — add caching for heavy endpoints","description":"Load avg 51, 74 concurrent connections, pages timing out. Add response caching for expensive DB queries on /senate, /forge, /atlas, /resources, /demo, /agents, /artifacts which all take >2s.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-13T23:08:28.984977+00:00","updated_at":"2026-04-13T23:08:28.984977+00:00","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/936fae01_e37_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"completion_shas\": [\"da9cc3013a45ef21ef62a0acd82932c0a2d6e8c6\", \"7aace34d3581e6a89b5c472280186a56941cb698\"], \"completion_shas_checked_at\": \"2026-04-13T23:08:28.965446+00:00\"}"},{"id":"87cab3b8-d87e-4aca-bbb3-e5a96ca99e9a","title":"[UI] Fix case-insensitive analysis ID lookups in API endpoints","description":"The /api/graph/{analysis_id} endpoint returns 404 for valid analysis IDs due to case sensitivity mismatch. Database stores IDs in lowercase (e.g., 'sda-2026-04-01...') but API receives uppercase requests (e.g., 'SDA-2026-04-01...'). Affects 144 broken links across the site. Fix: Use LOWER(id) in SQL queries or normalize input.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-13T22:02:40.901873+00:00","updated_at":"2026-04-13T22:02:40.901873+00:00","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/87cab3b8_d87_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"d4fd9a93b0d8d1779c8f7dd4da3cfdb917a052d7\", \"bf2a3e18dc8bcb90cea96d26dc67aa1616e52ce5\"], \"completion_shas_checked_at\": \"2026-04-13T22:02:40.882206+00:00\"}"},{"id":"a60027d6-027b-4b31-9667-08e85da27c2b","title":"[UI] Add SciDEX logo/icon home link and shared navigation menu to all pages","description":"Add to nav_html() in api.py:\n1. SciDEX icon/logo (text-based is fine: \"SciDEX\" in gradient) as leftmost nav element, always links to /\n2. Hamburger menu for mobile that expands to show all nav links\n3. Group nav links: Main (Dashboard, Analyses, Exchange), Knowledge (Wiki, Graph, Atlas), System (Senate, Quests, Resources, Forge), Info (How, Pitch)\n4. Active page highlight (already exists but improve)\n5. Ensure this shared nav appears on ALL pages including static HTML pages\nThis is the highest priority UI task — do it first and simple.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-13T21:26:45.113366+00:00","updated_at":"2026-04-13T21:26:45.113366+00:00","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\": [\"890e8ec677721217b3bcbb5bbbf0fe7eb9879352\"], \"completion_shas_checked_at\": \"2026-04-13T21:26:45.097028+00:00\"}"},{"id":"1ad717d4-0adb-492f-8df6-bf86ecd1bf64","title":"[UI] Fix 500 errors on /atlas and /notebooks pages","description":"The /atlas page returns 500 due to NameError: _cache_page not defined. The /notebooks page returns 500 due to NoneType subscript error. Both are critical demo pages that need to work.","status":"archived","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 00:45:42","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1ad717d4_0ad_spec.md","provider":"any","payload_json":"{}"},{"id":"5b0d6a48-62ee-4c51-ab6f-9aacfe017d85","title":"[UI] Fix analysis_detail notebooks query - column name mismatch","description":"Fix line 1291 in api.py: analysis_detail() uses 'analysis_id' but database column is 'associated_analysis_id'. Causing 500 errors on /analysis/* routes. Simple one-line fix.","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 05:55:15","updated_at":"2026-04-02T05:54:03.938233+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5b0d6a48_62e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"98b8a425-bb25-4733-9034-bea77bd70aa6","title":"[UI] Fix /analyses/ page timeout — optimize slow correlated subqueries","description":"The /analyses/ page takes 20+ seconds to load because of correlated subqueries with LOWER() in the main analyses listing query. Replace with JOINs or precomputed counts. Demo-critical page linked from demo walkthrough.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:12:33.355753+00:00","updated_at":"2026-04-14T02:12:33.355753+00:00","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/98b8a425_bb2_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"225bdf35fa92259367d9f176a3cbd55fe4031abd\", \"81f93f31bd3a265c9a829e9975edbd763a6a25f8\"], \"completion_shas_checked_at\": \"2026-04-14T02:12:33.336681+00:00\"}"},{"id":"341e9fcc-c42d-4786-89e0-76d619086b79","title":"[UI] Optimize /entity page query performance (2.2s -> <500ms)","description":"The /entity/TREM2 page takes 2.2 seconds to load. Likely has N+1 queries or unindexed lookups. Profile and optimize the SQL queries in the entity detail handler to bring load time under 500ms. This is a key demo page linked from /demo.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T01:08:55.945373+00:00","updated_at":"2026-04-16T01:08:55.945373+00:00","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/341e9fcc_c42_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 03:33:19\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"8644e8c9f20c283644c55e0f4fa446c1296fe7a0\", \"2fd5e89a80b47711fe494bdbbf610b2692a0646d\", \"a81809576c1478e9d464a1dfc847f510d974f8c1\"], \"completion_shas_checked_at\": \"2026-04-16T01:08:55.927031+00:00\"}"},{"id":"48b9bc76-9296-4867-8e45-31f263e57a02","title":"[UI] Fix demo page broken links and template bugs","description":"Fix href=${r.link} template bug, /atlas.html→/atlas link, and verify all demo page links work\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T04:10:49.872978+00:00","updated_at":"2026-04-14T04:10:49.872978+00:00","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/48b9bc76_929_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"c419417ffe26d0e8c9cb644fd98405adf46cb6be\"], \"completion_shas_checked_at\": \"2026-04-14T04:10:49.852962+00:00\"}"},{"id":"0e3fc944-94b2-4b76-b5b7-7ecefc1b2d13","title":"[UI] Fix nav links pointing to /atlas.html instead of /atlas","description":"Navigation links across the site point to /atlas.html (old static page) instead of /atlas (dynamic Atlas dashboard with stats, entity browser, edge type breakdowns). This misdirects users to an inferior page. Fix all nav references.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:58:27.693125+00:00","updated_at":"2026-04-14T03:58:27.693125+00:00","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/0e3fc944_94b_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"ddbbf8e77d86e521b839ddf2ce18c6957526904b\"], \"completion_shas_checked_at\": \"2026-04-14T03:58:27.674482+00:00\"}"},{"id":"099ca612-357f-4844-b518-b3c35495cade","title":"[UI] Fix hypothesis detail page timeout — remove blocking ClinicalTrials.gov API call","description":"The /hypothesis/{id} page has a blocking call to ClinicalTrials.gov API with only a 5s timeout, causing page loads to take 5+ seconds or timeout entirely. The visual regression test also times out on this page. Solution: remove the live-fetch and rely on cached clinical_trials data, or move to async loading.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:24:01.058062+00:00","updated_at":"2026-04-14T03:24:01.058062+00:00","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/099ca612_357_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"57bc798ac4e209edea1f63ff0961436f315470a3\"], \"completion_shas_checked_at\": \"2026-04-14T03:24:01.039895+00:00\"}"},{"id":"34b64eff-cac8-4a22-af1c-bc0406b07a50","title":"[UI] Add pathway diagrams and evidence strength matrix to hypothesis detail pages","description":"Quest 16/17: Enhance hypothesis detail pages with mermaid pathway diagrams rendered from hypothesis mechanism data, and visual evidence strength matrices showing citation quality vs relevance. These are the hero pages visitors click 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":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:17:26.404961+00:00","updated_at":"2026-04-14T03:17:26.404961+00:00","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/34b64eff_cac_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"8dc4adfc097606968b052c812f71dc9ffa99edb7\"], \"completion_shas_checked_at\": \"2026-04-14T03:17:26.388419+00:00\"}"},{"id":"60a1a63f-176a-4d4e-a005-16ef9ce70889","title":"[UI] Fix /notebooks route returning 500 Internal Server Error","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T07:38:14.379536+00:00","updated_at":"2026-04-16T07:38:14.379536+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/60a1a63f_176_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"fa8fe4d7-5986-4a9f-af9c-21dc664f5bc4","title":"[UI] Fix /experiments 500 error and /hypotheses 404","description":"The /experiments page returns 500 Internal Server Error and /hypotheses returns 404. Both are linked from the homepage and are critical demo pages. Previous fix attempt (445f3420) did not resolve.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T06:51:38.760903+00:00","updated_at":"2026-04-16T06:51:38.760903+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/fa8fe4d7_598_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"548af5d2-7a43-41ce-b2d0-4d777f83ffc5","title":"[UI] Add DB connection cleanup middleware to prevent file descriptor exhaustion","description":"The #1 production error is 'unable to open database file' (19K/hr) caused by get_db() creating connections that are never closed. Add FastAPI middleware to auto-close DB connections after each request.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T05:54:09.272596+00:00","updated_at":"2026-04-16T05:54:09.272596+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/548af5d2_7a4_spec.md","provider":"any","payload_json":"{}"},{"id":"1c986ccf-13cd-4d39-b3de-e7d7d60b5683","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T05:51:46.253035+00:00","updated_at":"2026-04-16T05:51:46.253035+00:00","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/1c986ccf-13c_ui_improve_analyses_page_add_cards_with_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 9}, \"completion_shas\": [\"6fbeaff2201e10ee05b632e770374bc4ff5a36b1\"], \"completion_shas_checked_at\": \"2026-04-16T05:51:46.212127+00:00\"}"},{"id":"e14a3683-4380-4651-9a9b-c06bda733625","title":"[UI] Fix /notebooks 500 error - TypeError in entity parsing","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T05:16:51.791764+00:00","updated_at":"2026-04-16T05:16:51.791764+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e14a3683_438_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"11ba0ced-cf7d-4eca-b377-b18820985ab0","title":"[UI] Build /showcase page — curated top analyses with rich cards","description":"The /showcase link exists in sidebar nav but returns 404. Build a polished showcase page highlighting top analyses with debate scores, key findings, and visual appeal for demo purposes.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T04:34:09.267583+00:00","updated_at":"2026-04-16T04:34:09.267583+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/11ba0ced_cf7_spec.md","provider":"any","payload_json":"{}"},{"id":"bb296f89-43d2-4831-9e09-500d17976cb1","title":"[UI] Fix duplicate route definitions in api.py causing dead routes","description":"api.py has duplicate route definitions for /agora, /api/coverage, /api/feedback, /api/webhooks, /hypotheses/{hyp_id}, /status. FastAPI uses the first definition and ignores later ones. Need to remove duplicates or rename the conflicting routes.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T04:28:32.138421+00:00","updated_at":"2026-04-16T04:28:32.138421+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/bb296f89_43d_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"a7934e54-4aa8-46fc-9dd9-e8bfa64466f4","title":"[UI] Fix 500 errors on entity pages due to NULL field access","description":"Entity pages like /entity/CASP1 crash with TypeError: NoneType not subscriptable. Multiple places in _entity_detail_render access DB fields without None guards: h[title][:60], h[composite_score] > 0.7, html.escape(e[relation]), etc. Fix all None access patterns.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T04:10:25.723690+00:00","updated_at":"2026-04-16T04:10:25.723690+00:00","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/a7934e54_4aa_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"f5224f3cbfe132399bf5cfd64ca9fdf80a9c2be0\"], \"completion_shas_checked_at\": \"2026-04-16T04:10:25.705003+00:00\"}"},{"id":"6d789cd7-0823-427d-892f-f199633a6a99","title":"[UI] Build /experiments listing page for 188 experiments","description":"Quest 10/16: The /experiments route returns 404. There are 188 experiments in the DB with no listing page. Individual experiment detail pages exist at /experiment/{id}. Need a listing page similar to /analyses with cards, search, filtering by type/disease, and key metrics.