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@@ -52,7 +52,7 @@
{"id":"gt-3x0z.11","title":"Phase 5.1: Document ephemeral architecture","description":"Update docs with ephemeral molecule architecture.\n\n## Files to Update\n\n### docs/architecture.md\n- Add Ephemeral Molecules section\n- Diagram: Proto → Ephemeral → Digest flow\n- Explain inversion of control for summaries\n\n### docs/molecules.md (new or update)\n- Proto molecule catalog\n- Ephemeral vs main beads\n- Molecule lifecycle\n- Summary generation guidelines\n\n### Agent CLAUDE.md files\n- Polecat: molecule workflow protocol\n- Deacon: patrol cycle pattern\n- Witness: patrol cycle pattern\n- Refinery: patrol cycle pattern\n\n## Key Concepts to Document\n\n1. Everything is a molecule\n2. Orchestration molecules are ephemeral\n3. Only digests reach main beads\n4. Agents generate their own summaries\n5. Crash recovery via ephemeral persistence","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-21T14:34:30.074147-08:00","updated_at":"2025-12-21T14:34:30.074147-08:00","dependencies":[{"issue_id":"gt-3x0z.11","depends_on_id":"gt-3x0z","type":"parent-child","created_at":"2025-12-21T14:34:30.075854-08:00","created_by":"daemon"},{"issue_id":"gt-3x0z.11","depends_on_id":"gt-3x0z.10","type":"blocks","created_at":"2025-12-21T14:34:40.812635-08:00","created_by":"daemon"}]}
{"id":"gt-3x0z.12","title":"Phase 5.2: Ephemeral error handling and recovery","description":"Handle edge cases in ephemeral molecule lifecycle.\n\n## Scenarios\n\n### Agent dies mid-molecule\n- Ephemeral state persists\n- Witness detects stall (no heartbeat)\n- Options:\n a. Nudge agent to resume\n b. Reassign to new agent\n c. Escalate to Mayor\n\n### Squash fails\n- Retry with exponential backoff\n- If persistent failure, escalate\n- Don't lose the ephemeral state until squash succeeds\n\n### Orphaned molecules\n- Molecule started, never completed\n- gt doctor detects (\u003e24h old with no activity)\n- Options:\n a. Manual review\n b. Auto-abandon with 'abandoned' digest\n c. Reassign\n\n### Ephemeral repo corruption\n- Re-init from scratch\n- Active molecules are lost\n- Main beads is source of truth for assigned work\n\n## Implementation\n\nAdd error handling to:\n- bd mol bond (handle init failures)\n- bd squash (retry logic)\n- gt doctor (recovery suggestions)","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-21T14:34:30.158784-08:00","updated_at":"2025-12-21T14:34:30.158784-08:00","dependencies":[{"issue_id":"gt-3x0z.12","depends_on_id":"gt-3x0z","type":"parent-child","created_at":"2025-12-21T14:34:30.15923-08:00","created_by":"daemon"},{"issue_id":"gt-3x0z.12","depends_on_id":"gt-3x0z.9","type":"blocks","created_at":"2025-12-21T14:34:40.886432-08:00","created_by":"daemon"}]}
{"id":"gt-3x0z.2","title":"Phase 1.2: Configure bd for ephemeral molecule bonding","description":"Ensure bd mol bond --ephemeral works with Gas Town setup.\n\n## Questions for Dave\n\n1. Does bd automatically find .beads-ephemeral/ or need explicit path?\n2. How does bd mol bond --ephemeral know which repo to use?\n3. Is there a redirect mechanism for ephemeral like main beads?