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>
Git hooks are shared across all worktrees and live in the common git
directory (e.g., /repo/.git/hooks), not the worktree-specific directory
(e.g., /repo/.git/worktrees/feature/hooks).
The core issue was in GetGitHooksDir() which used GetGitDir() instead
of GetGitCommonDir(). This caused hooks to be installed to/read from
the wrong location when running in a worktree.
Additionally, several places in the codebase manually constructed
hooks paths using gitDir + "hooks" instead of calling GetGitHooksDir().
These have been updated to use the proper worktree-aware path.
Affected areas:
- GetGitHooksDir() now uses GetGitCommonDir()
- CheckGitHooks() uses GetGitHooksDir()
- installHooks/uninstallHooks use GetGitHooksDir()
- runChainedHook() uses GetGitHooksDir()
- Doctor checks use git-common-dir for hooks paths
- Reset command uses GetGitCommonDir() for hooks and beads-worktrees
Symptoms that this fixes:
- Chained hooks (pre-commit.old) not running in worktrees
- bd hooks install not finding/installing hooks correctly in worktrees
- bd hooks list showing incorrect status in worktrees
- bd doctor reporting incorrect hooks status in worktrees
Co-authored-by: Zain Rizvi <4468967+ZainRizvi@users.noreply.github.com>
WSL doesn't fully respect Unix file permission semantics - the file
owner can bypass read-only restrictions, similar to macOS. Add isWSL()
helper and skip TestMergeDriverWithLockedConfig_E2E on WSL.
Fixes bd-srv
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
prek (https://prek.j178.dev) is a faster Rust-based alternative to
pre-commit that uses the same .pre-commit-config.yaml config files.
Changes:
- Add prek detection pattern in hookManagerPatterns (before pre-commit
to ensure correct detection since prek hooks may contain 'pre-commit')
- Handle prek in checkManagerBdIntegration using same config parser
- Update init_git_hooks.go to recognize prek-installed hooks
- Rename isPreCommit field to isPreCommitFramework for clarity
- Use regex pattern matching all pre-commit/prek signatures consistently
- Add test cases for prek run and prek hook-impl signatures
Co-authored-by: Ismar Iljazovic <ismar@gmail.com>
Add support for lefthook v1.10.0+ jobs array syntax in addition to
the older commands map syntax. Both syntaxes are now checked for
bd hooks run integration.
Fixes#981
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Executed-By: beads/crew/dave
Rig: beads
Role: crew
* fix(doctor): handle 's' status in combined git flags
Problem:
- Git status detection failed when 's' was combined with other flags
- Branch synchronization checks produced incorrect results due to missing flag parsing
Solution:
- Update detection logic to correctly identify the 's' status within combined flag strings
Impact:
- Ensures branch synchronization state is accurately reported during doctor checks
* test(doctor): add unit tests for git flag parsing
- Extract git flag parsing logic into parseGitLsFilesFlag helper
- Add unit tests for git flag parsing logic
Coverage: Git flag parsing in sync_branch.go
- Extract inode function to platform-specific files (inode_unix.go,
inode_windows.go) to fix syscall.Stat_t compile error on Windows
- Add skipOnWindows helper and skip Unix permission/symlink tests
on Windows where chmod semantics differ
- Increase Windows test timeout from 10m to 20m since full test
suite runs slower without race detector
Fixes Windows CI failures introduced when PR #904 expanded Windows
testing from smoke tests to full test suite.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add config parsing for .pre-commit-config.yaml to detect if bd hooks are
configured. pre-commit is popular enough to warrant full support alongside
lefthook and husky.
Changes:
- Add CheckPrecommitBdIntegration() function to parse YAML config
- Check hooks.*.entry field for 'bd hooks run' pattern
- Handle stages field to determine which git hooks are configured
- Support legacy stage names (commit -> pre-commit, push -> pre-push)
- Add pre-commit to checkManagerBdIntegration switch statement
- Add comprehensive tests for all scenarios
Now supported managers with deep integration checks:
- lefthook (YAML, TOML, JSON)
- husky (.husky/ scripts)
- pre-commit (.pre-commit-config.yaml)
Detection-only managers (cannot verify config):
- overcommit, yorkie, simple-git-hooks
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When bd doctor detects hook managers we can't fully check (pre-commit,
overcommit, yorkie, simple-git-hooks), it now shows an informational
message instead of a warning:
✓ pre-commit detected (cannot verify bd integration)
└─ Ensure your hook config calls 'bd hooks run <hook>'
Previously it incorrectly warned that these managers were "not calling bd"
when we simply couldn't verify their config.