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T04:09:49.892298+00:00","updated_at":"2026-04-16T04:09:49.892298+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6d789cd7_082_spec.md","provider":"any","payload_json":"{}"},{"id":"7fc7b480-0952-413b-a288-f9de26909835","title":"[UI] Render stored pathway_diagram mermaid on hypothesis pages","description":"110 hypotheses have curated mermaid pathway diagrams stored in the pathway_diagram DB field (graph TD format). These are NOT rendered on hypothesis pages - only auto-generated KG-edge diagrams are shown. Add rendering of the stored pathway_diagram as a 'Curated Mechanism Diagram' section above the auto-generated one, with proper mermaid initialization.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T04:05:56.473414+00:00","updated_at":"2026-04-16T04:05:56.473414+00:00","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/7fc7b480_095_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"4e8818126fde97d282431cc147bb3fbda613318d\"], \"completion_shas_checked_at\": \"2026-04-16T04:05:56.445771+00:00\"}"},{"id":"46597930-d558-49ef-a448-8eaaf1d05381","title":"[UI] Fix hypothesis page performance - reduce DB queries and optimize rendering","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T04:02:09.044391+00:00","updated_at":"2026-04-16T04:02:09.044391+00:00","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/46597930_d55_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"18973443037245856eb63de66583228b220f8ec8\"], \"completion_shas_checked_at\": \"2026-04-16T04:02:09.026016+00:00\"}"},{"id":"0f2c20d4-e85d-45d4-8a26-31d366cb1a48","title":"[UI] Fix slow hypothesis page rendering (3-7s, target <2s)","description":"Hypothesis detail pages take 3-7 seconds to render, exceeding the 2s quality bar. Profile and optimize the /hypothesis/{id} endpoint to achieve sub-2s load times.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T03:50:34.520896+00:00","updated_at":"2026-04-16T03:50:34.520896+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0f2c20d4_e85_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"727c5c9f-5bdd-4cb1-8d85-e45abd9fc7e7","title":"[UI] Fix slow hypothesis detail page load (>3s, target <2s)","description":"Hypothesis detail pages take 3.3s to load (e.g. /hypothesis/h-de0d4364). Quality bar requires <2s. Profile the route handler to find bottlenecks and optimize. This is critical for demo showcase - hypothesis pages are the hero pages visitors click 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":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T03:13:52.901839+00:00","updated_at":"2026-04-16T03:13:52.901839+00:00","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/727c5c9f_5bd_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"ffdac4c9cb2fb6fd6ba0fb205daf3205b1fbd9a0\", \"87b8d95057a19893033a32ef5f186156fae4363c\"], \"completion_shas_checked_at\": \"2026-04-16T03:13:52.886945+00:00\"}"},{"id":"a831d3bc-17a1-4efb-9102-9014ff952dbc","title":"[UI] Fix /exchange page timeout — optimize slow queries and rendering","description":"The /exchange page times out. The sync handler builds enormous HTML server-side with multiple DB queries including correlated subqueries in market movers. Optimize the queries and rendering.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T03:13:32.083424+00:00","updated_at":"2026-04-16T03:13:32.083424+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a831d3bc_17a_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"e48c060e-124a-41e0-9e59-946602b03607","title":"[UI] Ensure all 5 layer pages load without errors and have meaningful content","description":"Spot-check: /agora (debates), /exchange (hypotheses), /forge (tools), /atlas (KG), /senate (governance). Fix any 500/502 errors, broken layouts, or empty content areas.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T02:05:19.540362+00:00","updated_at":"2026-04-16T02:05:19.540362+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"54d54ecc-ee02-4847-a1ec-292f8138b08a","title":"[UI] Polish dashboard with live metrics and demo highlights","description":"Quest 10 demo priority: Enhance the main dashboard (/) with better live metrics display, highlight the top 3 demo hypotheses prominently, add quick links to demo-relevant analyses and notebooks. The homepage is the first thing visitors see.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T10:53:18.504099+00:00","updated_at":"2026-04-16T10:53:18.504099+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/54d54ecc_ee0_spec.md","provider":"any","payload_json":"{}"},{"id":"60d315c6-3c1f-4b51-9f8e-d1d0f104a5c6","title":"[UI] Global search bar with autocomplete in nav — Quest 8 S8.2","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:44:11.782637+00:00","updated_at":"2026-04-16T10:44:11.782637+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/60d315c6_3c1_spec.md","provider":"any","payload_json":"{}"},{"id":"a11c3add-3d48-4de7-8ee1-5ecfea4176f6","title":"[UI] Enrich dashboard with live stats, top hypotheses, and recent activity feed","description":"Dashboard currently shows minimal info. Add: platform stats (hypotheses, analyses, targets, experiments, wiki pages, KG edges), top 5 hypotheses by score with mini-cards, recent 5 analyses with status, and quick action links. Makes the dashboard a compelling landing page for demos.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:41:32.986088+00:00","updated_at":"2026-04-16T10:41:32.986088+00:00","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/a11c3add_3d4_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"04a0e5a2-c968-4fbf-b5ab-df44c71a91d0","title":"[UI] Render gene_expression_context on hypothesis pages","description":"69 hypotheses have rich gene expression context data (markdown with Allen Human Brain Atlas data, GTEx FPKM values, cell-type expression patterns) stored in gene_expression_context DB field. This data is NOT rendered anywhere on hypothesis pages. Add a Gene Expression Context section to hypothesis detail pages, rendering the markdown content.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:28:17.821860+00:00","updated_at":"2026-04-16T10:28:17.821860+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/04a0e5a2_c96_spec.md","provider":"any","payload_json":"{}"},{"id":"aa0bc26e-281b-48f1-a599-f0a7e628e077","title":"[UI] Fix entity page 500 — NoneType subscript error on papers with NULL authors/title/journal","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":"2026-04-16T14:16:43.428763+00:00","updated_at":"2026-04-16T14:16:43.428763+00:00","summary":"","completion_notes":"Investigated entity page (_entity_detail_impl) papers rendering. Found proper NULL guards already in place at lines 46374-46379: (p.get('authors') or 'Unknown'), (p.get('title') or 'Untitled'), (p.get('journal') or ''). These or-defaults handle NULL authors correctly (None or 'Unknown' = 'Unknown'). Database has 5 papers with NULL authors but code handles them safely. No code change needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/aa0bc26e_281_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"909c0688-ec05-4d81-9048-2f9d2b900c74","title":"[UI] Add search box to navigation bar for quick search from any page","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T14:14:38.466783+00:00","updated_at":"2026-04-16T14:14:38.466783+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/909c0688_ec0_spec.md","provider":"any","payload_json":"{}"},{"id":"c8c5076c-b3a4-4ac5-bc28-6a52ed4d87fc","title":"[UI] Add /demo/walkthrough redirect and fix /notebooks 500 error in production","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":"2026-04-16T14:14:34.811107+00:00","updated_at":"2026-04-16T14:14:34.811107+00:00","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/c8c5076c_b3a_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"609f3013-8d3b-4a1b-896a-107c53ed1fe3","title":"[UI] Add API auto-reload on code changes via uvicorn --reload","description":"The scidex-api systemd service runs uvicorn without --reload. When api.py is updated via git merges, the running process still serves stale code, causing 500 errors on /atlas and /notebooks. Fix: add --reload to the uvicorn command in the systemd service. This will auto-restart when api.py changes, eliminating stale-code 500s.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T14:12:24.506405+00:00","updated_at":"2026-04-16T14:12:24.506405+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/609f3013_8d3_spec.md","provider":"any","payload_json":"{}"},{"id":"ac43d84f-7c45-4df9-947c-3fb50f8fffd4","title":"[UI] Optimize entity page queries — most entities taking 0.8-1.6s","description":"Entity pages for APOE (1.6s), APP (1.5s), MAPT (1.3s), BDNF (1.2s), LRP1/NLRP3 (1.1s) are too slow. Profile and optimize SQL queries on the entity detail page. Target: <500ms for all entities. Previous optimization on TREM2 worked (cached at 3ms) but the optimizations need to apply to all entities.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T14:08:27.333578+00:00","updated_at":"2026-04-16T14:08:27.333578+00:00","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/ac43d84f_7c4_spec.md","provider":"any","payload_json":"{}"},{"id":"62b509d8-facc-441d-b39d-d8a7b4e469cc","title":"[UI] Fix /notebooks 500 error — StaticFiles mount conflicts with page route","description":"The app.mount('/notebooks', StaticFiles(...)) on line 17640 overrides the @app.get('/notebooks') HTML page route on line 14657, causing a 500. Fix by changing the static files mount path to /notebooks-files or similar to avoid the conflict.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T14:06:13.890036+00:00","updated_at":"2026-04-16T14:06:13.890036+00:00","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/62b509d8_fac_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"7b92e4e2-470a-4830-ab71-5b2fe8a1e291","title":"[UI] Add global search bar with autocomplete to navigation on all pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T14:02:42.865082+00:00","updated_at":"2026-04-16T14:02:42.865082+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7b92e4e2_470_spec.md","provider":"any","payload_json":"{}"},{"id":"0c12f008-ddbc-4745-af7f-7deca66b8d50","title":"[UI] Render mermaid diagrams in hypothesis descriptions instead of showing raw code","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":"2026-04-16T13:56:36.463494+00:00","updated_at":"2026-04-16T13:56:36.463494+00:00","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/0c12f008_ddb_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}}"},{"id":"b8fe5306-8e4d-429c-a2af-99184c6b5135","title":"[UI] Fix /showcase page — route defined but not active in running API","description":"The /showcase endpoint is defined in api.py at line 14264 but returns 404 because it was added after the last API restart. Verify the route code is correct and will work once the API is restarted. Also check for other routes that may be defined but not active.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T13:41:54.048641+00:00","updated_at":"2026-04-16T13:41:54.048641+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b8fe5306_8e4_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"cc807612-4836-4b40-8a84-ed84f22bf32e","title":"[UI] Remove duplicate route definitions in api.py","description":"api.py has 5 duplicate route definitions: /agora, /api/coverage, /debates, /hypotheses/{hyp_id}, /status. FastAPI uses first definition, making subsequent ones unreachable dead code. Removed 431 lines. Branch: worktree-fix-debates-dupe\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T13:37:21.634491+00:00","updated_at":"2026-04-16T13:37:21.634491+00:00","summary":"","completion_notes":"Verified cea4f100d is on origin/main — 425 lines of duplicate route definitions already removed from api.py","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/cc807612_483_spec.md","provider":"any","payload_json":"{}"},{"id":"a41440f1-74d0-46ae-93ed-93eb1e4fcb61","title":"[UI] Build /targets listing page for 150 drug targets","description":"Quest 2/10: 150 targets exist with druggability data but /targets returns 404. Need a listing page with cards showing gene symbol, druggability bucket, target class, score, and hypothesis count.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T13:33:56.040811+00:00","updated_at":"2026-04-16T13:33:56.040811+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a41440f1_74d_spec.md","provider":"any","payload_json":"{}"},{"id":"fcf2de19-e005-45d8-ab57-b2459f930d2d","title":"[UI] Add hypothesis comparison modal to Exchange page","description":"Quest 2/16: Exchange page already has compare checkboxes (compare-cb class) but no comparison modal/panel. Add a comparison view that shows 2-3 selected hypotheses side-by-side with scores, evidence counts, and pathway diagrams.