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>
Add support for claude.local.md and .claude/claude.local.md as local-only
alternatives to CLAUDE.md. These files are intended to be gitignored for
personal customizations that should not be committed to the repo.
Changes:
- Update CheckAgentDocumentation to detect claude.local.md files
- Update CheckLegacyBeadsSlashCommands to check claude.local.md files
- Update CheckDocumentationBdPrimeReference to check claude.local.md files
- Add fix message mentioning claude.local.md as an option
- Add test cases for claude.local.md support
Closes#488🤖 Generated with [Claude Code](https://claude.com/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
The .beads/.gitignore now ignores everything by default and explicitly
whitelists tracked files. This fixes confusion about which files to
commit when using protected branches workflow.
Changes:
- Use `*` to ignore all by default, then `!file` to whitelist
- Fix config.json -> config.yaml (wrong filename in negation)
- Update doctor check to validate new patterns
- Update PROTECTED_BRANCHES.md documentation
- Simplify git add instructions to just `git add .beads/`
Fixes#473🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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>
Add comprehensive validation for config values in bd doctor:
YAML config (config.yaml) validations:
- actor: alphanumeric with dashes, underscores, dots, @
- db: valid database extension (.db, .sqlite, .sqlite3)
- Boolean flags: json, no-daemon, no-auto-flush, no-auto-import,
no-db, auto-start-daemon validate as true/false/yes/no/1/0/on/off
- sync.require_confirmation_on_mass_delete: boolean validation
- repos.primary: must be a directory if path exists
- repos.additional: paths must be directories if they exist
Database config validations:
- status.custom: validates custom status names are lowercase
alphanumeric with underscores, checks for conflicts with built-in
statuses (open, in_progress, blocked, closed)
- sync.branch (legacy): validates as git branch name
Includes tests for all new validation functions.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* fix: use os.Lstat for symlink-safe mtime and permission checks
On NixOS and other systems using symlinks heavily (e.g., home-manager),
os.Stat follows symlinks and returns the target's metadata. This causes:
1. False staleness detection when JSONL is symlinked - mtime of target
changes unpredictably when symlinks are recreated
2. os.Chmod failing or changing wrong file's permissions when target
is in read-only location (e.g., /nix/store)
3. os.Chtimes modifying target's times instead of the symlink itself
Changes:
- autoimport.go: Use Lstat for JSONL mtime in CheckStaleness()
- import.go: Use Lstat in TouchDatabaseFile() for JSONL mtime
- export.go: Skip chmod for symlinked files
- multirepo.go: Use Lstat for JSONL mtime cache
- multirepo_export.go: Use Lstat for mtime, skip chmod for symlinks
- doctor/fix/permissions.go: Skip permission fixes for symlinked paths
These changes are safe cross-platform:
- On systems without symlinks, Lstat behaves identically to Stat
- Symlink permission bits are ignored on Unix anyway
- The extra Lstat syscall overhead is negligible
Fixes symlink-related data loss on NixOS. See GitHub issue #379.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
* test: add symlink behavior tests for NixOS compatibility
Add tests that verify symlink handling behavior:
- TestCheckStaleness_SymlinkedJSONL: verifies mtime detection uses
symlink's own mtime (os.Lstat), not target's mtime (os.Stat)
- TestPermissions_SkipsSymlinkedBeadsDir: verifies chmod is skipped
for symlinked .beads directories
- TestPermissions_SkipsSymlinkedDatabase: verifies chmod is skipped
for symlinked database files while still fixing .beads dir perms
Also adds devShell to flake.nix for local development with go, gopls,
golangci-lint, and sqlite tools.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
---------
Co-authored-by: Claude <noreply@anthropic.com>
The beads plugin now provides SessionStart and PreCompact hooks directly
via plugin.json. Users no longer need to run 'bd setup claude' when using
the plugin - hooks are automatically available.
Changes:
- Add hooks section to .claude-plugin/plugin.json with SessionStart and
PreCompact hooks that run 'bd prime'
- Update doctor/claude.go to recognize plugin-provided hooks as valid
- Update tips.go to check for plugin installation when determining if
Claude integration is complete
- Update messaging to recommend plugin installation as primary option
The 'bd setup claude' command remains available for CLI-only users who
do not want to install the plugin.
Closes#462🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Fixes#460 - .local_version was added for version tracking but not
included in the gitignore template, causing it to show as untracked.
