bd sync: 2025-12-24 12:58:10

.beads/issues.jsonl

@@ -597,7 +597,7 @@
 {"id":"gt-in3x","title":"gt spawn --continue for resuming parked molecules","description":"Add `--continue` flag to gt spawn for resuming parked molecules:\n\n```bash\ngt spawn --continue gt-mol-root\n```\n\nThis:\n1. Finds molecule root\n2. Verifies molecule is in \"parked\" state (in_progress, no assignee)\n3. Checks external deps are now satisfied\n4. Spawns polecat with molecule context\n5. Polecat reads handoff mail and continues from blocked step\n\nPart of cross-project dependency system.\nSee: docs/cross-project-deps.md\n\nDepends on: gt-zniu (gt park)\nDepends on Beads: bd-zmmy (bd ready resolution)","status":"open","priority":2,"issue_type":"feature","created_at":"2025-12-21T22:39:13.154462-08:00","updated_at":"2025-12-21T22:39:13.154462-08:00","dependencies":[{"issue_id":"gt-in3x","depends_on_id":"gt-zniu","type":"blocks","created_at":"2025-12-21T22:39:44.707231-08:00","created_by":"daemon"}]}
 {"id":"gt-in7b","title":"gt sling: nudge crew/mayor if session is running","description":"When slinging to crew or mayor, if they have an active tmux session, send a nudge notification so they know work has landed on their hook.\n\nCurrently only slingToPolecat nudges (lines 514-521 in internal/cmd/sling.go).\n\nMissing nudge in:\n- slingToCrew (line ~669)\n- slingToMayor (line ~876)\n\nNOT applicable to patrol-based agents (witness, refinery, deacon) - they run on cycles and pick up work via hook check, not interactive nudge.\n\nImplementation:\n1. For crew: need to determine session name (e.g., gastown-crew-max)\n2. Check if session running via tmux\n3. If running, call t.NudgeSession() with appropriate message","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-23T15:56:22.30857-08:00","updated_at":"2025-12-23T15:57:01.19806-08:00"}
 {"id":"gt-ingm","title":"Molecular Chemistry Cleanup: Fix inaccurate molecule depictions","description":"## The Correct Model\n\nAccording to molecular-chemistry.md, the hierarchy is:\n\nFormula (YAML DSL) --cook--\u003e Proto (template beads) --pour/wisp--\u003e Mol/Wisp (actual work)\n\n- **Formulas**: YAML files in .beads/formulas/ that define workflow structure\n- **Cook**: Transform formula to proto beads (with [template] label)\n- **Proto**: Template beads with child beads for each step\n- **Pour**: Proto to Mol (persistent liquid)\n- **Wisp**: Proto to Wisp (ephemeral vapor)\n\n## What's Wrong\n\nWe have legacy code and docs that use the OLD model where molecules are defined\nin Go code as structs with embedded markdown, instead of as formula YAML cooked into proto beads.\n\n---\n\n## MAJOR ISSUES\n\n### 1. Go Code: molecules_*.go (DELETE OR REWRITE)\n\n**Files:**\n- internal/beads/builtin_molecules.go\n- internal/beads/molecules_patrol.go (19KB!)\n- internal/beads/molecules_session.go (13KB)\n- internal/beads/molecules_work.go (13KB)\n\n**Problem:** Defines molecules as Go structs with embedded markdown descriptions.\nThis is completely wrong. Molecules should come from:\n1. Formula YAML files cooked into proto beads\n2. Proto beads with child beads for each step\n\n**Used by:**\n- install.go:seedBuiltinMolecules() - seeds during install\n- catalog.go - includes in catalog\n- molecule_list.go:ExportBuiltinMolecules()\n\n**Fix:** Delete these files. Create formula YAML files instead. Update seeding\nto cook formulas into protos.\n\n### 2. Role Templates: Steps Listed in Markdown (REWRITE)\n\n**Files:**\n- prompts/roles/deacon.md - Lists 7 patrol steps\n- prompts/roles/refinery.md - Lists 10 patrol steps\n- prompts/roles/witness.md - Procedural \"Heartbeat Protocol\" (not molecule-based!)