\n\n## Integration\n\nFrom polecat/crew working directory:\n```bash\nbd mol bond mol-polecat-work --ephemeral --assignee $(gt whoami)\n```\n\nShould create molecule in rig's .beads-ephemeral/, not main beads.","status":"closed","priority":1,"issue_type":"task","assignee":"gastown/nux","created_at":"2025-12-21T14:33:23.777969-08:00","updated_at":"2025-12-21T15:59:40.899659-08:00","closed_at":"2025-12-21T15:59:40.899659-08:00","close_reason":"Blocked: bd mol bond --ephemeral does not exist. The --ephemeral flag needs to be implemented in the beads repo first. See analysis comment for full details and recommendations.","dependencies":[{"issue_id":"gt-3x0z.2","depends_on_id":"gt-3x0z","type":"parent-child","created_at":"2025-12-21T14:33:23.77835-08:00","created_by":"daemon"}],"comments":[{"id":1,"issue_id":"gt-3x0z.2","author":"stevey","text":"## Analysis: bd mol bond --ephemeral\n\n### Current State\n\n1. **No --ephemeral flag exists** on `bd mol bond`\n - The help shows: --as, --dry-run, --type, --var\n - No ephemeral option\n\n2. **mol run has implicit ephemeral behavior**\n - In mol_run.go:93, spawnMolecule is called with ephemeral=true\n - This marks spawned issues with wisp=true field\n\n3. **Current wisp implementation is field-based, not storage-based**\n - Wisps are stored in the SAME database as regular issues\n - The wisp field just marks them for cleanup when closed\n - No separate `.beads-ephemeral/` directory exists\n\n### Architecture Gap\n\nThe architecture.md describes (lines 487-491):\n```\nWisps are stored in a per-rig ephemeral database:\n- \u003crig\u003e/.beads-ephemeral/ - Separate from permanent beads\n- Fast writes, no sync overhead\n- Auto-cleaned on squash/burn\n- Digests write to permanent beads\n```\n\nThis is NOT implemented. Current state:\n- Wisps go to same .beads/beads.db\n- Wisps are synced with everything else\n- No separate ephemeral store\n\n### Answers to Dave's Questions\n\n1. **Does bd automatically find .beads-ephemeral/?**\n NO - This directory concept is not yet implemented. bd only finds .beads/\n\n2. **How does bd mol bond --ephemeral know which repo to use?**\n N/A - The flag doesn't exist yet. Would need to be implemented.\n\n3. **Is there a redirect mechanism for ephemeral?**\n NO - Only BEADS_DIR env var exists for redirecting regular beads.\n\n### Recommendations\n\n**Option A: Minimal (Phase 1)**\n- Add --ephemeral flag to mol bond\n- Use existing wisp field (just marks issues)\n- No separate storage yet\n\n**Option B: Full Architecture**\n- Create .beads-ephemeral/ storage layer\n- Add findEphemeralBeadsDir() discovery\n- Route --ephemeral operations there\n- Implement squash/burn cleanup\n\n### For Gas Town Integration\n\nCurrent workaround using mol run:\n```bash\n# mol run already sets ephemeral=true internally\nbd mol run mol-polecat-work --var assignee=$(gt whoami)\n```\n\nFull integration would need beads changes first.","created_at":"2025-12-21T23:59:33Z"}]}
{"id":"gt-3x0z.3","title":"Phase 1.3: gt doctor checks for ephemeral health","description":"Add doctor checks for ephemeral beads repo.\n\n## Checks\n\n1. **ephemeral-exists**: .beads-ephemeral/ directory exists for each rig\n2. **ephemeral-git**: It's a valid git repo\n3. **ephemeral-orphans**: Molecules started but never squashed (\u003e24h old)\n4. **ephemeral-size**: Warn if ephemeral repo is \u003e100MB (should be cleaned)\n5. **ephemeral-stale**: Molecules with no activity in last hour\n\n## Auto-fix\n\n--fix can:\n- Create missing ephemeral repo\n- Clean up old completed molecules (already squashed)\n- NOT auto-squash incomplete molecules (needs AI summary)","status":"in_progress","priority":2,"issue_type":"task","assignee":"gastown/rictus","created_at":"2025-12-21T14:33:23.864314-08:00","updated_at":"2025-12-21T15:55:25.877899-08:00","dependencies":[{"issue_id":"gt-3x0z.3","depends_on_id":"gt-3x0z","type":"parent-child","created_at":"2025-12-21T14:33:23.864678-08:00","created_by":"daemon"}]}