Changes:
- Add DetectionOnly field to HookIntegrationStatus
- Set DetectionOnly=true for unsupported managers in CheckExternalHookManagerIntegration
- Update CheckGitHooks and CheckSyncBranchHookCompatibility to show
informational message for detection-only managers
- Add test coverage for DetectionOnly behavior
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add detection for external git hook managers (lefthook, husky, pre-commit,
overcommit, yorkie, simple-git-hooks) and check if they have bd hooks
integration configured.
- Detect manager config files in various locations/formats
- Parse lefthook YAML/TOML/JSON to check for `bd hooks run` commands
- Check husky hook scripts for bd integration
- Report which hooks have bd integration vs missing
- Use --chain flag in `bd doctor --fix` when external managers detected
- Detect active manager from git hooks when multiple present
Executed-By: mayor
Role: mayor
Review findings addressed:
1. Fixed HasSyncBranchGitignoreFlags() - now correctly returns (hasAnyFlag,
hasSkipWorktree) since skip-worktree takes precedence in git ls-files -v
2. Added interactions.jsonl to list of files to hide (was only issues.jsonl)
3. Added idempotency check - skips setting flags if already set (checks for S)
4. Made output conditional - only prints when flags actually changed
5. Fixed addToGitExclude() pattern matching - now uses exact line match
instead of substring to prevent false positives
6. Refactored to use setGitIndexFlags() helper to reduce duplication
🤖 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
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
Post-merge cleanup of PR #805:
1. Extract duplicate error classification logic into classifyDatabaseError()
helper function (was duplicated in two places in database.go)
2. Fix semantic conflict between --force and --source=db flags:
- --force implies "database is broken, rebuild from JSONL"
- --source=db implies "use database as source of truth"
- These are contradictory; now errors with clear message
- --force with --source=auto or --source=jsonl works as expected
🤖 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
- Rename followRedirect to FollowRedirect in internal/beads (export it)
- Update doctor/maintenance.go to use beads.FollowRedirect
- Update doctor/fix/common.go to use beads.FollowRedirect
- Remove 66 lines of duplicated code across 3 implementations
This ensures consistent redirect handling with path canonicalization,
chain prevention, and proper error warnings.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- 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>
Strip (bd-xxx), (gt-xxx) suffixes from code comments and changelog
entries. The descriptions remain meaningful without the ephemeral
issue IDs.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Analysis found these commands are dead code:
- gt never calls `bd pin` - uses `bd update --status=pinned` instead
- Beads.Pin() wrapper exists but is never called
- bd hook functionality duplicated by gt mol status
- Code comment says "pinned field is cosmetic for bd hook visibility"
Removed:
- cmd/bd/pin.go
- cmd/bd/unpin.go
- cmd/bd/hook.go
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds automatic database recovery when bd doctor --fix detects corruption:
- Detects SQLite corruption (malformed database, SQLITE_CORRUPT errors)
- Backs up corrupted database before recovery attempt
- Rebuilds from JSONL if available (issues.jsonl, deletions.jsonl)
- Falls back to fresh database if JSONL unavailable
- Reports recovery results (issues imported, success/failure)
Recovery is triggered automatically by --fix when corruption is detected.
No manual intervention required.
The CheckChildParentDependencies detection and ChildParentDependencies fix
were flagging ALL child→parent dependencies, including legitimate
'parent-child' type structural hierarchy relationships.
Now only blocking types (blocks, conditional-blocks, waits-for) are
detected as anti-patterns. The 'parent-child' type is a legitimate
hierarchy marker used for:
- Tracking parent-child relationships
- Transitive block propagation (if parent blocked, children blocked)
- Hierarchy visualization in external tools
Changes:
- Add type filter to SELECT queries (only blocking types)
- Add type filter to DELETE statement (preserve parent-child)
- Add regression test TestChildParentDependencies_PreservesParentChildType
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
GH#740: bd doctor --fix was auto-removing child→parent dependencies,
calling them an 'anti-pattern'. While these often indicate modeling
mistakes (deadlock), they may be intentional in some workflows.
Changes:
- Add --fix-child-parent flag (required to remove child→parent deps)
- Remove ChildParentDependencies from default --fix set
- Update warning message to reference new flag
- Update comments to reflect more nuanced understanding
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This prevents a common mistake where users add dependencies from child
issues to their parent epics. This creates a deadlock:
- Child can't start (blocked by open parent)
- Parent can't close (children not done)
Changes:
- dep.go: Reject child→parent deps at creation time with clear error
- server_labels_deps_comments.go: Same check for daemon RPC
- doctor/validation.go: New check detects existing bad deps
- doctor/fix/validation.go: Auto-fix removes bad deps
- doctor.go: Wire up check and fix handler
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When 'bd doctor --fix' detects DB has more issues than JSONL, it runs
'bd export' to sync them. However, 'bd export' without -o flag outputs
to stdout instead of writing to .beads/issues.jsonl, making the fix a
no-op.