\n- prompts/roles/polecat.md - References molecule steps\n\n**Problem:** The steps are listed in the markdown template, but they should be\ndiscovered from the proto beads via bd mol current. Templates should say\n\"check your hook, run your patrol\" without duplicating step definitions.\n\n**Fix:** Templates should describe HOW to run a patrol (propulsion principle,\nbd mol current, bd close --continue), not WHAT the steps are.\n\n### 3. Protos are Empty/Missing (CREATE)\n\n**Current state:**\n- gt-iep9 (mol-deacon-patrol) - Only 2 child steps\n- gt-qflq (mol-witness-patrol) - EMPTY (0 children)\n- mol-refinery-patrol - DOESN'T EXIST\n\n**Fix:** Create formula YAML files for each patrol, cook them into proper protos\nwith child beads for each step.\n\n---\n\n## MEDIUM ISSUES\n\n### 4. Command Confusion: spawn vs pour/wisp\n\n**Files:**\n- prompts/roles/deacon.md - Uses bd mol spawn ... --assignee=deacon\n- prompts/roles/refinery.md - Uses bd mol spawn ... --wisp\n- Various docs\n\n**Problem:** The correct commands per molecular-chemistry.md:\n- bd pour proto - Create persistent mol (liquid)\n- bd wisp proto - Create ephemeral wisp (vapor)\n- bd mol spawn - Old/deprecated\n\n**Fix:** Update all references to use bd wisp for patrols, bd pour for\npersistent work.\n\n### 5. Command Confusion: gt mol vs bd mol\n\n**Files:** Various docs and templates\n\n**Problem:** Some use gt mol status, others bd mol status. Need to clarify:\n- gt mol = Gas Town wrapper (if it exists, what does it add?)\n- bd mol = Beads molecule commands (authoritative)\n\n**Fix:** Audit and standardize. If gt mol is a thin wrapper, remove it.\n\n### 6. polecat-wisp-architecture.md (UPDATE OR DELETE)\n\n**File:** docs/polecat-wisp-architecture.md\n\n**Problem:** References adding molecules to builtin_molecules.go - old model.\n\n### 7. manager.go (UPDATE)\n\n**File:** internal/rig/manager.go\n\n**Problem:** Comment references \"subset of builtin_molecules.go for seeding\"\n\n---\n\n## IMPLEMENTATION ORDER\n\n1. **Create formula YAML files** for the 3 patrol molecules:\n   - mol-deacon-patrol.formula.yaml\n   - mol-witness-patrol.formula.yaml\n   - mol-refinery-patrol.formula.yaml\n\n2. **Implement bd cook** if not already working to create protos from formulas\n\n3. **Cook the formulas** into proto beads with proper child beads\n\n4. **Update role templates** to use propulsion principle without step lists\n\n5. **Delete molecules_*.go** once formulas are working\n\n6. **Update install.go** to cook formulas instead of seeding Go structs\n\n7. **Audit gt mol vs bd mol** and standardize","status":"open","priority":1,"issue_type":"epic","created_at":"2025-12-24T12:37:49.601971-08:00","updated_at":"2025-12-24T12:37:49.601971-08:00"}
-{"id":"gt-ingm.1","title":"Create patrol formula YAML files","description":"Create formula YAML files for:\n- mol-deacon-patrol.formula.yaml\n- mol-witness-patrol.formula.yaml  \n- mol-refinery-patrol.formula.yaml\n\nUse the step definitions currently in molecules_patrol.go as reference.\nStore in .beads/formulas/","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-24T12:38:10.472804-08:00","updated_at":"2025-12-24T12:38:10.472804-08:00"}
+{"id":"gt-ingm.1","title":"Create patrol formula YAML files","description":"Create formula YAML files for:\n- mol-deacon-patrol.formula.yaml\n- mol-witness-patrol.formula.yaml  \n- mol-refinery-patrol.formula.yaml\n\nUse the step definitions currently in molecules_patrol.go as reference.\nStore in .beads/formulas/","status":"in_progress","priority":1,"issue_type":"task","created_at":"2025-12-24T12:38:10.472804-08:00","updated_at":"2025-12-24T12:56:28.825557-08:00"}