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T13:33:39.443568+00:00","updated_at":"2026-04-16T13:33:39.443568+00:00","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/fcf2de19_e00_spec.md","provider":"any","payload_json":"{}"},{"id":"a31c1245-2c2d-4da0-a47e-b147a2c0c078","title":"[UI] Optimize hypothesis detail page — reduce 17 DB queries and add connection pooling","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":"2026-04-16T13:32:03.840030+00:00","updated_at":"2026-04-16T13:32:03.840030+00:00","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/a31c1245_2c2_spec.md","provider":"any","payload_json":"{}"},{"id":"32db7caa-c28e-46cf-baf9-59e4eae03b86","title":"[UI] Fix TypeError in entity page edge rendering","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":"2026-04-16T13:27:36.448072+00:00","updated_at":"2026-04-16T13:27:36.448072+00:00","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/32db7caa_c28_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"763524e5-035c-4acd-8677-3937ec917ab4","title":"[UI] Add Open Graph meta tags for social sharing previews","description":"No Open Graph (og:title, og:description, og:image) or Twitter Card meta tags exist on any page. When SciDEX URLs are shared on social media/Slack/etc, no preview appears. Add OG meta tags to hypothesis pages, analysis pages, wiki pages, and the homepage for rich link previews.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T13:27:05.419159+00:00","updated_at":"2026-04-16T13:27:05.419159+00:00","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/763524e5_035_spec.md","provider":"any","payload_json":"{}"},{"id":"5e083da5-03ea-4567-b98f-9bdf4123ad22","title":"[UI] Fix link checker to handle transient 502 errors","description":"Problem: Link checker creates P90-P100 tasks for 502 errors during API restarts, creating task spam (18K+ false positives in last run).\n\nRoot cause: check_link() doesn't retry transient failures or check API health before crawling.\n\nFix needed:\n1. Add retry logic with exponential backoff for 502/503 errors\n2. Check /api/status before starting full crawl\n3. Filter 502 errors from high-priority task creation\n4. Add --verify flag to re-check broken links before creating tasks\n\nAcceptance:\n- 502 errors retried 3x with backoff before reporting\n- Link checker skips or defers crawl if API unhealthy\n- No P90+ tasks created for transient infrastructure issues\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T13:10:54.724224+00:00","updated_at":"2026-04-16T13:10:54.724224+00:00","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/5e083da5_03e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"f949d28f-175e-4e2e-8e00-96ad096f8453","title":"[UI] Add universal search bar with autocomplete to navigation","description":"Add a compact search input to the top nav bar that queries /api/search?q=...&limit=5 on keyup (debounced 300ms), showing a dropdown with type-grouped results (hypotheses, wiki, entities). Clicking a result navigates to it. This is Quest 8 S8.2 - critical for demo experience.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T13:05:57.786338+00:00","updated_at":"2026-04-16T13:05:57.786338+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f949d28f_175_spec.md","provider":"any","payload_json":"{}"},{"id":"9e24306d-1adc-48c2-8a1e-e1501aec575f","title":"[UI] Add --workers 2 to uvicorn for parallel request handling","description":"Single uvicorn worker causes all requests to serialize. Under load from health checkers and crawlers, pages stall 5-10s waiting in queue. Adding --workers 2 to /etc/systemd/system/scidex-api.service would allow parallel request processing. Requires human operator to restart API.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T13:03:49.783219+00:00","updated_at":"2026-04-16T13:03:49.783219+00:00","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/9e24306d_1ad_spec.md","provider":"any","payload_json":"{}"},{"id":"6ae96e37-21a8-4ed5-bf2f-33ea2493fcaa","title":"[UI] Add /dashboard page with platform overview stats and quick links","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":"2026-04-16T12:56:34.830889+00:00","updated_at":"2026-04-16T12:56:34.830889+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6ae96e37_21a_spec.md","provider":"any","payload_json":"{}"},{"id":"c15f105f-4e1b-4708-aa00-3ff847c35a2e","title":"[UI] Fix /api/graph/{analysis_id} endpoint returning 404s","description":"Link checker found 17 broken links to /api/graph/{analysis_id}. Two analyses (SDA-2026-04-02-gap-tau-prop-20260402003221 and SDA-2026-04-01-gap-lipid-rafts-2026-04-01) exist in DB with completed status but endpoint returns 404. Need to fix endpoint to properly handle case-insensitive analysis ID lookup and return graph 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":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T12:35:22.642622+00:00","updated_at":"2026-04-16T12:35:22.642622+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c15f105f_4e1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"1d56aaa3-9774-4144-aa84-e47eb58e3f63","title":"[UI] Create missing Senate dashboard frontend","description":"The /api/coverage endpoint exists and returns orphan work metrics, but site/senate.html is missing (returns 404). Need to create the Senate dashboard HTML page to display coverage monitoring with auto-refresh. This was marked complete in task 6d500cfd but the deliverable wasn't actually created.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 04:06:13","updated_at":"2026-04-02T04:02:44.439178+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1d56aaa3_977_spec.md","provider":"any","payload_json":"{}"},{"id":"q10-u1-DB649BF2","title":"[UI] Polish all pages for demo readiness","description":"Audit all pages (/,/analyses/,/exchange,/wiki,/graph,/senate,/quests,/resources,/forge,/gaps) for: consistent nav, no 500 errors, no broken links, fast loading, consistent card/table styling. Fix any issues found. Ensure hamburger menu works.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:47:50","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":"0dce4c3a-5624-4968-aa75-8b18e4433d87","title":"[UI] Add breadcrumbs and back-navigation to all detail pages","description":"Entity, hypothesis, analysis, experiment, and target pages should have breadcrumbs showing navigation path.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T23:55:08.735448+00:00","updated_at":"2026-04-16T23:55:08.735448+00:00","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/0dce4c3a-562_ui_add_breadcrumbs_and_back_navigation_spec.md","provider":"any","payload_json":"{}"},{"id":"60827c16-12ec-4c7a-98f6-aa541b819eb0","title":"[UI] Fix analysis detail pages to show wiki cross-links from improved query","description":"The wiki cross-link query was fixed for hypothesis pages (JOIN directly from artifact_links to wiki_pages instead of going through artifacts table). Verify the fix also works correctly on analysis detail pages and experiment detail pages by testing with TestClient.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T23:48:09.091640+00:00","updated_at":"2026-04-16T23:48:09.091640+00:00","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/60827c16_12e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"a1c9c112e\"], \"completion_shas_checked_at\": \"2026-04-16T23:47:55.065962+00:00\"}"},{"id":"993baf5b-a932-4a30-a8e7-d8681d80317d","title":"[UI] Fix broken CRISPR walkthrough link from demo page — add to WALKTHROUGH_IDS","description":"The demo page links to /walkthrough/SDA-2026-04-02-gap-crispr-neurodegeneration-20260402 but it returns 404 because the analysis is not in WALKTHROUGH_IDS. Add it.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T23:38:55.497974+00:00","updated_at":"2026-04-16T23:38:55.497974+00:00","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/993baf5b_a93_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"5408489e-930a-498d-b069-9a67f2dbfcdc","title":"[UI] Optimize /gaps page query performance (1.4s)","description":"The /gaps page takes 1.4 seconds to load. Profile and optimize SQL queries.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T23:22:22.126932+00:00","updated_at":"2026-04-16T23:22:22.126932+00:00","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/5408489e_930_spec.md","provider":"any","payload_json":"{}"},{"id":"5320432c-bf55-4ff6-b957-5ad5b0f93e41","title":"[UI] Fix /gaps page slow loading (1.8s) — optimize queries","description":"The /gaps page takes 1.8s to load, close to the 2s quality bar. Investigate and optimize the SQL queries to bring load time under 0.5s.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T23:02:47.801048+00:00","updated_at":"2026-04-16T23:02:47.801048+00:00","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/5320432c_bf5_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"d5c7c383-2ed0-446c-80ab-a79203fa793e","title":"[UI] Add /status system health page with DB stats, service health, and recent activity","description":"Add a public /status page showing: DB size, table counts, service health, recent analyses/debates, storage usage, uptime. Useful for demo and operations monitoring.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:37:50.957458+00:00","updated_at":"2026-04-16T22:37:50.957458+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d5c7c383_2ed_spec.md","provider":"any","payload_json":"{}"},{"id":"ef9d02c5-8631-460c-b2a8-d27229648684","title":"[UI] Search page: support URL parameters for deep linking","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":"2026-04-16T21:29:37.128902+00:00","updated_at":"2026-04-16T21:29:37.128902+00:00","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/ef9d02c5_863_spec.md","provider":"any","payload_json":"{}"},{"id":"efacabd6-da8b-434d-961b-566151158b3f","title":"[UI] Add /experiments listing page with filterable table","description":"Create the /experiments endpoint showing all 188 experiments in a searchable, filterable table. Include status, title, linked hypotheses. This is critical 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":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:25:20.971489+00:00","updated_at":"2026-04-16T21:25:20.971489+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/efacabd6_da8_spec.md","provider":"any","payload_json":"{}"},{"id":"f605325e-dd96-42a7-b964-2a3b2f8f9ddb","title":"[UI] Add /experiments listing page with filterable experiment cards","description":"Create a browsable /experiments page showing all 188 experiments with filtering by type, target gene, and disease. Cards should show title, score, cost, and linked hypothesis count.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T21:23:03.978103+00:00","updated_at":"2026-04-16T21:23:03.978103+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f605325e_dd9_spec.md","provider":"any","payload_json":"{}"},{"id":"aa945ffb-6cc0-47c1-a836-50c9b4b451cb","title":"[UI] Add page caching to slow pages (exchange, senate, quests)","description":"Exchange (342ms), Senate (1338ms), and Quests (253ms) pages lack caching. Add _get_cached_page/_set_cached_page with 60s TTL.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T21:11:36.735504+00:00","updated_at":"2026-04-16T21:11:36.735504+00:00","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/aa945ffb_6cc_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}}"},{"id":"dec65421-e6db-4ef8-a9ef-dbbc2a8b6be8","title":"[UI] Add styled 404 error page with navigation","description":"Currently 404 errors show raw JSON: {\"detail\":\"Not Found\"}. Add a custom exception handler that returns a styled HTML 404 page with SciDEX branding, navigation, and helpful links back to main pages. Important for demo polish.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T21:08:59.468056+00:00","updated_at":"2026-04-16T21:08:59.468056+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/dec65421_e6d_spec.md","provider":"any","payload_json":"{}"},{"id":"6cfd32be-46be-41e2-a771-4d3d82d23786","title":"[UI] Fix 404 errors on /showcase and /experiments pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T20:43:06.043848+00:00","updated_at":"2026-04-16T20:43:06.043848+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6cfd32be_46b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"8a4e5f9ba\"], \"completion_shas_checked_at\": \"2026-04-16T20:43:06.022529+00:00\"}"},{"id":"d65788b7-3267-4e7a-af9d-dcb476c0641c","title":"[UI] Fix broken wiki links — hardcoded slugs and improve fallback matching","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":"2026-04-16T17:51:54.779708+00:00","updated_at":"2026-04-16T17:51:54.779708+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d65788b7_326_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"6a650f80-8a68-43bd-8bce-cb98c7c66d3c","title":"[UI] Fix /notebooks 500 error: add missing is_spotlight and tags columns","description":"The /notebooks page returns 500 because api.py queries for n.is_spotlight and n.tags columns that don't exist in the notebooks table schema. Need to create a migration to add these columns.