bd sync: 2026-01-04 15:14:11

.beads/issues.jsonl

@@ -301,6 +301,7 @@
 {"id":"bd-beads-crew-giles","title":"Crew worker giles in beads - human-managed persistent workspace.","description":"Crew worker giles in beads - human-managed persistent workspace.\n\nrole_type: crew\nrig: beads\nagent_state: idle\nhook_bead: null\nrole_bead: gt-crew-role\ncleanup_status: null\nactive_mr: null\nnotification_level: null","status":"open","priority":2,"issue_type":"agent","created_at":"2026-01-04T11:22:11.009942-08:00","created_by":"mayor","updated_at":"2026-01-04T11:22:11.009942-08:00"}
 {"id":"bd-beads-crew-grip","title":"Crew worker grip in beads - human-managed persistent workspace.","description":"Crew worker grip in beads - human-managed persistent workspace.\n\nrole_type: crew\nrig: beads\nagent_state: idle\nhook_bead: null\nrole_bead: gt-crew-role\ncleanup_status: null","status":"open","priority":2,"issue_type":"agent","created_at":"2025-12-30T23:14:04.739788-08:00","created_by":"deacon","updated_at":"2026-01-04T11:14:56.280175-08:00"}
 {"id":"bd-beads-crew-wolf","title":"Crew worker wolf in beads - human-managed persistent workspace.","description":"Crew worker wolf in beads - human-managed persistent workspace.\n\nrole_type: crew\nrig: beads\nagent_state: idle\nhook_bead: null\nrole_bead: gt-crew-role\ncleanup_status: null","status":"open","priority":2,"issue_type":"agent","created_at":"2025-12-30T23:14:04.805884-08:00","created_by":"deacon","updated_at":"2026-01-04T11:15:02.743259-08:00"}
+{"id":"bd-beads-polecat-garnet","title":"bd-beads-polecat-garnet","description":"bd-beads-polecat-garnet\n\nrole_type: polecat\nrig: beads\nagent_state: spawning\nhook_bead: bd-hmeb\nrole_bead: hq-polecat-role\ncleanup_status: null\nactive_mr: null\nnotification_level: null","status":"open","priority":2,"issue_type":"agent","created_at":"2026-01-04T15:12:49.812132-08:00","created_by":"mayor","updated_at":"2026-01-04T15:12:51.950599-08:00"}
 {"id":"bd-beads-polecat-jasper","title":"bd-beads-polecat-jasper","description":"bd-beads-polecat-jasper\n\nrole_type: polecat\nrig: beads\nagent_state: spawning\nhook_bead: bd-oos3\nrole_bead: gt-polecat-role\ncleanup_status: null\nactive_mr: bd-srhu\nnotification_level: null","status":"tombstone","priority":2,"issue_type":"agent","created_at":"2026-01-02T12:41:56.3782-08:00","created_by":"mayor","updated_at":"2026-01-04T11:27:04.41339-08:00","deleted_at":"2026-01-02T16:57:50.038825-08:00","deleted_by":"mayor","delete_reason":"delete","original_type":"agent"}
 {"id":"bd-beads-polecat-newbot","title":"Agent: bd-beads-polecat-newbot","status":"tombstone","priority":0,"issue_type":"agent","created_at":"2026-01-02T12:25:10.273273-08:00","created_by":"beads/polecats/obsidian","updated_at":"2026-01-02T12:25:42.678762-08:00","labels":["rig:beads","role_type:polecat"],"deleted_at":"2026-01-02T12:25:42.678762-08:00","deleted_by":"batch delete","delete_reason":"batch delete","original_type":"agent"}
 {"id":"bd-beads-polecat-obsidian","title":"bd-beads-polecat-obsidian","description":"bd-beads-polecat-obsidian\n\nrole_type: polecat\nrig: beads\nagent_state: spawning\nhook_bead: null\nrole_bead: gt-polecat-role\ncleanup_status: null\nactive_mr: bd-xntk\nnotification_level: null","status":"tombstone","priority":2,"issue_type":"agent","created_at":"2026-01-01T11:10:14.972102-08:00","created_by":"mayor","updated_at":"2026-01-04T11:30:56.737474-08:00","deleted_at":"2026-01-02T16:57:50.357825-08:00","deleted_by":"mayor","delete_reason":"delete","original_type":"agent"}
@@ -402,7 +403,6 @@