{"id":"gt-3x0z.3","title":"Phase 1.3: gt doctor checks for ephemeral health","description":"Add doctor checks for ephemeral beads repo.\n\n## Checks\n\n1. **ephemeral-exists**: .beads-ephemeral/ directory exists for each rig\n2. **ephemeral-git**: It's a valid git repo\n3. **ephemeral-orphans**: Molecules started but never squashed (\u003e24h old)\n4. **ephemeral-size**: Warn if ephemeral repo is \u003e100MB (should be cleaned)\n5. **ephemeral-stale**: Molecules with no activity in last hour\n\n## Auto-fix\n\n--fix can:\n- Create missing ephemeral repo\n- Clean up old completed molecules (already squashed)\n- NOT auto-squash incomplete molecules (needs AI summary)","status":"closed","priority":2,"issue_type":"task","assignee":"gastown/rictus","created_at":"2025-12-21T14:33:23.864314-08:00","updated_at":"2025-12-21T16:03:03.287627-08:00","closed_at":"2025-12-21T16:03:03.287627-08:00","close_reason":"Implemented all 5 ephemeral health checks: ephemeral-exists (fixable), ephemeral-git (fixable), ephemeral-orphans, ephemeral-size, ephemeral-stale","dependencies":[{"issue_id":"gt-3x0z.3","depends_on_id":"gt-3x0z","type":"parent-child","created_at":"2025-12-21T14:33:23.864678-08:00","created_by":"daemon"}]}
{"id":"gt-3x0z.4","title":"Phase 2.1: gt spawn --molecule bonds in ephemeral","description":"Make gt spawn molecule-aware with ephemeral bonding.\n\n## New Flag\n\n```bash\ngt spawn --issue gt-xxx --molecule mol-polecat-work\n```\n\n## Behavior\n\n1. Create polecat with fresh worktree (existing)\n2. Bond molecule in ephemeral: `bd mol bond mol-polecat-work --ephemeral`\n3. Link molecule root to source issue\n4. Include molecule context in work assignment mail\n5. Start session\n\n## Work Assignment Mail\n\n```\nSubject: Work Assignment: Fix lifecycle bug [MOLECULE]\n\nYou are working on gt-rixa as part of molecule mol-polecat-work.\n\nMolecule instance: eph-abc123\nCurrent step: read-assignment (1/8)\n\nFollow the molecule workflow. When complete, generate summary and squash.\n```","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-21T14:33:45.082722-08:00","updated_at":"2025-12-21T14:33:45.082722-08:00","dependencies":[{"issue_id":"gt-3x0z.4","depends_on_id":"gt-3x0z","type":"parent-child","created_at":"2025-12-21T14:33:45.084965-08:00","created_by":"daemon"},{"issue_id":"gt-3x0z.4","depends_on_id":"gt-3x0z.1","type":"blocks","created_at":"2025-12-21T14:34:40.385365-08:00","created_by":"daemon"},{"issue_id":"gt-3x0z.4","depends_on_id":"gt-3x0z.2","type":"blocks","created_at":"2025-12-21T14:34:40.457259-08:00","created_by":"daemon"}]}
{"id":"gt-3x0z.5","title":"Phase 2.2: gt prime shows ephemeral molecule context","description":"Update gt prime to detect and display ephemeral molecule state.\n\n## Detection\n\n1. Check for active ephemeral molecule assigned to current identity\n2. Parse molecule progress (current step, total steps)\n3. Show in prime output\n\n## Output\n\n```\n🔧 Polecat furiosa, checking in.\n\n📦 Molecule: mol-polecat-work (eph-abc123)\n Step 3/8: do-work\n Source: gt-rixa\n Started: 10 minutes ago\n\nRun 'bd mol status' for full molecule state.\n```","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-21T14:33:45.164431-08:00","updated_at":"2025-12-21T14:33:45.164431-08:00","dependencies":[{"issue_id":"gt-3x0z.5","depends_on_id":"gt-3x0z","type":"parent-child","created_at":"2025-12-21T14:33:45.16487-08:00","created_by":"daemon"},{"issue_id":"gt-3x0z.5","depends_on_id":"gt-3x0z.4","type":"blocks","created_at":"2025-12-21T15:22:46.151626-08:00","created_by":"daemon"}]}