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:43:21.948165+00:00","updated_at":"2026-04-16T16:43:21.948165+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6a650f80_8a6_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"059ef936-0414-4456-9f20-8c1e641bbcfd","title":"[UI] Fix top nav alignment and deploy merged nav changes","description":"Update worktree nav_html to current main navbar structure, fix horizontal alignment of top nav items, then merge/push/restart API.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:24:55.659815+00:00","updated_at":"2026-04-16T16:24:55.659815+00:00","summary":"","completion_notes":"Verification: HEAD (6e831b74b) is on origin/main; api_shared/nav.py matches origin/main exactly (min-height:34px for both nav-top-link and nav-top-separator); prior task commits 555c797e7 and e58b797d7 confirmed on main. Work already shipped.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/059ef936_041_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"a140d6f5-bfd1-42f9-a816-d28f5158202c","title":"[UI] Add hypothesis evidence strength matrix with citation quality scoring","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:20:05.347936+00:00","updated_at":"2026-04-16T16:20:05.347936+00:00","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/a140d6f5_bfd_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"65f92687-5a57-4653-b0bc-9e5e3d84695b","title":"[UI] Fix navigation links pointing to wrong atlas URL","description":"Nav sidebar links to /atlas.html (static file) instead of /atlas (dynamic route with live stats). Fix nav to use /atlas.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:16:53.797719+00:00","updated_at":"2026-04-16T16:16:53.797719+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/65f92687_5a5_spec.md","provider":"any","payload_json":"{}"},{"id":"18a73eb3-7268-48e8-a9db-04abdd01cb20","title":"[UI] Create missing feedback table — prevents OperationalError on /api/feedback","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:09:23.271686+00:00","updated_at":"2026-04-16T16:09:23.271686+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/18a73eb3_726_spec.md","provider":"any","payload_json":"{}"},{"id":"e273532b-f6e4-4436-a86e-8df0dbc84736","title":"[UI] Add /notebooks to nav sidebar under Knowledge section","description":"The nav sidebar links to /artifacts (Artifact Gallery) but not /notebooks, which has 99 Jupyter notebook analyses. Visitors can only find notebooks through /demo or /artifacts pages. Add Notebooks link to the Knowledge section of sidebar nav for better discoverability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:05:12.114755+00:00","updated_at":"2026-04-16T16:05:12.114755+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e273532b_f6e_spec.md","provider":"any","payload_json":"{}"},{"id":"3acd73a2-c12a-43d0-bc4c-8fa1d8b782c8","title":"[UI] Fix entity detail 500 errors — add None-safety and error boundary","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":"2026-04-16T15:55:35.634518+00:00","updated_at":"2026-04-16T15:55:35.634518+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3acd73a2_c12_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"a1c23b8f-57a2-4a19-a1a7-ed84e5db5ab3","title":"[UI] Add /debates listing page — browse all 47 debate sessions","description":"Add a /debates page that lists all debate sessions with quality scores, persona badges, hypothesis outcomes, and links to full transcripts. Currently the only way to find debates is via hypothesis pages. This page makes the Agora layer navigable. Data: 47 debate sessions, 4 personas, quality scores.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:53:51.742909+00:00","updated_at":"2026-04-16T15:53:51.742909+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a1c23b8f_57a_spec.md","provider":"any","payload_json":"{}"},{"id":"c66969ce-ab0d-4b64-af44-49f425079c52","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03T05:55:07.283606","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"49611990-b63e-4776-b633-6b23108fa92b","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 13:34:48","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":"0a6a8553-2955-4ff1-bec3-304c69239a63","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:05:07","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"86f62c69-dc00-4e2f-a71e-e50247348968","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:56:40","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":"48460d8e-eba5-4742-9c76-ca85291e23d7","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:11:36","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":"9a39517f-19d1-4169-b11e-6e370262ec5a","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, 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KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:06:31","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"100baf53-b0dc-4cc8-83bd-d6f9bb19ab3e","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:12:50","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":"956a3217-6ea6-4dff-81f3-57379eb70b83","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:22:37","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":"0e6223b6-dbef-4a32-ae75-c52f09ee21d8","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:32:43","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"caef4f61-958e-498e-8367-451c1f69a866","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:34:32","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"155e9556-a33b-4698-8762-99899fc9c198","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:45:28","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"8381bbb1-68d6-4055-a0c6-2d53b67dc801","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 08:05:44","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":"1bd9f6f1-4929-43cf-9aea-7cc7404c31c3","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:22:20","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"3bdd9bd2-8a3a-4c15-a791-67d0e4ca0f2f","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:39:40","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":"88d32103-2a28-46b4-a174-f4ca177a1e6e","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:46:55","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"8ab0b96d-c3be-4311-977f-3c3e1f3b82f3","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:54:45","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":"edce1968-50b4-4786-891a-02018560cd93","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:59:01","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"49fa743f-22c5-4c21-8c5d-1d2f72625776","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:40:35","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"73461b32-43d1-46fd-998b-01b6fb3ec6ad","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:40:36","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":"2eac3b19-2374-4903-8eea-3b8350aff5b4","title":"[UI] Improve /analyses page — add cards with key metrics and debate status","description":"The analyses list page should show richer cards: hypothesis count, debate status, top score, KG edge count, creation date.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:46:56","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"445f3420-931e-4339-a981-a90d49185b0e","title":"[UI] Fix /experiments 500 error and /hypotheses 404","description":"The /experiments page returns HTTP 500 and /hypotheses returns 404. These are core navigation pages that must work for demo quality.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 04:40:07","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/445f3420_931_spec.md","provider":"any","payload_json":"{}"},{"id":"58be9a95-c650-4862-8d0f-81531af2239a","title":"[UI] Optimize entity and analysis page query performance","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T19:25:15.179201+00:00","updated_at":"2026-04-16T19:25:15.179201+00:00","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/58be9a95_c65_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"0fb66e79-45ed-4121-af46-180ba7d9d3cd","title":"[UI] CI: Smoke-test all pages and fix any broken links or 500s","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":"2026-04-17T04:56:29.645439+00:00","updated_at":"2026-04-17T04:56:29.645439+00:00","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/0fb66e79_45e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"64c4130e-9c6b-44f8-b26e-19e5b997dde5","title":"[UI] Fix artifact version history None crash and cache corruption recovery","description":"Fix two bugs: (1) artifact_detail crashes with AttributeError when version_tag/changelog are null in DB, (2) page_cache.db corruption silently fails without recovery. Fix: null coalescing for version history fields, _init_disk_cache deletes and recreates corrupt DB file.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:17:07.820080+00:00","updated_at":"2026-04-16T21:17:07.820080+00:00","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/64c4130e_9c6_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"164a3c5a-9479-4f31-8ae0-326384af322e","title":"[UI] Fix /notebooks route: add missing tags and is_spotlight columns","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:15:51.062081+00:00","updated_at":"2026-04-16T21:15:51.062081+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/164a3c5a_947_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"f38b1b34-9df1-4ae1-814d-fdeecdc1aec6","title":"[UI] Harden link checker against transient API restart cascades","description":"Reduce false broken links and runtime blowups when scidex-api restarts mid-crawl by adding outage-aware retry behavior and clear reporting.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:14:13.876504+00:00","updated_at":"2026-04-16T21:14:13.876504+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f38b1b34_9df_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"935d3ab5-8319-46bb-ac10-b24a33ec849c","title":"[UI] Make Mermaid diagrams pan by drag at native size","description":"Update shared Mermaid rendering so pathway diagrams render at normal intrinsic size inside a bounded viewport and can be inspected by click-drag panning across hypothesis, analysis, and wiki pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:12:33.910704+00:00","updated_at":"2026-04-16T21:12:33.910704+00:00","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/935d3ab5_831_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}}"},{"id":"a266c543-c42e-4a53-941e-fed8c594dec7","title":"[UI] Add missing type colors to nav search dropdown (notebook, debate, gap)","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:02:37.671587+00:00","updated_at":"2026-04-16T21:02:37.671587+00:00","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/a266c543_c42_spec.md","provider":"any","payload_json":"{}"},{"id":"6c4a33ec-cebb-486c-8369-e14afbcf8459","title":"[UI] Fix /experiments 500 error: html module UnboundLocalError","description":"The /experiments page returns 500 due to UnboundLocalError on html module in the running server. The on-disk code appears correct but the running server has a stale version. Need to verify on-disk code is clean and ensure next restart resolves the issue. Also check for any html variable shadowing in the experiments_listing function.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:59:44.110382+00:00","updated_at":"2026-04-16T20:59:44.110382+00:00","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/6c4a33ec_ceb_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"d5cd9059-26fb-4642-aa7f-92f5ce4943ce","title":"[UI] Add /forge/pubmed-pipeline HTML page for PubMed evidence pipeline","description":"Create HTML page for /forge/pubmed-pipeline that shows PubMed pipeline status, recent runs, and trigger button. Currently linked from sidebar but returns 404.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:59:03.736747+00:00","updated_at":"2026-04-16T20:59:03.736747+00:00","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/d5cd9059_26f_spec.md","provider":"any","payload_json":"{}"},{"id":"5ed34d52-d413-4a0c-8518-96801235c9d4","title":"[UI] Add 500 error handler with traceback display and fix stale cache issues","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":"2026-04-16T20:56:32.736867+00:00","updated_at":"2026-04-16T20:56:32.736867+00:00","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/5ed34d52_d41_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}}"},{"id":"2904cc7b-c6f5-443c-8e17-be2298217255","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:55:02.552899+00:00","updated_at":"2026-04-16T20:55:02.552899+00:00","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/2904cc7b-c6f_ui_add_hypothesis_comparison_view_to_ex_spec.md","provider":"any","payload_json":"{}"},{"id":"2a172292-fe0f-4101-898d-647717aebc1c","title":"[UI] Fix site-wide broken links and 404 pages","description":"Run link_checker.py to identify all broken links across the site, then fix routing issues in api.py and broken href references in templates. This improves demo quality by ensuring every page is navigable.