 {"id":"bd-eijl","title":"bd ship command for publishing capabilities","description":"Add `bd ship \u003ccapability\u003e` command that:\n\n1. Finds issue with `export:\u003ccapability\u003e` label\n2. Validates issue is closed (or --force to override)\n3. Adds `provides:\u003ccapability\u003e` label\n4. Protects `provides:*` namespace (only bd ship can add these labels)\n\nExample:\n```bash\nbd ship mol-run-assignee\n# Output: Shipped mol-run-assignee (bd-xyz)\n```\n\nPart of cross-project dependency system.\nSee: gastown/docs/cross-project-deps.md","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-12-21T22:37:19.123024-08:00","updated_at":"2025-12-21T23:11:47.498859-08:00","closed_at":"2025-12-21T23:11:47.498859-08:00"}
 {"id":"bd-eko4","title":"Add pre-migration orphan cleanup to avoid chicken-and-egg fix failure","description":"## Problem\n\nWhen the database has orphaned foreign key references (dependencies or labels pointing to non-existent issues), the migration invariant check fails, preventing the database from opening. This creates a chicken-and-egg problem:\n\n1. `bd doctor --fix` tries to open the database\n2. Opening triggers migrations with invariant checks\n3. Invariant check fails due to orphaned refs\n4. Fix never runs because database won't open\n\n## Root Cause\n\nAggressive tombstone deletion (e.g., deleting ~1000 old tombstones) left behind orphaned:\n- 218+ dependencies where issue_id not in issues\n- 222+ dependencies where depends_on_id not in issues  \n- 30+ labels where issue_id not in issues\n\n## Current Workaround\n\nDirect SQL to clean up before bd can run:\n```sql\nDELETE FROM dependencies WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = issue_id);\nDELETE FROM dependencies WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = depends_on_id) AND depends_on_id NOT LIKE 'external:%';\nDELETE FROM labels WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = issue_id);\n```\n\n## Proposed Fix\n\nAdd a pre-migration cleanup step that runs BEFORE invariant checks:\n1. Option A: Run orphan cleanup as part of migrations (before invariant check)\n2. Option B: Add `bd doctor --force-fix` that bypasses invariant checks\n3. Option C: Have invariant check auto-clean orphans instead of failing\n\nOption A is cleanest - orphan cleanup should be part of normal migration.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-12-28T23:18:24.65227-08:00","created_by":"beads/crew/dave","updated_at":"2025-12-29T13:46:30.625571-08:00","closed_at":"2025-12-29T13:46:30.625571-08:00","close_reason":"Implemented Option A: CleanOrphanedRefs runs before captureSnapshot in RunMigrations, preventing chicken-and-egg problem"}
 {"id":"bd-elqd","title":"Systematic bd sync stability investigation","description":"## Context\n\nbd sync has chronic instability issues that have persisted since inception:\n- issues.jsonl is always dirty after push\n- bd sync often creates messes requiring manual cleanup\n- Problems escalating despite accumulated bug fixes\n- Workarounds are getting increasingly draconian\n\n## Goal\n\nSystematically observe and diagnose bd sync failures rather than applying band-aid fixes.\n\n## Approach\n\n1. Start fresh session with latest binary (all fixes applied)\n2. Run bd sync and carefully observe what happens\n3. Document exact sequence of events when things go wrong\n4. File specific issues for each discrete problem identified\n5. Track the root causes, not just symptoms\n\n## Test Environment\n\n- Fresh clone or clean state\n- Latest bd binary with all bug fixes\n- Monitor both local and remote JSONL state\n- Check for timing issues, race conditions, merge conflicts\n\n## Success Criteria\n\n- Identify root causes of sync instability\n- Create actionable issues for each problem\n- Eventually achieve stable bd sync (no manual intervention needed)","status":"tombstone","priority":1,"issue_type":"task","created_at":"2025-12-16T22:57:25.35289-08:00","updated_at":"2025-12-17T16:11:17.070763-08:00","deleted_at":"2025-12-17T16:11:17.070763-08:00","deleted_by":"batch delete","delete_reason":"batch delete","original_type":"task"}