{"id":"gt-3x0z.6","title":"Phase 2.3: Polecat CLAUDE.md molecule workflow protocol","description":"Update polecat prompting for molecule-based work.\n\n## CLAUDE.md Updates\n\nAdd section on molecule workflow:\n\n```markdown\n## Molecule Workflow\n\nWhen assigned a molecule (check gt prime output):\n\n1. Follow molecule steps in order\n2. Mark steps complete: bd mol step complete \u003cstep-id\u003e\n3. Before signaling done:\n a. Generate summary of work performed\n b. Run: bd squash \u003cmolecule-root\u003e --summary \"\u003cyour summary\u003e\"\n4. Then signal done as normal\n\n### Summary Guidelines\n\nYour summary should include:\n- What was the task?\n- What did you do?\n- What was the outcome?\n- Any issues or follow-ups?\n\nKeep it to 2-4 sentences. This becomes the permanent record.\n```","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-21T14:33:45.24122-08:00","updated_at":"2025-12-21T14:33:45.24122-08:00","dependencies":[{"issue_id":"gt-3x0z.6","depends_on_id":"gt-3x0z","type":"parent-child","created_at":"2025-12-21T14:33:45.241575-08:00","created_by":"daemon"},{"issue_id":"gt-3x0z.6","depends_on_id":"gt-3x0z.4","type":"blocks","created_at":"2025-12-21T15:22:47.355729-08:00","created_by":"daemon"}]}
@@ -289,6 +289,7 @@
{"id":"gt-h5n.9","title":"Per-epic config overrides: custom merge settings","description":"Allow per-epic merge configuration overrides.\n\nEpic can specify merge_config in its description:\n merge_config:\n run_tests: true\n test_command: 'go test -race ./...'\n on_conflict: assign_back\n\nWhen processing MRs for an epic:\n1. Load rig-level merge_queue config\n2. Check if epic has merge_config\n3. Merge epic config over rig config\n4. Use merged config for processing\n\nUse cases:\n- Risky refactors: more thorough testing\n- Urgent fixes: skip some checks\n- Experimental work: different test suite\n\nReference: docs/merge-queue-design.md#per-epic-overrides","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-17T13:52:02.32832-08:00","updated_at":"2025-12-17T13:52:02.32832-08:00","dependencies":[{"issue_id":"gt-h5n.9","depends_on_id":"gt-h5n","type":"parent-child","created_at":"2025-12-17T13:52:02.32997-08:00","created_by":"daemon"}]}
{"id":"gt-hcc0","title":"gt polecat remove --all: bulk polecat teardown","description":"Currently gt polecat remove only accepts one polecat at a time. Need bulk operations:\n\n## Requested\n- `gt polecat remove gastown --all` - remove all polecats from a rig\n- `gt polecat remove gastown/A gastown/B ...` - remove multiple by name\n\n## Context\nAfter a swarm completes, tearing down 20 polecats one at a time is tedious.\nEphemeral workers should be easy to create and destroy in bulk.\n\n## Related\n- gt-c92: CLI: all command for batch polecat operations","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-12-19T14:06:43.892225-08:00","updated_at":"2025-12-20T13:16:06.901839-08:00","closed_at":"2025-12-20T13:16:06.901839-08:00"}