Co-Authored-By: Claude <noreply@anthropic.com>
Add ability to save doctor diagnostics to a JSON file for historical
analysis and bug reporting. The export includes timestamp and platform
info (OS, Go version, SQLite version) for tracking intermittent issues.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Add a new Config Values check to bd doctor that validates:
- flush-debounce: must be a valid duration (e.g., 30s, 1m)
- issue-prefix: must start with letter, alphanumeric with dashes/underscores
- routing.mode: must be auto, maintainer, or contributor
- sync-branch: must be a valid git branch name
- routing paths: warns if configured paths do not exist
- metadata.json database: should be filename (not path), with db extension
- metadata.json jsonl_export: should have .jsonl extension
- deletions_retention_days: must be non-negative if set
This catches misconfigurations before they cause runtime errors.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Add 'Sync Branch Health' check that detects:
1. Local sync branch diverged from remote (after force-push reset)
2. Sync branch significantly behind main on source files (20+ commits, 50+ files)
Add --fix support that:
- Handles worktree case (resets within worktree)
- Handles regular branch case (deletes and recreates from main)
- Pushes the reset branch to remote
This helps contributors whose local beads-sync becomes orphaned after
someone else resets the branch.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Previously, bd init blocked when JSONL existed with issues but no database,
telling users to run 'bd doctor --fix'. But doctor --fix just ran bd migrate
which requires an existing database - creating a circular dependency.
Now:
- bd init allows fresh clones (JSONL exists, no database) to proceed
- bd init creates the database and imports from JSONL automatically
- bd doctor --fix runs bd init (not migrate) when there's no database
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Use `git rev-parse --git-dir` instead of hardcoded `.git` path to find
the actual git directory. In worktrees, `.git` is a file containing a
gitdir pointer, not a directory.
Changes:
- Add getGitDir() helper in hooks.go
- Update installHooks(), uninstallHooks(), CheckGitHooks() to use it
- Update hooksInstalled(), detectExistingHooks(), installGitHooks() in init.go
- Update checkHooksQuick() in doctor.go
- Update GitHooks() in doctor/fix/hooks.go
- Update tests to use real git repos via `git init`
Fixes bd-63l
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Fixes from maphew including:
- Remove test for deleted isPathWithinDir function
- Add gosec nolint directives for safe file operations
- Add rm -rf .beads before init in CI workflow
- Simplify panic handling and file operations
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: maphew <maphew@users.noreply.github.com>
Co-Authored-By: Claude <noreply@anthropic.com>
Add CheckFreshClone function that detects when JSONL contains issues
but no database exists. Recommends 'bd init --prefix <detected-prefix>'
to hydrate the database. This check appears early in doctor output
to guide users on fresh clones.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Verify that beads.base.jsonl and beads.left.jsonl patterns are correctly
excluded from the 'multiple JSONL files' warning, same as issues.base.jsonl.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- bound fresh-clone JSONL discovery to the .beads dir (abs path, traversal guard) before reading counts
- add safeWorkspacePath/isWithinWorkspace helpers and use in doctor fixes (database_config, untracked) to reject absolute/traversal inputs and confine .gitattributes edits
- normalize git status paths and path-guard tests for cross-OS (Windows) compatibility
- add regression tests for the new guards
Add .base.jsonl, .left.jsonl, and .right.jsonl patterns to the skip list
in CheckLegacyJSONLFilename. These are legitimate git merge conflict
artifacts that should not trigger a warning about multiple JSONL files.
Fixes: bd-nsb
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Fix doctor to treat empty deletions.jsonl as valid (0 entries OK status)
- Fix HydrateDeletionsManifest to create empty file when no deletions found
- Add --parent flag documentation to onboard command
- Add CLI --help tip throughout onboard documentation
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Change default JSONL filename from beads.jsonl to issues.jsonl
- Add bd doctor check and fix to auto-migrate legacy beads.jsonl configs
- Update FindJSONLPath to prefer issues.jsonl over beads.jsonl
- Add CheckLegacyJSONLConfig and CheckLegacyJSONLFilename checks
- Add LegacyJSONLConfig fix to rename files and update config
- Update .gitattributes to reference issues.jsonl
- Fix tests to expect new canonical filename
- Add bd-6xd to v0.25.1 release notes
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
The multiple JSONL files check was incorrectly flagging deletions.jsonl
as a problem, even though it is a valid system file for tracking deleted
issues. Added deletions.jsonl to the skip list alongside backups and
merge artifacts.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Add JSONL sanitization after git pull to remove deleted issues that
git's 3-way merge may resurrect. Also add bd doctor check to hydrate
deletions.jsonl from git history for pre-v0.25.0 deletions.