-{"id":"bd-eph-5h2","title":"beads-release","description":"Beads release workflow - from version bump to verified release.\n\nThis formula orchestrates a complete release cycle:\n1. Preflight checks (clean git, up to date)\n2. Documentation updates (CHANGELOG, info.go)\n3. Version bump (all components)\n4. Git operations (commit, tag, push)\n5. CI verification (GitHub Actions)\n6. Artifact verification (GitHub, npm, PyPI)\n7. Local installation update\n8. Daemon restart\n\n## Usage\n\n```bash\nbd wisp create beads-release --var version=0.37.0\n```\n\nOr assign to a polecat:\n```bash\ngt sling beads/polecats/p1 --formula beads-release --var version=0.37.0\n```","status":"tombstone","priority":2,"issue_type":"epic","assignee":"beads/crew/emma","created_at":"2025-12-30T21:17:38.213979-08:00","updated_at":"2026-01-01T11:14:44.070596-08:00","deleted_at":"2026-01-01T11:14:44.070596-08:00","deleted_by":"beads/crew/wolf","delete_reason":"misfiled - should have been a wisp","original_type":"epic","ephemeral":true}
 {"id":"bd-epww","title":"Document pinned status in CLI_REFERENCE.md","description":"## Task\n\nThe `pinned` status is a valid issue status but is not documented in CLI_REFERENCE.md.\n\n## Current Status Values (from types.go:295-301)\n\n- open\n- in_progress\n- blocked\n- deferred\n- closed\n- tombstone\n- **pinned** ← undocumented\n\n## Definition\n\n`StatusPinned Status = \"pinned\" // Persistent bead that stays open indefinitely (bd-6v2)`\n\n## Where to Document\n\nAdd to the 'Issue Types' or create a new 'Issue Statuses' section in docs/CLI_REFERENCE.md.\n\n## Related\n\nThe pinned status is heavily used by gt for hook management (`--status=pinned`).","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-27T17:12:35.296002-08:00","created_by":"gastown/crew/joe","updated_at":"2025-12-27T19:13:05.640767-08:00","closed_at":"2025-12-27T19:13:05.640767-08:00"}
 {"id":"bd-etyv","title":"Smart --var detection for mol distill","description":"Implemented bidirectional syntax support for mol distill --var flag.\n\n**Problem:**\n- spawn uses: --var variable=value (assignment style)\n- distill used: --var value=variable (substitution style)\n- Agents would naturally guess spawn-style for both\n\n**Solution:**\nSmart detection that accepts BOTH syntaxes by checking which side appears in the epic text:\n- --var branch=feature-auth → finds 'feature-auth' in text → works\n- --var feature-auth=branch → finds 'feature-auth' in text → also works\n\n**Changes:**\n- Added parseDistillVar() with smart detection\n- Added collectSubgraphText() helper\n- Restructured runMolDistill to load subgraph before parsing vars\n- Updated help text to document both syntaxes\n- Added comprehensive tests in mol_test.go\n\n**Edge cases handled:**\n- Both sides found: prefers spawn-style (more common guess)\n- Neither found: helpful error message\n- Empty sides: validation error\n- Values containing '=' (e.g., KEY=VALUE): works via SplitN\n\nEmbodies the Beads philosophy: watch what agents do, make their guess correct.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-21T11:08:50.83923-08:00","updated_at":"2025-12-21T11:08:56.432536-08:00","closed_at":"2025-12-21T11:08:56.432536-08:00"}
 {"id":"bd-ewcd","title":"Merge: onyx-mjxcs6um","description":"branch: polecat/onyx-mjxcs6um\ntarget: main\nsource_issue: onyx-mjxcs6um\nrig: beads\nagent_bead: bd-beads-polecat-onyx","status":"closed","priority":2,"issue_type":"merge-request","created_at":"2026-01-02T13:07:05.288722-08:00","created_by":"beads/polecats/onyx","updated_at":"2026-01-02T13:41:56.622999-08:00","closed_at":"2026-01-02T13:41:56.622999-08:00","close_reason":"Branches merged, cleaning up stale MR beads"}