Add -o .beads/issues.jsonl --force to the export command to ensure the
JSONL file is actually updated.
- Add _ = prefix for ignored Close/Remove return values
- Fix unused cmd parameter in runMoleculeReady
- Add nolint:misspell for intentional British "cancelled" spelling
- Update comments to use US spelling where not intentional
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add new Maintenance category to bd doctor with checks for:
- Stale closed issues (older than 30 days)
- Expired tombstones (older than TTL)
- Compaction candidates (info only)
Add fix handlers for cleanup and tombstone pruning via bd doctor --fix.
Add deprecation hints to cleanup, compact, and detect-pollution commands
suggesting users try bd doctor instead.
This consolidation reduces cognitive load - users just need to remember
'bd doctor' for health checks and 'bd doctor --fix' for maintenance.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* fix(doctor): UX improvements for diagnostics and daemon
- Add Repo Fingerprint check to detect when database belongs to a
different repository (copied .beads dir or git remote URL change)
- Add interactive fix for repo fingerprint with options: update repo ID,
reinitialize database, or skip
- Add visible warning when daemon takes >5s to start, recommending
'bd doctor' for diagnosis
- Detect install method (Homebrew vs script) and show only relevant
upgrade command
- Improve WARNINGS section:
- Add icons (⚠ or ✖) next to each item
- Color numbers by severity (yellow for warnings, red for errors)
- Render entire error lines in red
- Sort by severity (errors first)
- Fix alignment with checkmarks above
- Use heavier fail icon (✖) for better visibility
- Add integration and validation tests for doctor fixes
* fix(lint): address errcheck and gosec warnings
- mol_bond.go: explicitly ignore ephStore.Close() error
- beads.go: add nosec for .gitignore file permissions (0644 is standard)
- Modified fix.DBJSONLSync() to detect which direction to sync:
- If DB > JSONL: run 'bd export' to sync JSONL (DB has newer data)
- If JSONL > DB: run 'bd sync --import-only' to import (JSONL is source of truth)
- If equal but different timestamps: use file mtime to decide direction
- Updated CheckDatabaseJSONLSync() error messages to recommend correct fix direction:
- Shows different guidance based on whether DB or JSONL has more issues
- Added helper functions:
- countDatabaseIssues() to count issues in SQLite
- countJSONLIssues() to count issues in JSONL (local, avoids circular import)
- Added tests for countJSONLIssues() with edge cases
Fixes issue where 'bd doctor --fix' would recommend 'bd sync --import-only'
when DB > JSONL, which would be a no-op since JSONL hasn't changed.
Adds configuration options for beads git commits:
- git.author: Override commit author (e.g., "beads-bot <beads@example.com>")
- git.no-gpg-sign: Disable GPG signing for beads commits
This is useful for users with Touch ID commit signing (like Secretive)
who get prompted for every beads auto-commit.
Config example:
```yaml
git:
author: "beads-bot <beads@example.com>"
no-gpg-sign: true
```
Environment variables: BD_GIT_AUTHOR, BD_GIT_NO_GPG_SIGN
Closes#600🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* test(doctor): add comprehensive tests for fix and check functions
Add edge case tests, e2e tests, and improve test coverage for:
- database_test.go: database integrity and sync checks
- git_test.go: git hooks, merge driver, sync branch tests
- gitignore_test.go: gitignore validation
- prefix_test.go: ID prefix handling
- fix/fix_test.go: fix operations
- fix/e2e_test.go: end-to-end fix scenarios
- fix/fix_edge_cases_test.go: edge case handling
* docs: add testing philosophy and anti-patterns guide
- Create TESTING_PHILOSOPHY.md covering test pyramid, priority matrix,
what NOT to test, and 5 anti-patterns with code examples
- Add cross-reference from README_TESTING.md
- Document beads-specific guidance (well-covered areas vs gaps)
- Include target metrics (test-to-code ratio, execution time targets)
* chore: revert .beads/ to upstream/main state
* refactor(doctor): add category grouping and Ayu theme colors
- Add Category field to DoctorCheck for organizing checks by type
- Define category constants: Core, Git, Runtime, Data, Integration, Metadata
- Update thanks command to use shared Ayu color palette from internal/ui
- Simplify test fixtures by removing redundant test cases
* fix(doctor): prevent test fork bomb and fix test failures
- Add ErrTestBinary guard in getBdBinary() to prevent tests from
recursively executing the test binary when calling bd subcommands
- Update claude_test.go to use new check names (CLI Availability,
Prime Documentation)
- Fix syncbranch test path comparison by resolving symlinks
(/var vs /private/var on macOS)
- Fix permissions check to use exact comparison instead of bitmask
- Fix UntrackedJSONL to use git commit --only to preserve staged changes
- Fix MergeDriver edge case test by making both .git dir and config
read-only
- Add skipIfTestBinary helper for E2E tests that need real bd binary
* test(doctor): skip read-only config test in CI environments
GitHub Actions containers may have CAP_DAC_OVERRIDE or similar
capabilities that allow writing to read-only files, causing
the test to fail. Skip the test when CI=true or GITHUB_ACTIONS=true.