Changes:
- Add sanitizeJSONLWithDeletions() in sync.go (Step 3.6)
- Add checkDeletionsManifest() in doctor.go (Check 18)
- Add HydrateDeletionsManifest() fix in doctor/fix/deletions.go
- Add looksLikeIssueID() validation to prevent false positives
- Add comprehensive tests for sanitization logic
🤖 Generated with Claude Code
Co-Authored-By: Claude <noreply@anthropic.com>
Windows doesn't support Unix-style file permissions, so these tests
will always fail. Skip the permission verification on Windows while
still testing the core functionality (file creation, content).
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Add two new checks to verify Claude Code integration:
- CheckBdInPath: verifies 'bd' is in PATH (needed for hooks)
- CheckDocumentationBdPrimeReference: checks if docs reference 'bd prime'
and verifies the command exists (detects version mismatches)
Closes bd-o78
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
## Summary
When metadata.json gets deleted (git clean, merge conflict, rebase), the
version tracking code auto-recreates it using DefaultConfig() which hardcoded
jsonl_export to 'issues.jsonl'. But many repos (including beads itself) use
'beads.jsonl', causing a mismatch between config and actual JSONL file.
## Changes
1. **bd doctor --fix auto-detection** (cmd/bd/doctor/fix/database_config.go)
- New DatabaseConfig() fix function that auto-detects actual JSONL file
- Prefers beads.jsonl over issues.jsonl (canonical name)
- Skips backup files and merge artifacts
- Wired into doctor.go applyFixes()
2. **Version tracking auto-detection** (cmd/bd/version_tracking.go)
- trackBdVersion() now scans for existing JSONL files before defaulting
- Prevents mismatches when metadata.json gets recreated
- Added findActualJSONLFile() helper function
3. **Canonical default name** (internal/configfile/configfile.go)
- DefaultConfig() changed from issues.jsonl to beads.jsonl
- Aligns with canonical naming convention
4. **FindJSONLPath preference** (internal/beads/beads.go)
- Now prefers beads.jsonl over issues.jsonl when scanning
- Default changed from issues.jsonl to beads.jsonl
5. **Test coverage**
- Added comprehensive tests for DatabaseConfig fix
- Updated configfile tests for new default
- Verified backup file skipping logic
## Testing
- All existing tests pass
- New tests verify auto-fix behavior
- Integration tested with simulated mismatches
Closes: bd-afd
Resolves bd-ee1: Add security tests for WriteFile permissions in doctor command
Added comprehensive security tests for the FixGitignore function to verify:
- Files are created with 0600 permissions (secure, owner-only read/write)
- Existing files with insecure permissions are fixed
- Read-only files can be updated (permissions fixed first)
- File ownership is correct
- Permissions are enforced even on systems that respect umask
Also improved FixGitignore implementation to:
- Handle read-only files by fixing permissions before writing
- Explicitly set permissions after write to ensure 0600 regardless of umask
- Maintain secure permissions throughout the operation
Tests verify the gosec G306 security concern is properly addressed.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Problem: Existing beads repositories initialized before commit a4c38d5 don't have sync.branch configured. This causes 'bd sync --status' to fail with a confusing error.
Solution: Added new check in 'bd doctor' that detects when sync.branch is not configured and provides automatic fix via 'bd doctor --fix'. The fix automatically sets sync.branch to the current branch using 'git symbolic-ref --short HEAD'.
Changes:
- Added checkSyncBranchConfig() function in doctor.go
- Created fix/sync_branch.go with SyncBranchConfig() fix handler
- Added comprehensive test coverage in doctor_test.go
- Integrated check into applyFixes() switch statement
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Previously bd doctor warned about using beads.jsonl vs issues.jsonl, but
users should be free to configure any name they want. The real problems are:
1. Having multiple JSONL files (sync/merge conflicts)
2. Configuration not matching reality
Changes:
- Rewrote CheckLegacyJSONLFilename to scan for ALL .jsonl files
- Now filters out merge artifacts (backup, .orig, .bak, etc.)
- Warns only when multiple real JSONL files exist
- Added CheckDatabaseConfig to detect when configured paths do not match
what actually exists on disk
- Updated tests to verify backup files are ignored
- Added test cases for custom JSONL filenames
🤖 Generated with Claude Code
Co-Authored-By: Claude <noreply@anthropic.com>
The canonical beads database name is issues.jsonl. Tens of thousands of users
have issues.jsonl, and beads.jsonl was only used by the Beads project itself
due to git history pollution.
