Add CheckPatrolPollution to detect stale patrol beads:
- Patrol digests matching 'Digest: mol-*-patrol'
- Session ended beads matching 'Session ended: *'
Includes auto-fix via 'bd doctor --fix' to clean up pollution.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add bd doctor check that detects legacy gastown merge queue JSON files
in .beads/mq/. These files are local-only remnants from the old mrqueue
implementation and can safely be deleted since gt done already creates
merge-request wisps in beads.
- CheckStaleMQFiles() detects .beads/mq/*.json files
- FixStaleMQFiles() removes the entire mq directory
- Comprehensive tests for check and fix
This is the first step toward removing the mrqueue side-channel from
gastown. The follow-up convoy will update Refinery/Witness to use
beads exclusively.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add bd doctor check that warns if .beads/last-touched is tracked by git.
This file is local runtime state that should never be committed, as it
causes spurious diffs in other clones.
- CheckLastTouchedNotTracked() detects if file is git-tracked
- FixLastTouchedTracking() untracks with git rm --cached
- Comprehensive tests for all scenarios
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When sync.branch is configured, issues.jsonl appears modified in git status
even though changes go to the sync branch. This is confusing for users and
risks accidental commits to the wrong branch.
Implementation:
- Added SyncBranchGitignore() to set git index flags (assume-unchanged,
skip-worktree) on issues.jsonl when sync.branch is configured
- For untracked files, adds to .git/info/exclude instead
- Called automatically from bd sync after successful sync-branch sync
- Added bd doctor check and fix for this issue
- Added HasSyncBranchGitignoreFlags() to check current flag state
- Added ClearSyncBranchGitignore() to remove flags when sync.branch disabled
Fixes: GH#870 (duplicate of GH#797, GH#801)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Executed-By: beads/crew/dave
Rig: beads
Role: crew
- Add redirect to GitignoreTemplate with explanatory comment
- Add redirect to requiredPatterns for outdated gitignore detection
- Add CheckRedirectNotTracked() to detect already-tracked redirect files
- Add FixRedirectTracking() to untrack via git rm --cached
- Register check in bd doctor under Git Integration category
- Add 6 tests for the new functionality
The redirect file contains a relative path that only works in the
original worktree. When committed, it causes warnings in other clones:
"Warning: redirect target does not exist"
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Completes the work from #813 by actually calling the new functions:
- Add Check 14b in doctor.go for redirect file tracking detection
- Add Redirect Not Tracked case in doctor_fix.go switch statement
Without this wiring, bd doctor would not detect or fix already-tracked
redirect files, only prevent new ones via the updated .gitignore template.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Executed-By: beads/crew/dave
Rig: beads
Role: crew
Add comprehensive database corruption recovery capabilities to bd doctor.
## Changes
### New Command Flags
- --force: Force repair mode that bypasses database validation
- --source: Choose source of truth (auto/jsonl/db) for recovery
### Enhanced Error Classification
Improved CheckDatabaseIntegrity() to detect and classify:
- Database locked errors (suggests killing processes, removing locks)
- Invalid SQLite files (suggests JSONL recovery with exact commands)
- Migration/validation failures (orphaned dependencies, etc.)
- Generic database errors (context-aware suggestions)
Each error type provides:
- Specific diagnosis
- Step-by-step recovery instructions
- Appropriate command examples with new flags
### Force Recovery Implementation
New DatabaseCorruptionRecoveryWithOptions() function:
- Bypasses database validation when --force is used
- Supports explicit source of truth selection
- Auto-detects best recovery path when source=auto
- Comprehensive rollback on failure
- Uses --force --no-git-history in import during force mode
### Integration
Updated fix orchestration to pass force and source flags to recovery.
## Usage Examples
```bash
# Unopenable database with validation errors
bd doctor --fix --force --source=jsonl
# Choose specific source of truth
bd doctor --fix --source=jsonl # Trust JSONL
bd doctor --fix --source=db # Trust database
bd doctor --fix --source=auto # Auto-detect (default)
# Force recovery with auto-detection
bd doctor --fix --force
```
## Problem Solved
Before: When database had validation errors (orphaned dependencies,
foreign key violations), all bd commands failed in a catch-22 situation.
Could not open database to fix database. Users had to manually delete
database files and reinit.
After: bd doctor --fix --force detects unopenable databases, provides
clear recovery steps, and forces rebuild from JSONL even when database
validation fails.
## Backward Compatibility
- All new flags are optional with safe defaults
- --source defaults to 'auto' (existing behavior)
- --force is opt-in only
- Existing bd doctor behavior unchanged when flags not used
- DatabaseCorruptionRecovery() still exists for compatibility
Fixes: bd-pgza
- Add resolveBeadsDir helper to fix/common.go to follow redirect files
- Update OrphanedDependencies, ChildParentDependencies, and MergeArtifacts
to use resolveBeadsDir instead of hardcoded .beads path
- Add --verbose/-v flag to bd doctor command
- Only print individual items if verbose or count < 20, always show summary
(bd-dq74, bd-v55y)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