@@ -469,6 +469,7 @@
 {"id":"bd-hlsw.3","title":"Auto-recovery mode (bd sync --auto-recover)","description":"Add bd sync --auto-recover flag that: detects problematic sync state, backs up .beads/issues.db with timestamp, rebuilds DB from JSONL atomically, verifies consistency, reports what was fixed. Provides safety valve when sync integrity fails.","status":"closed","priority":3,"issue_type":"task","created_at":"2025-12-14T10:40:20.599836875-07:00","updated_at":"2025-12-30T15:44:43.352476-08:00","closed_at":"2025-12-30T07:02:42.636957-08:00","close_reason":"Implemented --auto-recover flag with detection, backup, rebuild, verify, and reporting. Added tests.","dependencies":[{"issue_id":"bd-hlsw.3","depends_on_id":"bd-hlsw","type":"parent-child","created_at":"2025-12-14T10:40:20.600435888-07:00","created_by":"daemon"}]}
 {"id":"bd-hlsw.4","title":"Sync branch integrity guards","description":"Track sync branch parent commit. If sync branch was force-pushed, warn user and require confirmation before proceeding. Add option to reset to remote if user accepts rebase. Prevents silent corruption from forced pushes.","status":"closed","priority":3,"issue_type":"task","created_at":"2025-12-14T10:40:20.645402352-07:00","updated_at":"2025-12-30T17:05:23.464495-08:00","closed_at":"2025-12-30T17:05:23.464495-08:00","close_reason":"Implemented sync branch integrity guards: (1) Added force-push detection via stored remote SHA tracking, (2) Added user warning and confirmation prompt when force-push detected, (3) Added --accept-rebase flag for non-interactive reset to remote, (4) Added tests for new functionality","dependencies":[{"issue_id":"bd-hlsw.4","depends_on_id":"bd-hlsw","type":"parent-child","created_at":"2025-12-14T10:40:20.646425761-07:00","created_by":"daemon"}]}
 {"id":"bd-hlyr","title":"Merge: bd-m8ro","description":"branch: polecat/max\ntarget: main\nsource_issue: bd-m8ro\nrig: beads","status":"closed","priority":2,"issue_type":"merge-request","created_at":"2025-12-23T20:45:40.218445-08:00","updated_at":"2025-12-23T21:21:57.69886-08:00","closed_at":"2025-12-23T21:21:57.69886-08:00"}
+{"id":"bd-hmeb","title":"bd slot set doesn't support cross-beads prefix routing","description":"## Problem\n\n`bd slot set` fails when setting a slot to a bead that lives in a different beads database (cross-db routing).\n\n## Evidence\n\nWhen spawning a polecat:\n```\nWarning: could not set role slot: bd slot set gt-gastown-polecat-chumbucket role hq-polecat-role: \nError: failed to resolve bead hq-polecat-role: no issue found matching \"hq-polecat-role\"\n```\n\nThe agent bead `gt-gastown-polecat-chumbucket` is in rig beads (`gastown/mayor/rig/.beads/`).\nThe role bead `hq-polecat-role` is in town beads (`~/gt/.beads/`).\n\n`bd show hq-polecat-role` works fine (uses prefix routing via routes.jsonl).\n`bd slot set ... hq-polecat-role` fails (does not use routing).\n\n## Root Cause\n\n`bd slot set` resolves the target bead in the current database only, ignoring the `hq-` prefix that should route to town beads.\n\n## Expected Behavior\n\n`bd slot set \u003cagent\u003e \u003cslot\u003e \u003cbead\u003e` should:\n1. Check if `\u003cbead\u003e` has a routable prefix (e.g., `hq-`, `gt-`, `bd-`)\n2. If so, resolve it via routes.jsonl like `bd show` does\n3. Store the bead reference (cross-db references are valid for slots)\n\n## Workaround\n\nCurrently the warning is non-fatal - the role slot just is not set. But this breaks role-based queries.\n\n## Files\n\n- `cmd/slot.go` - slot set command implementation\n- Need to add routing logic similar to `cmd/show.go`","status":"in_progress","priority":1,"issue_type":"bug","assignee":"beads/polecats/garnet","created_at":"2026-01-04T15:12:40.230597-08:00","created_by":"mayor","updated_at":"2026-01-04T15:13:33.548834-08:00"}