{"id":"gt-hgk","title":"Mail system: message types and threading","description":"GGT mail system needs message types and threading like PGT.\n\n## 1. Message Types\nAdd to internal/mail/types.go:\n```go\ntype MessageType string\nconst (\n TypeTask MessageType = \"task\" // Required processing\n TypeScavenge MessageType = \"scavenge\" // Optional first-come work\n TypeNotification MessageType = \"notification\" // Informational\n TypeReply MessageType = \"reply\" // Response to message\n)\n\n// Update Message struct\ntype Message struct {\n // existing fields...\n Type MessageType `json:\"type\"`\n ThreadID string `json:\"thread_id,omitempty\"`\n ReplyTo string `json:\"reply_to,omitempty\"`\n}\n```\n\n## 2. Priority Levels\nExpand from 2 to 4:\n```go\ntype Priority string\nconst (\n PriorityLow Priority = \"low\"\n PriorityNormal Priority = \"normal\"\n PriorityHigh Priority = \"high\"\n PriorityUrgent Priority = \"urgent\"\n)\n```\n\n## 3. CLI Updates\ninternal/cmd/mail.go:\n- Add --type flag to send: `gt mail send ... --type task`\n- Add --reply-to flag: `gt mail send ... --reply-to \u003cmsg-id\u003e`\n- Add thread command: `gt mail thread \u003cthread-id\u003e`\n\n## 4. Threading Logic\nNewMessage() should auto-generate thread_id if not a reply.\nReply messages inherit thread_id from original.\n\n## Files to Modify\n- internal/mail/types.go: Add types, expand Priority\n- internal/mail/mailbox.go: Thread filtering\n- internal/cmd/mail.go: CLI flags and thread command\n\n## PGT Reference\ngastown-py/src/gastown/mail/message.py\n\n## Acceptance Criteria\n- [ ] Messages have type field (default: notification)\n- [ ] 4 priority levels supported\n- [ ] Reply creates thread with shared thread_id\n- [ ] gt mail thread \u003cid\u003e shows conversation","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-16T14:46:55.29463-08:00","updated_at":"2025-12-18T20:14:28.308997-08:00","closed_at":"2025-12-18T20:14:28.308997-08:00"}
{"id":"gt-hj7f","title":"Merge: gt-3x0z.2","description":"branch: polecat/nux\ntarget: main\nsource_issue: gt-3x0z.2\nrig: gastown","status":"open","priority":1,"issue_type":"merge-request","created_at":"2025-12-21T16:01:27.529537-08:00","updated_at":"2025-12-21T16:01:27.529537-08:00"}
{"id":"gt-hoyd","title":"Merge: gt-rana.1","description":"branch: polecat/rictus\ntarget: main\nsource_issue: gt-rana.1\nrig: gastown","status":"closed","priority":1,"issue_type":"merge-request","created_at":"2025-12-21T15:51:03.089517-08:00","updated_at":"2025-12-21T15:54:12.41736-08:00","closed_at":"2025-12-21T15:54:12.41736-08:00","close_reason":"Merged to main by refinery"}
{"id":"gt-htto","title":"Heartbeat convention: simple liveness signal for agents","description":"Lightweight liveness signal extracted from Deacon epic (gt-5af).\n\n**Implementation**: Each agent writes a timestamp file on activity:\n```bash\necho '{\"ts\":\"'$(date -Iseconds)'\"}' \u003e ~/gt/\u003crole\u003e/heartbeat.json\n```\n\n**Integration points**:\n- SessionStart hook writes heartbeat\n- Periodic activity (mail check, work completion) refreshes it\n- `gt status` shows staleness (e.g., 'mayor: 5m ago')\n\n**Weight**: ~5 lines per agent\n**Value**: Quick debugging - see which agents are active at a glance\n\nNo monitoring daemon needed - human checks `gt status` when curious.","status":"open","priority":3,"issue_type":"task","created_at":"2025-12-20T20:40:45.459903-08:00","updated_at":"2025-12-20T20:40:45.459903-08:00"}
{"id":"gt-hw6","title":"GGT Command Parity: Complete gt command coverage","description":"Complete gt command set to match/exceed PGT town commands.\n\nCovers: uninstall, rig info, refinery attach, witness, session mgmt, mail UX, daemon.","status":"closed","priority":1,"issue_type":"epic","created_at":"2025-12-17T22:22:21.720078-08:00","updated_at":"2025-12-19T12:05:36.723692-08:00","closed_at":"2025-12-19T12:05:36.723692-08:00"}