Fixes Windows build by adding platform-specific inode handling via build tags. Also fixes gosec lint warnings in migrate_tombstones.go.
Thanks @deblasis!
- bd-6pni: Auto-filter tombstoned issues with mismatched prefixes during
import instead of failing. Tombstones from contributor PRs with different
test prefixes are pollution and safe to ignore.
- bd-ffr9: Stop recreating deletions.jsonl after tombstone migration.
Added IsTombstoneMigrationComplete() check to all code paths that write
to the legacy deletions manifest.
- bd-admx: Fix perpetual "JSONL file hash mismatch" warning. Now clears
both export_hashes AND jsonl_file_hash when mismatch detected, so the
warning doesn't repeat.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- bd-8v5o: When doctor --fix hydrates issues from git history, also
remove them from the deletions manifest to prevent perpetual skip
warnings during sync
- bd-wsqt: Remove verbose per-issue "Skipping bd-xxx" messages during
sync. Caller already shows summary of skipped issues.
Added RemoveDeletions() function to deletions package with tests.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When bd doctor detects legacy deletions.jsonl, --fix now runs the
tombstone migration automatically instead of requiring users to
manually run bd migrate-tombstones.
This makes the migration smoother for multi-clone scenarios where
only one clone needs to do the actual migration, but other clones
may still have local deletions.jsonl files that need cleanup.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The previous bd-in7q fix had backwards logic - by EXCLUDING tombstones
from currentIDs, they appeared missing when compared to historicalIDs,
causing HydrateDeletionsManifest to erroneously add them to deletions.jsonl.
This corruption manifested when:
1. Issues were migrated to tombstones via migrate-tombstones
2. Doctor hydration ran (directly or via sync)
3. Tombstones were seen as deleted and re-added to deletions.jsonl
4. Next import skipped thousands of issues with in deletions manifest
Fix: Include ALL issues (including tombstones) in currentIDs. Tombstones
represent migrated deletions that ARE accounted for - they should not
trigger new deletion records.
Generated with Claude Code
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Handle file.Close() errors in deletions.go and deletions_test.go
- Simplify boolean logic to apply De Morgan's law in common.go
- All golangci-lint checks now pass
Root cause: bd doctor hydrate was re-adding migrated tombstones to the
deletions manifest because getCurrentJSONLIDs() included all issues,
including tombstones. When compared against git history, tombstones
appeared as 'deleted' and were incorrectly added to the manifest as new
deletions, corrupting the database on next sync.
Fix: Skip tombstone-status issues in getCurrentJSONLIDs() so they don't
participate in deletion detection. Tombstones represent already-recorded
deletions/migrations and shouldn't be treated as active issues.
Changes:
- cmd/bd/doctor/fix/deletions.go: Skip tombstones in getCurrentJSONLIDs()
- cmd/bd/doctor/fix/deletions_test.go: New tests for tombstone skipping
- cmd/bd/migrate_tombstones_test.go: Test that tombstones are valid
This fixes the bug where 'bd migrate-tombstones' followed by 'bd sync'
would add thousands of deletion records with author 'bd-doctor-hydrate'
Adds comprehensive Git worktree support for beads issue tracking:
Core changes:
- New internal/git/gitdir.go package for worktree detection
- GetGitDir() returns proper .git location (main repo, not worktree)
- Updated all hooks to use git.GetGitDir() instead of local helper
- BeadsDir() now prioritizes main repository's .beads directory
Features:
- Hooks auto-install in main repo when run from worktree
- Shared .beads directory across all worktrees
- Config option no-install-hooks to disable auto-install
- New bd worktree subcommand for diagnostics
Documentation:
- New docs/WORKTREES.md with setup instructions
- Updated CHANGELOG.md and AGENT_INSTRUCTIONS.md
Testing:
- Updated tests to use exported git.GetGitDir()
- Added worktree detection tests
Co-authored-by: Claude <noreply@anthropic.com>
Closes: #478
These tests fail on Windows because:
- os.Symlink requires elevated privileges
- Unix-style permissions (0700, 0600) don't apply
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
