bd doctor v0.46.0

CORE SYSTEM
  ✓  Installation .beads/ directory found
  ✓  Fresh Clone Database exists
  ✓  Database version 0.46.0
     └─ Storage: SQLite
  ✓  Schema Compatibility All required tables and columns present
  ✓  Repo Fingerprint Verified (8bb5246b)
  ✓  Database Integrity No corruption detected
  ✓  Issue IDs hash-based ✓
  ✓  CLI Version 0.46.0 (latest)
  ✓  Permissions All permissions OK

DATA & CONFIG
  ✓  Database Files Single database file
  ⚠  JSONL Files Multiple JSONL files found: issues.jsonl, routes.jsonl
     └─ Having multiple JSONL files can cause sync and merge conflicts.
  Only one JSONL file should be used per repository.           
  ✓  JSONL Config Using issues.jsonl
  ✓  Database Config Configuration matches existing files
  ✓  Config Values All configuration values are valid
  ✓  JSONL Integrity issues.jsonl looks valid
  ⚠  DB-JSONL Sync Status mismatch: 6 issue(s) have different status in DB vs JSONL
     └─ Status mismatches detected:    
  hq-jr0: DB=closed, JSONL=open
  hq-n9c: DB=closed, JSONL=open
  hq-jxg: DB=closed, JSONL=open
  ... and 3 more               
                               
  ✖  Sync Divergence 2 sync divergence issue(s) detected
     └─ Database import time is newer than JSONL (2026-01-10T12:29:54-08:00 > 2026-01-10T12:05:48-08:00)
Uncommitted .beads/ changes (1 file(s))                                                         
  ✓  Untracked Files All .beads/*.jsonl files are tracked

GIT INTEGRATION
  ✓  Git Hooks All recommended hooks installed
     └─ Installed: pre-commit, post-merge, pre-push
  ✓  Sync Branch Hook Compatibility N/A (sync-branch not configured)
  ✓  Gitignore Up to date
  ✓  Issues Tracking issues.jsonl is tracked by git
  ✓  Redirect Tracking No redirect file present
  ✓  Git Merge Driver Correctly configured
     └─ bd merge %A %O %A %B
  ⚠  Git Working Tree Uncommitted changes present
     └─ ?? .beads/       
?? .claude/      
?? .events.jsonl 
?? .feed.jsonl   
?? .gitattributes
?? .gitignore    
?? AGENTS.md     
?? LexiconBlocks/
…                
  ⚠  Git Upstream No upstream configured for master
  ✓  Sync Branch Config N/A (no remote configured)
  ✓  Sync Branch Health N/A (no sync branch configured)
  ✓  Orphaned Issues No issues referenced in commits but still open
  ✓  Sync Branch Gitignore N/A (sync.branch not configured)

RUNTIME
  ✓  Git Sync Setup Git repository detected (sync-branch not configured)
     └─ Beads commits directly to current branch. For team collaboration or to keep beads changes isolated, consider using a sync-branch.
  ✓  Daemon Health Daemon running (PID 34279, version 0.46.0)
  ✓  Daemon Auto-Sync No sync-branch configured (auto-sync not applicable)
  ✓  Daemon Config Using current config format

INTEGRATIONS
  ⚠  Claude Plugin version 0.30.0 (latest: 0.46.0)
  ✓  Claude Integration Plugin installed
     └─ Slash commands and workflow hooks enabled via plugin
  ✓  Gemini CLI Integration Not configured
     └─ Run 'bd setup gemini' to enable Gemini CLI integration
  ✓  CLI Availability 'bd' command available in PATH
  ✓  Prime Documentation No bd prime references in documentation
  ✓  Agent Documentation Documentation found: AGENTS.md

METADATA
  ✓  Dependency Cycles No circular dependencies detected
  ✓  Legacy Commands No legacy beads slash commands detected
  ✓  Version Tracking Version tracking active (version: 0.46.0)
  ✓  Deletions Manifest Using inline tombstones
  ✓  Tombstones None (no deleted issues)
  ✓  Child-Parent Dependencies No child→parent dependencies

MAINTENANCE
  ✓  Stale Closed Issues No stale closed issues
  ✓  Stale Molecules No stale molecules
  ✓  Persistent Mol Issues No persistent mol- issues
  ✓  Expired Tombstones No expired tombstones
  ✓  Compaction Candidates No compaction candidates
  ✓  Pending Migrations None required

OTHER
  ✓  Merge Artifacts No merge artifacts found
  ✓  Orphaned Dependencies No orphaned dependencies
  ⚠  Duplicate Issues 1 duplicate issue(s) in 1 group(s)
     └─ Duplicates cannot be auto-fixed
  ✓  Test Pollution No test pollution detected
  ✓  Git Conflicts No git conflicts in JSONL
  ✓  Large Database 6 closed issues (threshold: 5000)