 {"id":"bd-hnkg","title":"GH#540: Add silent quick-capture mode (bd q)","description":"Add bd q alias for quick capture that outputs only issue ID. Useful for piping/scripting. See GitHub issue #540.","status":"tombstone","priority":2,"issue_type":"feature","created_at":"2025-12-16T01:03:38.260135-08:00","updated_at":"2025-12-17T16:11:17.070763-08:00","deleted_at":"2025-12-17T16:11:17.070763-08:00","deleted_by":"batch delete","delete_reason":"batch delete","original_type":"feature"}
 {"id":"bd-hobo","title":"Distinct prefixes for protos, molecules, wisps","description":"Template/workflow entities should have visually distinct prefixes from regular issues.\n\n**Problem:**\n- Protos (bd-7bs4) look like regular issues - invites squashing\n- Molecules (poured instances) also use bd- prefix\n- Wisps are in separate DB but still use bd- when referenced\n\n**Proposed Prefixes:**\n- `proto-` for templates (e.g., proto-release, proto-review)\n- `mol-` for active molecules (poured from protos)\n- `wisp-` for ephemeral wisps (vapor phase)\n\n**Benefits:**\n- Instant visual recognition of entity type\n- Prevents accidental modification of templates\n- Clear lifecycle: proto → mol → wisp → digest\n\n**Implementation options:**\n1. Separate databases with different prefixes\n2. Issue type determines prefix generation\n3. Naming convention enforced by bd pour/wisp commands","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-12-24T16:45:24.940809-08:00","updated_at":"2025-12-25T02:04:52.459233-08:00","closed_at":"2025-12-25T02:04:52.459233-08:00","labels":["workflow"]}
 {"id":"bd-hp8g","title":"gt sling should look up formulas from .beads/formulas/ registry","description":"## Problem\n\ngt sling \u003cformula-name\u003e doesn't find formulas from the registry that bd formula list shows.\n\n## What I tried\n\n1. gt sling beads/crew/emma --formula beads-release --var version=0.42.0\n   - Problem: --formula flag doesn't exist\n\n2. gt sling beads-release beads/crew/emma --var version=0.42.0\n   - Error: open .../beads-release: no such file or directory\n   - Problem: Looks for file in cwd, not formula registry\n\n## What worked\n\nbd mol wisp beads-release --var version=0.42.0 - correctly finds formula from .beads/formulas/\n\n## Expected\n\ngt sling should use the same formula lookup as bd mol wisp - checking .beads/formulas/*.formula.json\n\n## Documentation gap\n\nThe help shows examples like 'gt sling mol-release mayor/' suggesting formula slinging works, but it doesn't find registry formulas.","status":"closed","priority":2,"issue_type":"bug","assignee":"beads/polecats/jade","created_at":"2025-12-30T21:18:17.251292-08:00","created_by":"beads/crew/emma","updated_at":"2025-12-30T22:06:27.153176-08:00","closed_at":"2025-12-30T22:06:27.153176-08:00","close_reason":"Fixed in both repos: bd cook now looks up formulas from registry, and gt sling uses bd mol wisp"}
@@ -899,7 +900,7 @@
 {"id":"bd-vgi5","title":"Push version bump to GitHub","description":"git push origin main - triggers CI but no release yet.","status":"tombstone","priority":1,"issue_type":"task","created_at":"2025-12-18T22:43:05.363604-08:00","updated_at":"2025-12-24T16:25:30.019895-08:00","dependencies":[{"issue_id":"bd-vgi5","depends_on_id":"bd-qqc","type":"parent-child","created_at":"2025-12-18T22:43:16.87736-08:00","created_by":"daemon"},{"issue_id":"bd-vgi5","depends_on_id":"bd-3ggb","type":"blocks","created_at":"2025-12-18T22:43:21.078208-08:00","created_by":"daemon"}],"deleted_at":"2025-12-24T16:25:30.019895-08:00","deleted_by":"daemon","delete_reason":"delete","original_type":"task"}