 {"id":"gt-ingm.2","title":"Cook patrol formulas into proto beads","description":"Use bd cook to transform formula YAML into proto beads with proper child beads for each step.\n\nVerify with bd mol show that protos have all children.","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-24T12:38:11.762962-08:00","updated_at":"2025-12-24T12:38:11.762962-08:00","dependencies":[{"issue_id":"gt-ingm.2","depends_on_id":"gt-ingm.1","type":"blocks","created_at":"2025-12-24T12:38:23.880593-08:00","created_by":"daemon"}]}
 {"id":"gt-ingm.3","title":"Delete molecules_*.go files","description":"Remove legacy Go-defined molecules:\n- internal/beads/builtin_molecules.go\n- internal/beads/molecules_patrol.go\n- internal/beads/molecules_session.go\n- internal/beads/molecules_work.go\n\nUpdate install.go to cook formulas instead of seeding Go structs.\nUpdate catalog.go if needed.","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-24T12:38:13.028833-08:00","updated_at":"2025-12-24T12:38:13.028833-08:00","dependencies":[{"issue_id":"gt-ingm.3","depends_on_id":"gt-ingm.2","type":"blocks","created_at":"2025-12-24T12:38:23.964643-08:00","created_by":"daemon"}]}
 {"id":"gt-ingm.4","title":"Rewrite role templates without step lists","description":"Update:\n- prompts/roles/deacon.md\n- prompts/roles/refinery.md\n- prompts/roles/witness.md\n\nTemplates should describe HOW to run patrols (propulsion principle, bd mol current, bd close --continue) not WHAT the steps are. Steps come from proto beads.","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-24T12:38:14.388135-08:00","updated_at":"2025-12-24T12:38:14.388135-08:00","dependencies":[{"issue_id":"gt-ingm.4","depends_on_id":"gt-ingm.2","type":"blocks","created_at":"2025-12-24T12:38:24.049212-08:00","created_by":"daemon"}]}
@@ -747,7 +747,7 @@
 {"id":"gt-odfr","title":"Add WaitsFor parsing to molecule steps","description":"Add WaitsFor field to MoleculeStep struct and parse 'WaitsFor: all-children' (and future variants) from molecule descriptions.\n\nThis enables:\n- mol progress to understand fanout patterns\n- Validation that WaitsFor references valid constructs\n- Future automated orchestration\n\nImplementation:\n1. Add WaitsFor []string to MoleculeStep struct\n2. Add waitsForLineRegex to parse 'WaitsFor: ...' lines\n3. Update ParseMoleculeSteps to extract WaitsFor\n4. Update tests","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-23T21:35:55.004767-08:00","updated_at":"2025-12-23T21:41:27.539959-08:00","closed_at":"2025-12-23T21:41:27.539959-08:00","close_reason":"Implemented WaitsFor parsing with tests"}
 {"id":"gt-odvf","title":"Document bd mol bond/squash/burn CLI","description":"Create CLI reference documentation for molecule commands:\n\n## bd mol bond\n\nInstantiate a proto into a runnable molecule.\n\n```bash\nbd mol bond \u003cproto-id\u003e [--wisp] [--assignee=\u003caddr\u003e]\n```\n\n- Default: creates a Mol (durable, in main beads)\n- --wisp: creates a Wisp (ephemeral, in .beads-ephemeral/)\n- --assignee: who will execute this molecule\n\n## bd mol squash\n\nComplete a molecule and generate digest.\n\n```bash\nbd mol squash \u003cmol-id\u003e --summary='...'\n```\n\n- For Mol: creates digest in git history\n- For Wisp: evaporates (no permanent record)\n- --summary: required summary of what was accomplished\n\n## bd mol burn\n\nAbandon a molecule without completing.