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{"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":"in_progress","priority":1,"issue_type":"task","assignee":"gastown/nux","created_at":"2025-12-21T14:33:23.777969-08:00","updated_at":"2025-12-21T15:28:17.365238-08:00","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"}]}
{"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":"open","priority":2,"issue_type":"task","created_at":"2025-12-21T14:33:23.864314-08:00","updated_at":"2025-12-21T14:33:23.864314-08:00","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":"in_progress","priority":2,"issue_type":"task","assignee":"gastown/slit","created_at":"2025-12-21T14:33:23.864314-08:00","updated_at":"2025-12-21T15:28:35.498141-08:00","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.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"}]}