 {"id":"bd-vii9","title":"bd agent state fails when agent bead doesn't exist","description":"## Bug\n\n`bd agent state \u003cagent\u003e \u003cstate\u003e` fails if the agent doesn't already exist as a bead.\n\n## Reproduction\n\n```\ngt sling gt-nrpiq gastown\n...\nWarning: couldn't update agent gt-gastown-polecat-toast hook to gt-nrpiq: \n  updating agent state: bd agent state gt-gastown-polecat-toast running: \n  Error: failed to resolve agent gt-gastown-polecat-toast: \n  no issue found matching \"gt-gastown-polecat-toast\"\n```\n\n## Context from HOP Design\n\nFrom **docs/hop/CONTEXT.md**:\n\u003e \"Each polecat should have a chain: What work have they done? What's their success rate? What skills have they demonstrated?\"\n\nFrom **docs/PRIMING.md**:\n\u003e \"Polecats are ephemeral executors. Like K8s pods. They have names (for debugging, logs) but no persistent identity.\"\n\n**Resolution**: Polecat *sessions* are ephemeral, but polecat *names* (toast, nux, furiosa, etc.) are recycled and SHOULD have persistent identity beads. The name is the identity - sessions come and go.\n\nThink of it like K8s:\n- **Pod** = polecat session (ephemeral, killed after task)\n- **ServiceAccount** = polecat identity bead (persistent, accumulates history)\n\n## Solution\n\n`bd agent state` should **auto-create** the agent bead on first use:\n\n```go\n// If agent bead doesn't exist, create it\nif errors.Is(err, ErrNotFound) {\n    // Create identity bead for this agent\n    _, err = CreateIssue(Issue{\n        Title:    fmt.Sprintf(\"Agent: %s\", agentName),\n        Type:     \"agent\",\n        Status:   state,\n        Metadata: map[string]string{\n            \"role\": parseRole(agentName),  // polecat, witness, etc.\n            \"rig\":  parseRig(agentName),   // gastown, beads, etc.\n        },\n    })\n}\n```\n\nThis enables:\n1. Work history accumulation per polecat name\n2. Skill/success tracking over time\n3. CV chain for the polecat identity\n4. `bd list --type=agent` to see all agents\n\n## Non-goals\n\n- Session tracking (ephemeral, don't persist)\n- Work attribution to polecat (credits human owner)\n- Agent scheduling (Gas Town handles that)","status":"closed","priority":3,"issue_type":"bug","assignee":"beads/polecats/obsidian","created_at":"2026-01-02T12:16:39.116652-08:00","created_by":"mayor","updated_at":"2026-01-02T12:27:05.679183-08:00","closed_at":"2026-01-02T12:27:05.679183-08:00","close_reason":"Implemented auto-create logic in runAgentState to create agent beads on first use"}
 {"id":"bd-vjas","title":"Add --pretty flag to bd ready","description":"bd list has --pretty but bd ready doesn't. Should support same tree format with status/priority symbols for consistency.","status":"closed","priority":3,"issue_type":"feature","created_at":"2025-12-31T11:54:59.911409-08:00","created_by":"mayor","updated_at":"2026-01-01T11:16:53.096168-08:00","closed_at":"2026-01-01T11:16:53.096168-08:00","close_reason":"Implemented --pretty flag for bd ready"}
-{"id":"bd-vjdt","title":"Add bd doctor check for JSONL/SQLite/git divergence","description":"Part of GH#885 fix: recovery mechanism. Add new doctor check that detects: 1) JSONL on disk differs from git HEAD version, 2) SQLite last_import_time does not match JSONL mtime, 3) Uncommitted .beads/ changes exist. Auto-fix options: re-export from SQLite, re-import from JSONL, or commit pending changes. Key file: cmd/bd/doctor/fix/sync.go","status":"in_progress","priority":1,"issue_type":"task","assignee":"beads/crew/wolf","created_at":"2026-01-04T13:53:43.848369-08:00","created_by":"beads/crew/emma","updated_at":"2026-01-04T15:07:25.226194-08:00","dependencies":[{"issue_id":"bd-vjdt","depends_on_id":"bd-pnx2","type":"parent-child","created_at":"2026-01-04T13:53:55.84741-08:00","created_by":"beads/crew/emma"}]}