\n\n```bash\nbd mol burn \u003cmol-id\u003e [--reason='...']\n```\n\n- Discards molecule state\n- No digest created\n- Use when molecule is no longer needed","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-21T16:33:06.462105-08:00","updated_at":"2025-12-23T02:14:23.810794-08:00","closed_at":"2025-12-23T02:14:23.810794-08:00","close_reason":"Already documented in docs/molecules.md lines 70-235","dependencies":[{"issue_id":"gt-odvf","depends_on_id":"gt-62hm","type":"blocks","created_at":"2025-12-21T16:33:17.530156-08:00","created_by":"daemon"}]}
 {"id":"gt-odvr","title":"Merge: gt-r6td","description":"branch: polecat/furiosa\ntarget: main\nsource_issue: gt-r6td\nrig: gastown","status":"closed","priority":1,"issue_type":"merge-request","created_at":"2025-12-22T22:54:01.000047-08:00","updated_at":"2025-12-22T22:55:43.764376-08:00","closed_at":"2025-12-22T22:55:43.764376-08:00","close_reason":"Merged to main"}
-{"id":"gt-ofl2","title":"CRITICAL: ProcessMRFromQueue not implemented - Refinery merge logic stubbed","description":"File: internal/refinery/engineer.go:384\nThe ProcessMRFromQueue() function returns hardcoded failure with TODO comment.\nThis is a core refinery function that cannot process merges in current state.\nMust implement actual merge logic before OSS launch.","status":"open","priority":0,"issue_type":"bug","created_at":"2025-12-24T12:50:27.824454-08:00","updated_at":"2025-12-24T12:50:27.824454-08:00","dependencies":[{"issue_id":"gt-ofl2","depends_on_id":"gt-jo9n","type":"blocks","created_at":"2025-12-24T12:52:04.778532-08:00","created_by":"daemon"}]}
+{"id":"gt-ofl2","title":"CRITICAL: ProcessMRFromQueue not implemented - Refinery merge logic stubbed","description":"File: internal/refinery/engineer.go:384\nThe ProcessMRFromQueue() function returns hardcoded failure with TODO comment.\nThis is a core refinery function that cannot process merges in current state.\nMust implement actual merge logic before OSS launch.","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-12-24T12:50:27.824454-08:00","updated_at":"2025-12-24T12:58:06.150296-08:00","closed_at":"2025-12-24T12:58:06.150296-08:00","close_reason":"Not a blocker: Refinery agent manually executes git commands per role prompt. The stubbed ProcessMRFromQueue is for future beads-based automation, not currently in the active path. manager.ProcessMR() is also fully implemented if needed.","dependencies":[{"issue_id":"gt-ofl2","depends_on_id":"gt-jo9n","type":"blocks","created_at":"2025-12-24T12:52:04.778532-08:00","created_by":"daemon"}]}
 {"id":"gt-ogpk","title":"Add neighbor-check steps to all patrol molecules","description":"Part of the 'Gas Town is a Village' antifragility design.\n\nEvery patrol molecule should include optional neighbor-checking:\n- Deacon checks Witness and Refinery health\n- Witness checks Refinery health  \n- Refinery checks Witness health\n- Polecats can peek other polecats\n\nUse gt peek to check health states.\nIf stuck neighbor found, can nudge or escalate.\n\nThis creates distributed monitoring - no single point of failure.","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-22T22:01:16.358314-08:00","updated_at":"2025-12-22T22:01:16.358314-08:00"}
 {"id":"gt-oh90","title":"Test Patrol for Bonding","description":"Parent issue for mol bond CLI test","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-24T00:23:29.229339-08:00","updated_at":"2025-12-24T00:23:29.6136-08:00","closed_at":"2025-12-24T00:23:29.6136-08:00","close_reason":"Closed"}