Changes:
- Updated bd doctor to warn about beads.jsonl instead of issues.jsonl
- Changed default config from beads.jsonl to issues.jsonl
- Reversed precedence in checkGitForIssues to prefer issues.jsonl
- Updated git merge driver config to use issues.jsonl
- Updated all tests to expect issues.jsonl as the default
issues.jsonl is now the canonical default; beads.jsonl is legacy
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Git merge drivers only support three placeholders:
- %O (ancestor/base)
- %A (current version)
- %B (other branch's version)
The code was incorrectly using %L and %R, which don't exist in git,
causing them to be passed through literally and breaking JSONL merges.
Changes:
- Fixed merge driver config in init.go, merge.go, README.md, docs
- Added detection in bd doctor with clear error messages
- Added auto-fix in bd doctor --fix
- Added proactive warning in bd sync before git pull
- Added reactive error detection after merge failures
- Updated all tests to use correct placeholders
Now users get helpful guidance at every step:
1. bd doctor detects the issue
2. bd doctor --fix auto-corrects it
3. bd sync warns before pulling if misconfigured
4. Error messages suggest bd doctor --fix when merge fails
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Relocate documentation files to centralize all .md files in docs/ directory
(except those with historical precedent in specific locations like commands/,
examples/, integrations/, etc.).
Files moved:
- cmd/bd/doctor/claude.md -> docs/CLAUDE_INTEGRATION.md
- cmd/bd/MAIN_TEST_REFACTOR_NOTES.md -> docs/MAIN_TEST_REFACTOR_NOTES.md
- cmd/bd/TEST_SUITE_AUDIT.md -> docs/TEST_SUITE_AUDIT.md
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Add comprehensive detection and migration guidance for old beads integration
patterns. This helps users adopt the more efficient bd prime approach.
Changes:
- Enhanced CheckLegacyBeadsSlashCommands with detailed migration steps
and token efficiency benefits (99% reduction: ~10.5k → ~50 tokens)
- Added CheckAgentDocumentation to detect missing AGENTS.md/CLAUDE.md
and suggest bd onboard or bd setup claude
- Enhanced CheckClaude to recommend bd prime hooks for MCP-only setups
with clear token efficiency messaging
- Added comprehensive tests for all new checks
bd doctor now detects:
1. Old slash command patterns (/beads:*) and recommends bd prime hooks
2. Missing agent documentation and suggests creating it
3. MCP-only setups without hooks and shows token savings potential
4. Provides clear migration paths and benefits for all scenarios
Token efficiency messaging:
- MCP mode: ~50 tokens vs ~10.5k for full scan (99% reduction)
- CLI mode: ~1-2k tokens with automatic context recovery
- Hooks auto-refresh context on SessionStart and PreCompact
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Implements automatic fix capability for bd doctor with user confirmation
and security hardening.
Features:
- Organizes fix implementations under doctor/fix/ directory structure
- Shows all fixable issues and prompts for confirmation (Y/n) before applying
- Provides clear output about what was fixed and any errors encountered
- Re-runs diagnostics after fixes to show updated state
- Each fix is idempotent and safe to run multiple times
Automatic fixes implemented:
- Git hooks (runs bd hooks install)
- Daemon health issues (runs bd daemons killall)
- DB-JSONL sync problems (runs bd sync --import-only)
- File permissions (fixes .beads/ and database permissions)
- Database version mismatches (runs bd migrate)
- Schema compatibility issues (runs bd migrate)
- Gitignore updates (writes canonical template)
Security improvements:
- Prevents command injection by using os.Executable() instead of PATH lookup
- Prevents path traversal attacks with workspace validation
- Fixes race conditions by using cmd.Dir instead of os.Chdir()
- Corrects file permission logic (proper bit masking)
- Validates all operations run in beads workspaces only
Files changed:
- cmd/bd/doctor.go: Enhanced applyFixes() with confirmation and better UX
- cmd/bd/doctor/gitignore.go: Fixed permissions (0600 → 0644)
- cmd/bd/doctor/fix/common.go: Security helpers (getBdBinary, validateBeadsWorkspace)
- cmd/bd/doctor/fix/hooks.go: Git hooks fix
- cmd/bd/doctor/fix/daemon.go: Daemon health fix
- cmd/bd/doctor/fix/sync.go: DB-JSONL sync fix
- cmd/bd/doctor/fix/permissions.go: File permissions fix
- cmd/bd/doctor/fix/migrate.go: Database migration fixes
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