+{"id":"bd-vjdt","title":"Add bd doctor check for JSONL/SQLite/git divergence","description":"Part of GH#885 fix: recovery mechanism. Add new doctor check that detects: 1) JSONL on disk differs from git HEAD version, 2) SQLite last_import_time does not match JSONL mtime, 3) Uncommitted .beads/ changes exist. Auto-fix options: re-export from SQLite, re-import from JSONL, or commit pending changes. Key file: cmd/bd/doctor/fix/sync.go","status":"closed","priority":1,"issue_type":"task","assignee":"beads/crew/wolf","created_at":"2026-01-04T13:53:43.848369-08:00","created_by":"beads/crew/emma","updated_at":"2026-01-04T15:14:01.129418-08:00","closed_at":"2026-01-04T15:14:01.129418-08:00","close_reason":"Implemented CheckSyncDivergence doctor check","dependencies":[{"issue_id":"bd-vjdt","depends_on_id":"bd-pnx2","type":"parent-child","created_at":"2026-01-04T13:53:55.84741-08:00","created_by":"beads/crew/emma"}]}
 {"id":"bd-vks2","title":"bd dep tree doesn't display external dependencies","description":"GetDependencyTree (dependencies.go:464-624) uses a recursive CTE that JOINs with the issues table, which means external refs (external:project:capability) are invisible in the tree output.\n\nWhen an issue has an external blocking dependency, running 'bd dep tree \u003cid\u003e' won't show it.\n\nOptions:\n1. Query dependencies table separately for external refs and display them as leaf nodes\n2. Add a synthetic 'external' node type that shows the ref and resolution status\n3. Document that external deps aren't shown in tree view (use bd show for full deps)\n\nLower priority since bd show \u003cid\u003e displays all dependencies including external refs.","status":"closed","priority":3,"issue_type":"task","created_at":"2025-12-21T23:45:27.121934-08:00","updated_at":"2025-12-22T22:30:19.083652-08:00","closed_at":"2025-12-22T22:30:19.083652-08:00","dependencies":[{"issue_id":"bd-vks2","depends_on_id":"bd-zmmy","type":"discovered-from","created_at":"2025-12-21T23:45:27.122511-08:00","created_by":"daemon"}]}
 {"id":"bd-vln0","title":"Add display guards for large molecules in bd mol current","description":"When molecule has \u003e100 steps, show summary instead of list.\n\nChanges:\n1. Count children first\n2. If count \u003e 100: show summary + pointer to bd mol progress\n3. Add --range flag for viewing specific step ranges\n4. Add --limit flag for capping output","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-31T00:52:52.823925-08:00","created_by":"gastown/crew/max","updated_at":"2025-12-31T13:08:19.539445-08:00","closed_at":"2025-12-31T13:08:19.539445-08:00","close_reason":"Added display guards: threshold check, --limit and --range flags","dependencies":[{"issue_id":"bd-vln0","depends_on_id":"bd-5nu1","type":"parent-child","created_at":"2025-12-31T00:54:00.833563-08:00","created_by":"gastown/crew/max"}]}
 {"id":"bd-vpan","title":"Re: Thread Test 2","description":"Got your message. Testing reply feature.","status":"tombstone","priority":2,"issue_type":"message","created_at":"2025-12-16T18:21:29.144352-08:00","updated_at":"2025-12-17T16:11:17.070763-08:00","dependencies":[{"issue_id":"bd-vpan","depends_on_id":"bd-x36g","type":"replies-to","created_at":"2025-12-18T13:45:31.137191-08:00","created_by":"migration"}],"deleted_at":"2025-12-17T16:11:17.070763-08:00","deleted_by":"batch delete","delete_reason":"batch delete","original_type":"message"}