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:41:07.481474+00:00","updated_at":"2026-04-16T20:41:07.481474+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/2a172292_fe0_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"5012fd03-aa38-46b1-921a-175590291f01","title":"[UI] Add /api/experiments JSON endpoint with pagination and filtering","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":"2026-04-16T20:40:24.799704+00:00","updated_at":"2026-04-16T20:40:24.799704+00:00","summary":"","completion_notes":"The /api/experiments JSON endpoint with pagination and filtering already exists on main, implemented in commit 83b3ba921 [Forge] Add experiments registry list API with filtering and sorting [task:e10a1f53-c29e-46a1-8893-dd4f96965ac5]. The endpoint (line 9692 in api.py) supports ?limit, ?offset, ?exp_type, ?disease, ?q, ?sort parameters and returns JSON with experiments list, total, limit, offset, and has_more.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5012fd03_aa3_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"83b3ba921\"], \"completion_shas_checked_at\": \"2026-04-16T20:40:24.733906+00:00\"}"},{"id":"fc48c61d-8061-46aa-b85e-3fe39fbdc998","title":"[UI] Add /status to sidebar navigation under Operations","description":"Add /status link to sidebar nav Operations group\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:40:02.279167+00:00","updated_at":"2026-04-16T20:40:02.279167+00:00","summary":"","completion_notes":"Task was completed in commit 417ebc624 which added /status to sidebar navigation. The sidebar nav in api_shared/nav.py already has (\"/status\", \"Status\", \"🚦\") in the System group. No additional code changes needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/fc48c61d_806_spec.md","provider":"any","payload_json":"{}"},{"id":"4d6dc15f-8f53-4990-a6b7-8ad29e58052f","title":"[UI] Fix 404 on /agora route and verify all main navigation pages","description":"The /agora page returns 404. This is a core navigation page for the Agora debate layer. Investigate and fix. Verify all 5 layer pages render.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T20:39:55.806396+00:00","updated_at":"2026-04-16T20:39:55.806396+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4d6dc15f_8f5_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"5104ec7f-6a64-43b0-b222-9ca312ad2b68","title":"[UI] Add /api/experiments JSON endpoint and include experiments in search results","description":"Add /api/experiments JSON endpoint with pagination and filtering (type, disease, status). Also add experiments to the /api/search results so they appear in unified search. 188 experiments exist but have no API access.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:39:52.696627+00:00","updated_at":"2026-04-16T20:39:52.696627+00:00","summary":"","completion_notes":"Verified: commit 51a81098b ([UI] Add /api/experiments JSON endpoint with pagination and filtering [task:5104ec7f-6a64-43b0-b222-9ca312ad2b68]) is on origin/main. Both deliverables implemented: (1) /api/experiments JSON endpoint with limit/offset pagination and exp_type/disease/q/sort filtering, (2) experiments appear in /api/search results.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5104ec7f_6a6_spec.md","provider":"any","payload_json":"{}"},{"id":"ff9db36b-df93-40cf-b29d-12432875fef1","title":"[UI] Fix health endpoint — replace missing knowledge_nodes table with canonical_entities","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":"2026-04-16T20:39:32.507292+00:00","updated_at":"2026-04-16T20:39:32.507292+00:00","summary":"","completion_notes":"Verified on origin/gh/main: /api/health uses canonical_entities, /api/monitoring uses wiki_pages. No knowledge_nodes references exist in api.py. Task was addressed by commits 84e687f39 and 36db9bf5e (part of squash merge 2670d7c6a). Branch rebased to align with current main HEAD (518423aaa).","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ff9db36b_df9_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"2911d59b-19f7-4e9a-af46-6199cdf3e391","title":"[UI] Remove duplicate lowercase analyses that have no content","description":"There are duplicate analyses in the DB with lowercase IDs (e.g., sda-2026-04-01-gap-004) that mirror uppercase ones (SDA-2026-04-01-gap-004). The lowercase ones have 0 hypotheses and 0 debates. They clutter the /analyses/ page. Remove or hide the empty lowercase duplicates.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:37:33.012149+00:00","updated_at":"2026-04-16T20:37:33.012149+00:00","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/2911d59b_19f_spec.md","provider":"any","payload_json":"{}"},{"id":"81bd94ac-1aaa-4d29-b6ec-5d5510e60eaf","title":"[UI] Add /experiments listing page with search and filtering","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":"2026-04-16T20:37:03.972174+00:00","updated_at":"2026-04-16T20:37:03.972174+00:00","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/81bd94ac_1aa_spec.md","provider":"any","payload_json":"{}"},{"id":"4cbdc22a-abc7-4fbd-a605-51dd66a987b1","title":"[UI] Add /quests and /resources links to main navigation on all pages","description":"Update nav_html() in api.py to include links to /quests (Mission Control) and /resources (Resource Costs) in the navigation bar. These should be visible on every page. Coordinate with Quest 10 UI tasks for consistent nav design.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T20:33:16.215536+00:00","updated_at":"2026-04-16T20:33:16.215536+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"db5bc3f7-1c3f-403a-a0dc-d4b7cb385006","title":"[UI] Add /papers listing page — browse 2374 scientific papers","description":"Create a /papers page to browse all 2374 papers in the SciDEX database. Show title, authors, journal, year, citation count, and link to hypothesis connections. Support search, sort by citations/year, and pagination. This completes the Atlas layer navigation.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:31:00.417404+00:00","updated_at":"2026-04-16T20:31:00.417404+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/db5bc3f7_1c3_spec.md","provider":"any","payload_json":"{}"},{"id":"05c938c1-14ab-4c66-bdeb-1d74ec4478e7","title":"[UI] Add page caching to slow entity and wiki pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:24:04.558625+00:00","updated_at":"2026-04-16T20:24:04.558625+00:00","summary":"","completion_notes":"Verified on origin/main at e1515cd85: entity_detail (line ~46240) has `_get_cached_page(f\"entity:{entity_name}\")` and wiki_page (line ~48504) has `_get_cached_page(f\"wiki:{slug}\")` — both already cached. Task was done in commit 6489a6440.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/05c938c1_14a_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"completion_shas\": [\"6489a64401a8527850cc5b9798e5499a1a21a140\"], \"completion_shas_checked_at\": \"2026-04-16T20:24:04.539489+00:00\"}"},{"id":"4389919c-b605-4057-9dfa-48e064113a0c","title":"[UI] Add /experiments listing page for 188 experiments","description":"Individual experiment detail pages exist but there is no /experiments listing page. Visitors cannot discover experiments without going through the exchange. Add a listing page similar to /analyses/ with filtering.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:23:05.241220+00:00","updated_at":"2026-04-16T20:23:05.241220+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4389919c_b60_spec.md","provider":"any","payload_json":"{}"},{"id":"7d688f0f-d47a-414d-80f7-4e67de04b1df","title":"[UI] Fix link checker creating false P90+ tasks for transient 502s","description":"Link checker creates many P90+ tasks for 502 errors during service restarts. Per AGENTS.md: NEVER create P90+ bug tasks for 502 errors - they're transient. Fix: Add retry logic for 502s (wait 2min, retest), filter transient ones, cap 502 priority at 80.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:21:37.142180+00:00","updated_at":"2026-04-16T20:21:37.142180+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7d688f0f_d47_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"ee42db51-6055-4dc0-b0a0-8b1de86ebf65","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 13:43:02","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":"a164dc6d-1159-4327-8128-4c5b7bd1b420","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:10:46","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":"40ed8eda-d989-4c5f-b35a-e9dd8546b844","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:58:18","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"7d397d99-c26b-44c9-a2de-bb105917dfe5","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:16:14","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"7f51a77a-1263-4a7b-8292-b901994ef697","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:26:30","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"5aebca1c-ced7-4f9b-9067-ac93d3cbfbd9","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:25:43","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"292d2d91-d9b8-4c27-a2c2-f59b2673f9b1","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:18:58","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":"006da53b-d955-4ccf-83d4-ffd7fdc518ae","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:19:09","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"fe21fbc7-587e-4db7-be87-1e49bbfc3e73","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:26:31","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"dd3c47c5-2601-4f79-bf98-97d9d79e9a7f","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:54:28","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"3a09aca1-9b04-4d3b-a61d-05698f5c23b0","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:57:26","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"16778816-5ed6-4fbd-91b7-6afe1ae412be","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:05:17","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"0148e302-7a29-4f68-8375-e7321ea459ef","title":"[UI] Add hypothesis comparison view to 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15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"0303969a-08c8-4a4e-8ef2-afe4228f81e8","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:42:39","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":"c16b5643-e351-4c20-b05d-3978b516757e","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:41:02","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":"65be943b-e14d-42ec-8195-4eb25d45df60","title":"[UI] Add hypothesis comparison view to Exchange","description":"Allow selecting 2-3 hypotheses to compare side-by-side: radar charts, evidence, scores, debate excerpts.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:54:28","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"5f4855c0-4f61-465b-b045-85114b26bf8b","title":"[UI] Add /api/health JSON endpoint for monitoring","description":"Add a simple JSON health endpoint that returns DB connectivity, record counts, and service status for monitoring.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 19:21:39","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5f4855c0_4f6_spec.md","provider":"any","payload_json":"{}"},{"id":"c98a423d-0ad9-46a7-a0d7-0fd3d31e9405","title":"[UI] Fix orphan checker false positives for KG edges","description":"Bug: orphan_checker.py incorrectly reports 283/690 edges as orphaned (41% coverage) by checking for entity IDs in static HTML. Graph pages load data dynamically via /api/graph API, so entities won't be in static HTML. Fix: Change check_orphaned_kg_edges() to verify edges are accessible via API and properly structured, not text-search static files. All edges in DB are visualized, so true coverage should be ~100%.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 04:31:00","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c98a423d_0ad_spec.md","provider":"any","payload_json":"{}"},{"id":"f7aa0762-e2b1-4eec-a77e-5b13ae64d578","title":"[UI] Fix orphan checker false positives for KG edges","description":"Fix orphan_checker.py false positives: KG edges shown via /api/graph are incorrectly flagged as orphaned. See spec at docs/planning/specs/c98a423d_0ad_spec.md","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 04:38:11","updated_at":"2026-04-02T04:35:49.488553+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f7aa0762_e2b_spec.md","provider":"any","payload_json":"{}"},{"id":"5464c366-26a1-486a-979a-5247b1586e1e","title":"[UI] Fix orphan checker to use /api/graph endpoint","description":"Update orphan_checker.py check_orphaned_kg_edges() to query /api/graph endpoint instead of grepping static HTML files. Current heuristic fails because graph.html loads data dynamically via JavaScript. Fix: fetch from http://localhost:8000/api/graph, extract node IDs, check if edge source/target exist in returned nodes.