──────────────────────────────────────────
✓ 51 passed  ⚠ 6 warnings  ✖ 1 failed

⚠  WARNINGS
  ✖  1. Sync Divergence: 2 sync divergence issue(s) detected
        └─ bd export OR bd sync
  ⚠  2. JSONL Files: Multiple JSONL files found: issues.jsonl, routes.jsonl
        └─ Determine which file is current and remove the others:
  1. Check .beads/metadata.json for 'jsonl_export' setting
  2. Verify with 'git log .beads/*.jsonl' to see commit history
  3. Remove the unused file(s): git rm .beads/<unused>.jsonl
  4. Commit the change
  ⚠  3. DB-JSONL Sync: Status mismatch: 6 issue(s) have different status in DB vs JSONL
        └─ Run 'bd export -o issues.jsonl' to update JSONL from DB (DB is usually source of truth)
  ⚠  4. Git Working Tree: Uncommitted changes present
        └─ Commit or stash changes, then follow AGENTS.md: git pull --rebase && git push
  ⚠  5. Git Upstream: No upstream configured for master
        └─ Set upstream then push: git push -u origin master
  ⚠  6. Claude Plugin: version 0.30.0 (latest: 0.46.0)
        └─ Update plugin: /plugin update beads@beads-marketplace
Restart Claude Code after update
  ⚠  7. Duplicate Issues: 1 duplicate issue(s) in 1 group(s)
        └─ Run 'bd duplicates' to review and merge duplicates
bd doctor failed

✓ town-config-exists: mayor/town.json exists
✓ town-config-valid: mayor/town.json valid (name=gt, version=2)
✓ rigs-registry-exists: mayor/rigs.json exists
✓ rigs-registry-valid: All 1 registered rig(s) exist
✓ mayor-exists: mayor/ directory exists with required files
⚠ global-state: Global state not initialized
    → Run: gt enable
✓ town-git: Town root is under version control
✓ daemon: Daemon is running (PID 8564)
✓ repo-fingerprint: Repository fingerprints verified
✓ boot-health: Boot watchdog healthy
✓ beads-database: No issues.db file (will be created on first use)
✓ formulas: 25 formulas up-to-date
✓ bd-daemon: bd daemon is running and healthy
✓ prefix-conflict: No prefix conflicts found
✓ prefix-mismatch: No prefix mismatches found
✓ routes-config: Routes configured correctly (1 routes)
✓ orphan-sessions: All 1 Gas Town sessions are valid
⚠ orphan-processes: Found 2 runtime process(es) running outside tmux
    These may be your personal sessions or orphaned Gas Town processes.
    Verify these are expected before manually killing any:
      PID 54971: claude (parent: 73036)
      PID 43733: claude (parent: 4282)
⚠ gt-root-env: 1 session(s) missing GT_ROOT environment variable
    Missing GT_ROOT: gt-LexiconBlocks-witness
    
    Sessions without GT_ROOT cannot find town-level formulas.
    → Restart sessions to pick up GT_ROOT: gt shutdown && gt up
✓ wisp-gc: No abandoned wisps found
✓ persistent-role-branches: All 2 persistent roles on main branch
✓ beads-sync-orphans: No beads-sync branch (single-clone setup)
✓ clone-divergence: All 3 clones in sync with origin/main
✓ identity-collision: no worker locks found
✓ linked-panes: Not enough sessions to check for linking
✓ themes: 1 session(s) have correct themes
✓ patrol-molecules-exist: All 1 rig(s) have patrol molecules
✓ patrol-hooks-wired: Daemon configured with 3 patrol(s)
✓ patrol-not-stuck: No stuck patrol wisps found
✓ patrol-plugins-accessible: All plugin directories accessible
✓ patrol-roles-have-prompts: All patrol role prompt templates found
✓ agent-beads-exist: All 5 agent beads exist
✗ rig-beads-exist: 1 rig identity bead(s) missing
    le-rig-LexiconBlocks
    → Run 'gt doctor --fix' to create missing rig identity beads
✓ rig-settings: All 1 rig(s) have settings/ directory
✓ session-hooks: All 2 settings.json file(s) use proper session_id passthrough
✓ runtime-gitignore: .runtime/ properly gitignored
✓ legacy-gastown: No legacy .gastown/ directories found
✓ claude-settings: All Claude settings.json files are up to date
✓ crew-state: All 1 crew state files valid
✓ crew-worktrees: No cross-rig worktrees in crew directories
✓ commands-provisioned: Town-level slash commands provisioned (handoff.md)
✓ lifecycle-hygiene: No stale lifecycle messages found
✓ hook-attachment-valid: All hook attachments are valid
✓ hook-singleton: All handoff beads are unique
✓ orphaned-attachments: No orphaned handoff beads found

45 checks, 41 passed, 3 warnings, 1 errors
Error: doctor found 1 error(s)
Usage:
  gt doctor [flags]

Flags:
      --fix                Attempt to automatically fix issues
  -h, --help               help for doctor
      --restart-sessions   Restart patrol sessions when fixing stale settings (use with --fix)
      --rig string         Check specific rig only
  -v, --verbose            Show detailed output

gt doctor failed