 {"id":"gt-oh90.1","title":"Polecat Arm (arm-toast)","description":"Single polecat inspection and action cycle.\n\nThis molecule is bonded dynamically by mol-witness-patrol's survey-workers step.\nEach polecat being monitored gets one arm that runs in parallel with other arms.\n\n## Variables\n\n| Variable | Required | Description |\n|----------|----------|-------------|\n| polecat_name | Yes | Name of the polecat to inspect |\n| rig | Yes | Rig containing the polecat |\n\n## Step: capture\nCapture recent tmux output for toast.\n\n```bash\ntmux capture-pane -t gt-gastown-toast -p | tail -50\n```\n\nRecord:\n- Last activity timestamp (when was last tool call?)\n- Visible errors or stack traces\n- Completion indicators (\"Done\", \"Finished\", etc.)\n\n## Step: assess\nCategorize polecat state based on captured output.\n\nStates:\n- **working**: Recent tool calls, active processing\n- **idle**: At prompt, no recent activity\n- **error**: Showing errors or stack traces\n- **requesting_shutdown**: Sent LIFECYCLE/Shutdown mail\n- **done**: Showing completion indicators\n\nCalculate: minutes since last activity.\nNeeds: capture\n\n## Step: load-history\nRead nudge history for toast from patrol state.\n\n```\nnudge_count = state.nudges[toast].count\nlast_nudge_time = state.nudges[toast].timestamp\n```\n\nThis data was loaded by the parent patrol's load-state step and passed\nto the arm via the bonding context.\nNeeds: assess\n\n## Step: decide\nApply the nudge matrix to determine action for toast.\n\n| State | Idle Time | Nudge Count | Action |\n|-------|-----------|-------------|--------|\n| working | any | any | none |\n| idle | \u003c10min | any | none |\n| idle | 10-15min | 0 | nudge-1 (gentle) |\n| idle | 15-20min | 1 | nudge-2 (direct) |\n| idle | 20+min | 2 | nudge-3 (final) |\n| idle | any | 3 | escalate |\n| error | any | any | assess-severity |\n| requesting_shutdown | any | any | pre-kill-verify |\n| done | any | any | pre-kill-verify |\n\nNudge text:\n1. \"How's progress? Need any help?\"\n2. \"Please wrap up soon. What's blocking you?\"\n3. \"Final check. Will escalate in 5 min if no response.\"\n\nRecord decision and rationale.\nNeeds: load-history\n\n## Step: execute\nTake the decided action for toast.\n\n**nudge-N**:\n```bash\ntmux send-keys -t gt-gastown-toast \"{{nudge_text}}\" Enter\n```\n\n**pre-kill-verify**:\n```bash\ncd polecats/toast\ngit status                    # Must be clean\ngit log origin/main..HEAD     # Check for unpushed\nbd show \u003cassigned-issue\u003e      # Verify closed/deferred\n```\nIf clean: kill session, remove worktree, delete branch\nIf dirty: record failure, retry next cycle\n\n**escalate**:\n```bash\ngt mail send mayor/ -s \"Escalation: toast stuck\" -m \"...\"\n```\n\n**none**: No action needed.\n\nRecord: action taken, result, updated nudge count.\nNeeds: decide\n\n## Output\n\nThe arm completes with:\n- action_taken: none | nudge-1 | nudge-2 | nudge-3 | killed | escalated\n- result: success | failed | pending\n- updated_state: New nudge count and timestamp for toast\n\nThis data feeds back to the parent patrol's aggregate step.\n---\nbonded_from: mol-polecat-arm\nbonded_to: gt-oh90\nbonded_ref: arm-toast\nbonded_at: 2025-12-23T10:00:00Z\n","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-24T00:23:29.326738-08:00","updated_at":"2025-12-24T00:23:29.516266-08:00","closed_at":"2025-12-24T00:23:29.516266-08:00","close_reason":"Closed","dependencies":[{"issue_id":"gt-oh90.1","depends_on_id":"gt-oh90","type":"parent-child","created_at":"2025-12-24T00:23:29.327092-08:00","created_by":"daemon"}]}