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 04:34:22","updated_at":"2026-04-02T04:32:06.191037+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5464c366_26a_spec.md","provider":"any","payload_json":"{}"},{"id":"700f48d0-91c7-4377-9690-38696030c9bc","title":"[UI] Show commit metadata from commit hash links","description":"Improve commit hash links on quest and related pages so clicking or hovering reveals commit message and pertinent metadata instead of only the raw hash.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":84,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:44:19.644718+00:00","updated_at":"2026-04-16T22:44:19.644718+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/700f48d0_91c_spec.md","provider":"any","payload_json":"{}"},{"id":"56261b62-19cf-4ad8-ac86-f2bb49cc42c4","title":"[UI] Add /wiki endpoint for browsing imported NeuroWiki pages","description":"Create /wiki and /wiki/{slug} endpoints. /wiki shows a browsable index of all imported wiki pages grouped by type (genes, proteins, mechanisms, therapeutics). /wiki/{slug} renders the markdown content with SciDEX styling, KG sidebar, and related hypotheses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":84,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:41:17.976525+00:00","updated_at":"2026-04-16T22:41:17.976525+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"e563f807-5f68-446a-9822-c43513efeda0","title":"[UI] Mobile responsive improvements across all pages","description":"Test and fix mobile layout on all main pages. Ensure cards stack properly, tables scroll horizontally, nav works on mobile.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T05:26:58.748032+00:00","updated_at":"2026-04-17T05:26:58.748032+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{}"},{"id":"840112c6-224d-468b-b4a3-8d7446ea7793","title":"[UI] Optimize /atlas page performance — reduce 1.1s load time","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:08:59.981342+00:00","updated_at":"2026-04-16T23:08:59.981342+00:00","summary":"","completion_notes":"Verified: /atlas returns HTTP 200 in 0.003s (cached), code fixes on origin/main via commits 50f38aa71 and ab0d90c0e, indexes confirmed in /home/ubuntu/scidex/scidex.db","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/840112c6_224_spec.md","provider":"any","payload_json":"{}"},{"id":"931270aa-2278-4caf-8cd7-fdd2b7151f21","title":"[UI] Mobile responsive improvements across all pages","description":"Test and fix mobile layout on all main pages. Ensure cards stack properly, tables scroll horizontally, nav works on mobile.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:58:45.820730+00:00","updated_at":"2026-04-16T22:58:45.820730+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/931270aa-227_ui_mobile_responsive_improvements_acros_spec.md","provider":"any","payload_json":"{}"},{"id":"3db52188-8347-4d61-9d0e-050e4a3a3d85","title":"[UI] Add /search link to sidebar navigation and keyboard shortcut","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:52:01.905584+00:00","updated_at":"2026-04-16T22:52:01.905584+00:00","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/3db52188_834_spec.md","provider":"any","payload_json":"{}"},{"id":"0132bb21-2fe3-4313-b2af-ae60496eb051","title":"[UI] Add breadcrumb navigation to hypothesis, analysis, and wiki detail pages","description":"Add consistent breadcrumb navigation at the top of detail pages (hypothesis, analysis, wiki, experiment) showing the path like Home > Exchange > Hypothesis Name. Improves orientation and navigation especially for demo visitors. Check if breadcrumb_html() function exists and use it.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:46:39.655716+00:00","updated_at":"2026-04-16T22:46:39.655716+00:00","summary":"","completion_notes":"Already implemented on main. Verified: breadcrumb_html() exists in api_shared/nav.py, and all four detail pages (hypothesis at line 32506, analysis at line 35670, wiki at line 49837, experiment at line 33515) already use it with correct paths like Home > Exchange > Hypothesis Name.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0132bb21_2fe_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"0447ce63-efd1-4ef2-bb54-3481a0516d96","title":"[UI] Mobile responsive improvements across all pages","description":"Test and fix mobile layout on all main pages. Ensure cards stack properly, tables scroll horizontally, nav works on mobile.","status":"archived","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03T05:28:08.772855","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"68432c89-301c-4d8b-906d-9b2de8a24d55","title":"[UI] Mobile responsive improvements across all pages","description":"Test and fix mobile layout on all main pages. Ensure cards stack properly, tables scroll horizontally, nav works on mobile.","status":"archived","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 13:43:54","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"7f82a3b1-67e0-4892-8c81-be0a545d24b7","title":"[UI] Mobile responsive improvements across all pages","description":"Test and fix mobile layout on all main pages. Ensure cards stack properly, tables scroll horizontally, nav works on mobile.","status":"archived","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 13:59:49","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":"cd731ad6-7c4c-449f-a4c4-91401e648942","title":"[UI] Mobile responsive improvements across all pages","description":"Test and fix mobile layout on all main pages. Ensure cards stack properly, tables scroll horizontally, nav works on mobile.","status":"archived","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:01:43","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"59a2ea3e-943f-49ad-bc09-8ac409a8677b","title":"[UI] Mobile responsive improvements across all pages","description":"Test and fix mobile layout on all main pages. Ensure cards stack properly, tables scroll horizontally, nav works on mobile.","status":"archived","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:16:52","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"93f3f17a-4285-4f1a-90e3-7ce0fad0986f","title":"[UI] Mobile responsive improvements across all pages","description":"Test and fix mobile layout on all main pages. Ensure cards stack properly, tables scroll horizontally, nav works on mobile.","status":"archived","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:26:50","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":"d7a6e06d-f155-4043-bc2e-fa94be13bd33","title":"[UI] Mobile responsive improvements across all pages","description":"Test and fix mobile layout on all main pages. 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Ensure cards stack properly, tables scroll horizontally, nav works on mobile.","status":"archived","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:56:12","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"103f576e-406f-4c1c-970b-0f7b37150c14","title":"[UI] Mobile responsive improvements across all pages","description":"Test and fix mobile layout on all main pages. Ensure cards stack properly, tables scroll horizontally, nav works on mobile.","status":"archived","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:57:49","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":"29a336b4-a03d-4db1-9faf-7fce0ad76222","title":"[UI] Mobile responsive improvements across all pages","description":"Test and fix mobile layout on all main pages. Ensure cards stack properly, tables scroll horizontally, nav works on mobile.","status":"archived","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:40:00","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"1ba0c681-f92c-4ae2-8094-9014a37ad792","title":"[UI] Mobile responsive improvements across all pages","description":"Test and fix mobile layout on all main pages. Ensure cards stack properly, tables scroll horizontally, nav works on mobile.","status":"archived","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:41:04","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c3f6ceec-1b45-4f38-bbbc-77722f18da45","title":"[UI] Mobile responsive improvements across all pages","description":"Test and fix mobile layout on all main pages. Ensure cards stack properly, tables scroll horizontally, nav works on mobile.","status":"archived","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"7f0cb4c5-e318-4420-a668-d4c14401d7aa","title":"[UI] Add breadcrumbs and back-navigation to all detail pages","description":"Entity, hypothesis, analysis, experiment, and target pages should have breadcrumbs showing navigation path.","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T09:52:19.001386+00:00","updated_at":"2026-04-17T09:52:19.001386+00:00","summary":"","completion_notes":"Verified: All 5 detail pages (hypothesis at line 34495, experiment at 35505, target at 37007, analysis at 37698, entity at 50940) already have breadcrumb_html() calls showing navigation hierarchy, plus consistent \"← Back\" footer links. Task completed by prior agent (bca74295, commit dc6faff61).","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{}"},{"id":"a652be5a-460c-404c-98d6-0fe655dbea7a","title":"[UI] Backfill missing analysis HTML files","description":"Generate HTML reports for analyses that are completed but missing their HTML files. Run post_process.generate_report() for each missing file.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T09:07:17.981946+00:00","updated_at":"2026-04-17T09:07:17.981946+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a652be5a_460_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"f3085715-6cd6-4121-827d-d3ad63a065c8","title":"[UI] Clean up duplicate page cache definitions in api.py","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":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T05:35:43.249462+00:00","updated_at":"2026-04-17T05:35:43.249462+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f3085715_6cd_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}}"},{"id":"49c12054-0683-46ab-bb40-efb4daa11f51","title":"[UI] Add evidence matrix tables to hypothesis detail pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:50:43.287868+00:00","updated_at":"2026-04-16T23:50:43.287868+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/49c12054_068_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"f488e212-154b-43fb-8f36-c3b3c9f75e99","title":"[UI] Create shared CSS component and page template system","description":"Extract the inline CSS constant and create reusable components:\n1. Move CSS variable from api.py into a proper /static/style.css file served by nginx\n2. Create page_template() function that wraps content in consistent header/nav/footer\n3. Ensure dark theme consistency across all pages\n4. Add responsive breakpoints for mobile\n5. Test all pages render correctly after extraction.\nCoordinate with nav_html() changes.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:49:35.129703+00:00","updated_at":"2026-04-16T23:49:35.129703+00:00","summary":"","completion_notes":"Verified on origin/main (commit 91dc387a6): CSS extracted to site/style.css with dark theme CSS variables, page_template() at api_shared/nav.py:637, /style.css route at api.py:53773, nav_html() integrated, responsive breakpoints present. No broken work remains.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"93867984-e4a6-4096-9d63-409e3f2b8ee1","title":"[UI] Automated visual regression testing","description":"Build visual_inspector.py using Playwright to screenshot all key pages, compare against baselines, detect layout breakage >5%. Run every 6 hours via cron. Acceptance: screenshots for all routes; diff report on changes; /api/visual-report endpoint; Senate dashboard integration.","status":"archived","priority":80,"task_type":"recurring","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-12T18:09:49.891930+00:00","updated_at":"2026-04-16T19:47:42.283386+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/93867984-e4a_ui_automated_visual_regre_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6, \"safety\": 7}, \"completion_shas\": [\"f566069a678b1c0d7cdc1c76793cbadc1590f120\", \"d63e82e5fba41ca1e110ec4d5be36e714747db9e\", \"db6302474b342d56c9374fc02811730e1b0fefee\"], \"completion_shas_checked_at\": \"2026-04-12T18:09:49.881317+00:00\", \"completion_shas_missing\": [\"ca8ec8c766ee956a82a9d90d57a5173b2b3b352d\", 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15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"4c1336c2-eb44-4c34-8ac5-5873be63289c","title":"[UI] Add breadcrumbs and back-navigation to all detail pages","description":"Entity, hypothesis, analysis, experiment, and target pages should have breadcrumbs showing navigation path.","status":"archived","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:58:39","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":"c802ad66-3a5c-4205-98ee-0c975ae9fb61","title":"[UI] Add breadcrumbs and back-navigation to all detail pages","description":"Entity, hypothesis, analysis, experiment, and target pages should have breadcrumbs showing navigation path.","status":"archived","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:40:05","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":"eef9e581-2089-419b-a2f4-462c112d05f6","title":"[UI] Add breadcrumbs and back-navigation to all detail pages","description":"Entity, hypothesis, analysis, experiment, and target pages should have breadcrumbs showing navigation path.","status":"archived","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:41:04","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"08b8b4a6-793c-488a-a290-f46571da0e71","title":"[UI] Add breadcrumbs and back-navigation to all detail pages","description":"Entity, hypothesis, analysis, experiment, and target pages should have breadcrumbs showing navigation path.","status":"archived","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"e70b5abf-62a1-4589-b527-def6ffe4deb0","title":"[UI] Unified nav component across all pages","description":"UI6.1: Create single nav_html(active) function in api.py. All dynamic pages use it. Update static pages (how.html, atlas.html, graph.html, pitch.html) to share identical nav.\n\nAcceptance: All pages have identical nav with correct active highlighting.","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:58:23","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/e70b5abf_62a_unified_nav_componen_spec.md","provider":"any","payload_json":"{}"},{"id":"q10-u2-F37603C4","title":"[UI] Add loading states and error handling to all pages","description":"Add skeleton loaders or spinners for all client-side fetch() calls. Add error states (friendly error message, retry button). Currently pages show blank when API is slow. Priority: /exchange, /quests, /graph, /senate.","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:58:22","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":"9bd32798-ff72-47cc-8764-3135041f2272","title":"[UI] Add Option+Shift hamburger API restart shortcut","description":"Extend the navbar hamburger shortcut handling so Option+Shift+click triggers an API restart endpoint, while preserving Shift+click cache clear behavior.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":78,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:07:11.805941+00:00","updated_at":"2026-04-17T10:07:11.805941+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9bd32798_ff7_spec.md","provider":"any","payload_json":"{}"},{"id":"8ad4c451-bd35-4099-9b66-a39fe97da03e","title":"[UI] Fix nav Atlas link — /atlas.html to /atlas","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":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:39:44.523269+00:00","updated_at":"2026-04-17T10:39:44.523269+00:00","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/8ad4c451_bd3_spec.md","provider":"any","payload_json":"{}"},{"id":"22d979a5-baa8-492c-ac6b-db09d3b9c5e3","title":"[UI] Remove duplicate /clinical-trials route definition","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":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:36:56.628671+00:00","updated_at":"2026-04-17T10:36:56.628671+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/22d979a5_baa_spec.md","provider":"any","payload_json":"{}"},{"id":"81c62e13-becb-4d0e-ae78-292f42c87f96","title":"[UI] Fix remaining duplicate route definitions (/status, /hypotheses/{hyp_id}, /api/coverage)","description":"There are duplicate FastAPI route definitions that may cause confusion. /status has 2 definitions, /hypotheses/{hyp_id} has 2, /api/coverage has 2. Review and remove the older/less polished duplicates.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:21:53.977861+00:00","updated_at":"2026-04-17T10:21:53.977861+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/81c62e13_bec_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"0a2c411d-f510-41ae-b7c2-641fa57d1e1f","title":"[UI] Add search functionality across hypotheses, analyses, and entities","description":"Add a /search endpoint that accepts a query string and searches across hypotheses (title, description), analyses (title, question), and knowledge_edges (source, target). Return unified results with type indicators and links.","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:14:20","updated_at":"2026-04-02T06:09:46.402005+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"cba19c94-1724-4d5a-b89d-96c73c25f12a","title":"[UI] Nav links for all 5 layers","description":"UI6.2: Nav should include: Dashboard, Analyses (Agora), Exchange, Forge, Atlas, Senate, Gaps. Add Exchange prominently. Add Forge/Senate once pages exist.\n\nAcceptance: Nav reflects all 5 layers of SciDEX architecture.","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:02:13","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/cba19c94_172_nav_links_for_all_5_spec.md","provider":"any","payload_json":"{}"},{"id":"f576ae81-e879-4a3f-8979-df74d5faa49b","title":"[UI] Universal activity feed on dashboard","description":"Real-time activity feed on / showing last 50 actions: analyses, hypothesis scoring, KG edges, debates. Each entry links to detail page. Uses event_bus. Acceptance: visible on dashboard; actions appear within 60s; clickable links; auto-refresh via JS polling.","status":"done","priority":73,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:26:07","updated_at":"2026-04-02T03:05:17.609939+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f576ae81-e87_ui_universal_activity_fee_spec.md","provider":"any","payload_json":"{}"},{"id":"19703589-bdbf-4366-97fe-6fbaceca00c5","title":"[UI] Fix: SciDEX docs appear in entity search with wrong links","description":"wiki_entities view includes scidex_docs pages, causing them to appear in entity search results (type='entity', link='/entity/{slug}') instead of documentation results (type='documentation', link='/docs/{slug}'). Fix: filter entity_type='scidex_docs' from wiki_entities_fts search queries in api.py.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":72,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T11:28:16.352287+00:00","updated_at":"2026-04-17T11:28:16.352287+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/19703589_bdb_spec.md","provider":"any","payload_json":"{}"},{"id":"00739e13-fabf-4de6-8213-e7ee3994dfb8","title":"[UI] Simplify Showcase top navigation","description":"Remove Walkthroughs from the Showcase dropdown and remove the extra direct Showcase top-bar link, then deploy the nav cleanup.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":72,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:59:09.250448+00:00","updated_at":"2026-04-17T10:59:09.250448+00:00","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/00739e13_fab_spec.md","provider":"any","payload_json":"{}"},{"id":"ba90addf-4301-4401-9234-81c9001e1d6f","title":"[UI] Align top navbar items horizontally","description":"Normalize shared top navbar item styling so dropdowns, separator, Showcase, Demo, and Vision align cleanly on one horizontal axis.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":72,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:54:25.422904+00:00","updated_at":"2026-04-17T10:54:25.422904+00:00","summary":"","completion_notes":"Verification: nav_html() in api_shared/nav.py already implements horizontal navbar alignment. All 4 acceptance criteria are met in the spec. No additional code changes needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ba90addf_430_spec.md","provider":"any","payload_json":"{}"},{"id":"cdc83b67-782d-449f-99da-642fd88eafa3","title":"[UI] Tighten top nav spacing","description":"Move the hamburger and SciDEX branding closer to the first top-nav item and bring the search box closer to Vision by tightening shared nav spacing.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T12:06:14.693919+00:00","updated_at":"2026-04-17T12:06:14.693919+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/cdc83b67_782_spec.md","provider":"any","payload_json":"{}"},{"id":"c0eee311-f096-4ad8-90d0-d0c5609c98c8","title":"[UI] Normalize notebook action button heights","description":"Make notebook detail action buttons such as Show Code and Download .ipynb render at the same height and alignment.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T12:01:24.371648+00:00","updated_at":"2026-04-17T12:01:24.371648+00:00","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/c0eee311_f09_spec.md","provider":"any","payload_json":"{}"},{"id":"7c483e0e-5d15-4a51-ad71-449c293e98ca","title":"[UI] Fix duplicate Debates entry in sidebar navigation","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":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T11:47:59.848820+00:00","updated_at":"2026-04-17T11:47:59.848820+00:00","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/7c483e0e_5d1_spec.md","provider":"any","payload_json":"{}"},{"id":"3435e083-f54a-47c7-b721-8ba7156f8ae6","title":"[UI] Add loading spinners and error states to all dynamic pages","description":"Replace blank/broken pages during load with skeleton screens or spinners. Show friendly error messages instead of 500 traces. Implement retry logic in JavaScript fetch calls.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T11:45:26.689856+00:00","updated_at":"2026-04-17T11:45:26.689856+00:00","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":"475c2cfa-d8d9-4a54-8034-cfffc018a716","title":"[UI] Improve main dashboard with live growth metrics","description":"Update the main / dashboard to show: recent analyses, top hypotheses by score, knowledge growth rate (edges/day), recent papers added, active quests progress. Replace any stale/hardcoded numbers with live DB queries.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T11:41:09.101461+00:00","updated_at":"2026-04-17T11:41:09.101461+00:00","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":"81eca19b-5a7d-40fb-a5fa-2c2127afa0c1","title":"[UI] Add /api/health JSON endpoint for monitoring","description":"Add a lightweight JSON health endpoint that returns DB stats, service status, and uptime. Useful for Orchestra agents and external monitoring.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T11:25:23.315307+00:00","updated_at":"2026-04-17T11:25:23.315307+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/81eca19b_5a7_spec.md","provider":"any","payload_json":"{}"},{"id":"00e1917d-4890-45ce-886e-92694a3d0c19","title":"[UI] Dashboard stats accuracy - sync displayed counts with actual DB","description":"The main dashboard and /how.html show stats that may be stale or hardcoded. Verify all displayed numbers match actual DB counts: 23 analyses, 118 hypotheses, 665 KG edges, 22 gaps, 991 wiki entities. Fix any discrepancies.","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:44:01","updated_at":"2026-04-02T06:05:12.235648","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"e09ee1f9-d112-42e9-bc80-9eb5ed39a37f","title":"[UI] Add unified navigation bar across all pages","description":"Create a consistent navigation component used on all pages (index, exchange, graph, gaps, analyses, senate, atlas, how). Include links to all 5 layers. Acceptance: all pages share same nav; all layer links work.","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 05:38:41","updated_at":"2026-04-02T05:33:43.702848+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"7e9d24eb-ffbf-455e-8b51-0e26f0422e4b","title":"[UI] Entity detail pages with unified view","description":"Create /entity/{name} pages aggregating: wiki summary, all KG edges, targeting hypotheses, mentioning analyses, citing papers, mini subgraph viz. Every KG node becomes browsable. Acceptance: renders for ~62 entities; linked from graph viz; shows hypothesis count and top-scored.","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:29:00","updated_at":"2026-04-02T03:05:17.609939+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7e9d24eb-ffb_ui_entity_detail_pages_wi_spec.md","provider":"any","payload_json":"{}"},{"id":"ed11ca4e-8709-43bd-97bc-304e0de77265","title":"[UI] Add Showcase dropdown with Demo and Vision","description":"Update shared navigation to add a Showcase dropdown containing Showcase, Demo, and Vision, while keeping Showcase available as a direct top-level link.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":68,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T15:14:05.653982+00:00","updated_at":"2026-04-17T15:14:05.653982+00:00","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/ed11ca4e_870_spec.md","provider":"any","payload_json":"{}"},{"id":"bd8c1e40-d206-40e7-a9ab-50d3369ad084","title":"[UI] Make /how.html dynamic with live system stats","description":"Replace hardcoded stats on how.html with live data from /api/status. Show real counts for analyses, hypotheses, KG edges, tools, debates. Auto-refresh every 60s. Acceptance: all stats are live and accurate.","status":"done","priority":65,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:45:30","updated_at":"2026-04-02T05:33:43.702839+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":"{}"},{"id":"d62a776a-de83-49cd-8249-c8ee3f4aa129","title":"[UI] UX improvement -- navigation and discoverability","description":"Audit all pages for dead-ends. Implement: breadcrumb trails on detail pages, Related sidebars on hypothesis pages, Explore Further links on analysis pages. Acceptance: every page has path back to parent; no page >3 clicks from dashboard; related content links on all detail pages.","status":"done","priority":63,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:28:24","updated_at":"2026-04-02T03:05:17.609939+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d62a776a-de8_ui_ux_improvement___navig_spec.md","provider":"any","payload_json":"{}"},{"id":"8424ba01-97d1-4846-b479-97670600f6f8","title":"[UI] Display AI-generated images alongside existing figures in pages","description":"Update wiki, hypothesis, and analysis page templates to display AI-generated images (from image_generator.py) alongside existing matplotlib SVG figures. Images are optional — pages must work without them.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":62,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T15:29:09.211128+00:00","updated_at":"2026-04-17T15:29:09.211128+00:00","summary":"","completion_notes":"Verified: db4eef6eb (main commit) and 9980464b1 (spec log) already on origin/orchestra/task/8424ba01-display-ai-generated-images-alongside-ex. Work includes: hypothesis page AI badge, analysis page AI figure section, wiki page AI thumbnail grid. api.py loads OK. Push succeeds with \"Everything up-to-date\" — no pre-push hook actually blocks it.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8424ba01_97d_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"aff65180-61da-48f3-82c3-e92998c47072","title":"[UI] Fix gaps page stale statuses","description":"UI6.4: All 20 gaps show status=investigating but 0 are open (contradicts the UI text). Fix: after analysis completes on a gap, mark partially_filled. Only resolved after 2+ analyses. Reset stale investigating back to open.\n\nAcceptance: Gaps page shows realistic mix of open/investigating/filled.","status":"done","priority":60,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:57:51","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/aff65180_61d_fix_gaps_page_stale_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"d3978a8e-3fd4-44e2-970e-1cef3ef910e2","title":"[UI] Loading states + error handling in JS","description":"UI6.3: All fetch() calls in graph.html, exchange JS, and future JS pages get loading spinners and catch() error blocks.\n\nAcceptance: Slow API calls show spinner. Failures show user-friendly message.","status":"done","priority":60,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:04:23","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/d3978a8e_3fd_loading_states_error_spec.md","provider":"any","payload_json":"{}"},{"id":"5ef13316-a865-43c0-bfb6-4bb11e3b393c","title":"[UI] Mobile responsive improvements","description":"Audit all pages for mobile responsiveness. The site uses inline CSS. Ensure /exchange, /graph, /senate, /forge pages work on mobile screens. Fix any overflow, truncation, or unreadable text.","status":"done","priority":55,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:16:50","updated_at":"2026-04-02T06:09:46.402005+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"5a8ae947-aa53-48e4-8194-24dd10290ce1","title":"[UI] Fix SyntaxWarning in cli.py bundle script","description":"Fix invalid escape sequence $ warning in cli.py replicate command by using raw f-string","status":"done","priority":50,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:37:22","updated_at":"2026-04-02T03:35:49.120710+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5a8ae947_aa5_spec.md","provider":"any","payload_json":"{}"},{"id":"d7e9a9fc-e859-4440-ba04-d8b082157f9f","title":"[UI] Fix missing failure_reason column causing dashboard errors","description":"Database schema error: api.py queries failure_reason column that doesn't exist. The [Senate] Failed analysis tracking task (262b5f7) added the query but never ran the migration. Need to: 1) Create migration to add failure_reason column to analyses table, 2) Run migration on production DB, 3) Verify dashboard loads without errors.","status":"done","priority":50,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:31:55","updated_at":"2026-04-02T03:29:27.688909+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d7e9a9fc_e85_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"176f084a-7378-46ad-8883-04fc2c979a55","title":"[UI] Extract inline CSS to shared stylesheet","description":"Extract repeated inline CSS from api.py HTML generation into /static/style.css. All pages reference the shared stylesheet. Reduces code duplication and makes styling consistent.","status":"done","priority":45,"task_type":"one_shot","frequency":"","assigned_slot":"0","started_at":null,"completed_at":"2026-04-02 02:58:39","updated_at":"2026-04-02T02:39:58.767385","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/176f084a-737_ui_extract_inline_css_to__spec.md","provider":"any","payload_json":"{}"},{"id":"cdba659d-2592-4fc2-a78d-c4506b58fc77","title":"[UI] Fix SyntaxWarning in cli.py","description":"Change f-string to raw f-string (rf\"\"\") to fix '$' escape sequence warning in bundle_script. One-line fix, no functional changes.","status":"done","priority":40,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:40:22","updated_at":"2026-04-02T03:37:50.192629+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/cdba659d_259_spec.md","provider":"any","payload_json":"{}"}],"reviews":[{"task_count":9,"total_tokens":450000,"total_cost":1.35,"output_score":32033.6644,"efficiency_rating":"normal","reviewed_at":"2026-04-17T11:29:14.374676+00:00"}],"effectiveness":{"task_count":9,"total_lines_added":0,"total_lines_removed":0,"total_files_modified":0,"total_hypotheses":3908,"total_kg_edges":2830243,"total_papers":85997,"total_tokens":450000,"total_duration":9750819.321458999,"avg_impact":1601683.2222222222,"avg_effectiveness":32033.664444444443},"spec_content":"---\ntitle: \"Quest: UI\"\ndescription: \"UI/Infrastructure — consistent styling, responsive design, loading states\"\ntype: quest\nlayer: Cross-cutting\npriority: 75\nstatus: active\nquest_id: d5926799-267\nspec_path: docs/planning/specs/quest_ui_spec.md\n---\n\n# Quest: UI\n\n**Layer:** Cross-cutting \n**Priority:** P75 \n**Status:** active \n**Tasks:** 910 total (158 done, 6 open)\n\n## Vision\n\nUI/Infrastructure — consistent styling, responsive design, loading states\n\n## Open Tasks\n\n- [ ] [UI] Improve /analyses page — add cards with key metrics and debate status (P88)\n- [ ] [UI] Add hypothesis comparison view to Exchange (P85)\n- [ ] [UI] Orphan work detection and linking system (P80)\n- [ ] [UI] CI: Verify all main pages render without errors (P80)\n- [ ] [UI] CI: Site-wide link and render health check (P80)\n- [ ] [UI] Automated visual regression testing (P67)\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: UI

Layer: Cross-cutting \nPriority: P75 \nStatus: active \nTasks: 910 total (158 done, 6 open)

Vision

UI/Infrastructure — consistent styling, responsive design, loading states

Open Tasks

☐ [UI] Improve /analyses page — add cards with key metrics and debate status (P88)
\n
☐ [UI] Add hypothesis comparison view to Exchange (P85)
\n
☐ [UI] Orphan work detection and linking system (P80)
\n
☐ [UI] CI: Verify all main pages render without errors (P80)
\n
☐ [UI] CI: Site-wide link and render health check (P80)
\n
☐ [UI] Automated visual regression testing (P67)

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_ui_spec.md","commits":[{"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":"f39b5d3b0","message":"[Atlas] Fix broken /entity links: clean corrupted data + add cleanup script [task:326c7abd-3ad2-4ae5-9a0e-e9981d611890]","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":"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":"aa2d93a7b","message":"[Atlas] Verify /mission/als broken links: confirmed false positive, all pages HTTP 200 [task:67c9f93b-6399-4750-be74-6968cf5ec437]","date":"2026-04-17"},{"hash":"7294512ce","message":"[Atlas] Re-verify /figures broken links: all 10 HTTP 200, false positive confirmed [task:b28ea9ac-7721-47c3-b580-981fab4fd99e]","date":"2026-04-17"},{"hash":"9eccfd947","message":"[Atlas] Restore figure URL helpers + fix .gitignore","date":"2026-04-17"},{"hash":"a35a2b502","message":"[UI] Fix /api endpoints returning 503/timeout: add short busy_timeout for DB-locked scenarios [task:2b398777-c1e8-4188-a21a-cc65e9fc894f]","date":"2026-04-17"},{"hash":"9e2f78b19","message":"[Atlas] Filter deprecated figure artifacts from URL queries; clean up 10,241 stale artifacts [task:10faed1b-a808-4775-9841-5e3140e6fc9e]","date":"2026-04-17"},{"hash":"5cae0ccb6","message":"[Atlas] Verify /figures broken links: all 10 URLs HTTP 200, false positive confirmed [task:eec54272-a581-4863-ab2d-bd82541e6ad1]","date":"2026-04-17"},{"hash":"4fe296383","message":"[Senate] Improve repair_schema_corruption.py with targeted bogus-entry removal","date":"2026-04-17"},{"hash":"c24704ecb","message":"[Atlas] Document /analysis HTTP 0 links verification: all files exist [task:11b379ae-fef7-4314-91fd-d452fb53021d]","date":"2026-04-17"},{"hash":"3f428bd88","message":"[Forge] Update retraction-check spec with work log and verification [task:t-retraction-check]","date":"2026-04-17"},{"hash":"bd08ca4c6","message":"[Forge] Add retraction_check tool; wire into falsifier processing [task:t-retraction-check]","date":"2026-04-17"},{"hash":"d7707d003","message":"[Atlas] Re-confirm /mission broken links as false positive (third verification) [task:c0d66faa-91be-41e3-909d-d6359c5b936e]","date":"2026-04-17"},{"hash":"02741b075","message":"[Atlas] Document /experiment broken links verification: false positive, HTTP 200 confirmed [task:c5c954fe-c248-4d75-80df-2217edb56bf9]","date":"2026-04-17"},{"hash":"7154b9fbe","message":"[Atlas] Verify /analysis/SDA-2026-04-02-gap-seaad-v4-20260402065846 links working; document resolution [task:817257c0-aa87-4b40-a484-516f6ce868a3]","date":"2026-04-17"}],"related_quests":[{"name":"Epistemic Rigor","layer":"Cross-cutting","priority":95,"status":"active","description":"Evolve SciDEX toward rigorous scientific epistemology: 6-tier epistemic classification (T0 axiom → T5 contested) with asymmetric promotion/demotion (Gödel Machine principle), adversarial Falsifier persona as 5th debate round, proof-gated KG updates with contradiction checking against established knowledge, GFlowNet-inspired diverse hypothesis portfolio maintenance (anti-monoculture rules), pre-registration of predictions before analysis, replication status tracking (unreplicated/replicated/failed_replication), and calibration-adjusted believability weights. Every claim must be traceable to ground truth.","task_count":14,"done_count":14},{"name":"Search","layer":"Cross-cutting","priority":95,"status":"active","description":"Universal search across all SciDEX content with autocomplete","task_count":200,"done_count":13},{"name":"Economics","layer":"Cross-cutting","priority":94,"status":"active","description":"Resource economics — token/cost tracking, belief evolution, impact scoring. Extends to quadratic staking (agents stake reputation quadratically for high-confidence assertions), calibration tracking (per-persona hit rate on predictions vs outcomes), GFlowNet-inspired diversity bonuses (reward-proportional resource allocation preserving competing hypotheses), and contested claim prediction markets.","task_count":196,"done_count":9},{"name":"Evolutionary Arenas","layer":"Cross-cutting","priority":73,"status":"active","description":"Elo tournaments × LMSR markets × evolutionary operators for scientific artifacts. Pairwise LLM-judged matches produce quality signals that fuse with market prices; top-ranked artifacts spawn mutate/crossover/refine variants; adaptive loops dig deeper on winners. Bridges Bradley-Terry ≡ Elo ≡ LMSR via shared functional form. Spec: docs/planning/specs/q-evolutionary-arenas_spec.md","task_count":8,"done_count":7},{"name":"Resources","layer":"Cross-cutting","priority":70,"status":"active","description":"Resource tracking — Bedrock costs, API call logging, budget monitoring","task_count":1,"done_count":1},{"name":"Artifacts","layer":"Cross-cutting","priority":68,"status":"active","description":"Rich artifacts & computational notebooks. Artifact lifecycle governance: git-like versioning (version_number, parent_version_id, changelog), lifecycle states (active/deprecated/cold/superseded), supersession chains with forward reference resolution, dependency tracking, never-delete policy. Deduplication agent scans for duplicates and produces merge recommendations for governance review.","task_count":466,"done_count":89}]}