When `bd doctor --fix` fails to apply a fix, it was showing
"Manual fix: Run 'bd doctor --fix' ..." which is circular and unhelpful.
Now extracts just the manual command from the fix message:
- "..., or manually: <cmd>" -> extracts <cmd>
- "bd doctor --fix or <alt>" -> extracts <alt>
- No alternative available -> shows nothing
Closes GH#403
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
CloseIssue was storing the reason only in the events table, not in the
issues.close_reason column. This caused `bd show --json` to return an
empty close_reason even when one was provided.
- Update CloseIssue in queries.go and transaction.go to set close_reason
- Clear close_reason when reopening issues (in manageClosedAt)
- Add tests for close_reason in storage and CLI JSON output
- Document the dual-storage of close_reason (issues + events tables)
- 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 a new command that displays a thank you page listing all human
contributors to the beads project. Features:
- Static list of contributors (compiled into binary)
- Top 20 featured contributors displayed in columns
- Additional contributors in wrapped list
- Styled output using lipgloss (colored box, sections)
- Dynamic width based on content
- JSON output support (--json flag)
- Excludes bots and AI agents by email pattern
The sync sanitize process was incorrectly removing newly created issues
when they happened to have IDs matching entries in the deletions manifest.
This could occur with hash-based IDs when content is similar to previously
deleted issues.
The fix adds protection for issues that were in the left snapshot (local
export before pull). These represent local work and should not be removed
by sanitize, even if they match entries in the deletions manifest.
Changes:
- Load left snapshot in sanitizeJSONLWithDeletions() to build protection set
- Add protection check before removing issues from JSONL
- Add ProtectedCount/ProtectedIDs to SanitizeResult for tracking
- Log protected issues during sync for visibility
- Add comprehensive test coverage for the fix
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Fix bd-tnsq: executeDelete now sets closed_at=NULL when creating
tombstones, satisfying the CHECK constraint that requires
closed_at IS NULL when status != 'closed'
- Fix bd-08ea: cleanup command now also prunes expired tombstones
(older than 30 days) after converting closed issues to tombstones
- Add regression test for batch deletion of closed issues
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Fixes#543, #544, #545, #546 (no-db mode regressions)
Memory backend fixes:
- GetReadyWork now properly excludes issues with open blocks dependencies
- GetBlockedIssues now includes issues with status=blocked (even with 0 blockers)
- LoadFromIssues initializes hierarchical child counters from existing IDs
so repeated --parent creates bd-xxx.1, bd-xxx.2, etc.
JSONL path discovery:
- findJSONLPath works in no-db mode when dbPath is empty
- Honors BEADS_JSONL environment variable override
- Falls back to locating .beads directory
Based on PR #547 by @joelklabo - cherry-picked core fixes.
🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
Added onboard and hooks commands to the noDbCommands list so they
skip database and daemon initialization. These commands don't need
database access - they just output documentation or manage git hooks.
On Windows, if no .beads directory exists, the PersistentPreRun
would attempt database discovery (including git worktree detection)
which could hang due to git command issues.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Implements single-shot mode improvements for Windows and Docker scenarios:
- Add --lock-timeout global flag (default 30s, 0 = fail immediately)
- Add config file support: lock-timeout: 100ms
- Parameterize SQLite busy_timeout via NewWithTimeout() function
- In --sandbox mode: default lock-timeout to 100ms
- In --sandbox mode: skip FlushManager creation (no background goroutines)
This addresses bd.exe hanging on Windows and locking conflicts when
using beads across host + Docker containers.
Closes: bd-59er, bd-r4od, bd-dh8a
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add new bd doctor check that detects when sync-branch is configured
but the pre-push hook is too old (< 0.29.0) to support it. This causes
circular "bd sync" failures where the hook recommends running bd sync
but the user is already running bd sync.
The check:
- Returns error when hook version < 0.29.0 with sync-branch configured
- Returns warning for custom (non-bd) hooks that can't be verified
- Returns OK when hook is compatible or sync-branch not configured
Also adds checkSyncBranchHookQuick() for --check-health mode.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add JSONL-only mode detection in ensureStoreActive() with context-aware
error messages that suggest correct actions based on project state
- Improve error messages in main.go to detect JSONL presence and suggest
appropriate solutions (bd init, --no-db flag, or config.yaml setting)
- Update documentation to use issues.jsonl as canonical filename:
- AGENT_INSTRUCTIONS.md, README.md, resolve-beads-conflict.md
- docs/GIT_INTEGRATION.md
- Update hook template comments to clarify issues.jsonl is canonical
while maintaining backward compatibility for beads.jsonl
Fixes#534🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
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
Stealth mode was adding generic `.beads/` pattern to global gitignore,
which ignored ALL .beads/ folders across all repositories. Users who
want stealth mode in one project but open beads usage in others were
blocked.
Now uses absolute project paths instead:
- `/path/to/project/.beads/`
- `/path/to/project/.claude/settings.local.json`
This allows multiple stealth projects while other repos can use beads
openly.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Fix daemon auto-sync delete mutation not reflected in sync branch
When deleting an issue with `bd delete <id> --force`, the daemon auto-sync now properly removes the deleted issue from the sync branch.
**Problem:** The merge logic saw fewer local issues (due to deletion) and would re-add the deleted issue.
**Solution:** Add `ForceOverwrite` option to bypass merge logic when mutations occur. Mutation-triggered exports are authoritative and should overwrite, not merge.
Reviewed-by: stevey
When BEADS_DIR environment variable points to a separate git repository,
bd sync previously failed with "fatal: 'main' is already used by worktree"
because it computed repoRoot from cwd instead of the beads directory.
This fix detects when beads dir is in a different git repo than cwd and
uses direct git operations (add/commit/push/pull) instead of worktree-based
sync, bypassing the problematic worktree creation entirely.
Cherry-picked from PR #533 (cleaned up unrelated changes).
Co-Authored-By: dand-oss <dand-oss@users.noreply.github.com>
The sanitizeJSONLWithDeletions function was incorrectly removing ALL issues
whose ID appeared in deletions.jsonl, including tombstones. This caused:
1. Second sync after delete: tombstone removed from JSONL by sanitize
2. Import sees ID in deletions.jsonl but no tombstone in JSONL
3. Import creates new tombstone via convertDeletionToTombstone
4. UNIQUE constraint error: tombstone already exists in DB
The fix checks the issue status and only removes non-tombstone issues.
Tombstones are the proper representation of deletions and must be preserved.
Added test: TestSanitizeJSONLWithDeletions_PreservesTombstones
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add two new doctor checks for tombstone health:
1. Updated Deletions Manifest check:
- Warns when legacy deletions.jsonl has entries (suggests migration)
- Shows "Migrated to tombstones" when .migrated file exists
- Shows "Using inline tombstones" for new repos
2. New Tombstones check:
- Reports total tombstone count
- Warns about expired tombstones (older than 30 days)
- Shows tombstones expiring within 7 days
- Suggests 'bd compact' to prune expired tombstones
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The previous fix didn't handle the multi-repo case - it used bare
'jsonl_content_hash' key but daemon uses 'jsonl_content_hash:<repoKey>'.
Now properly computes repoKey for multi-repo support.
* fix(daemon): check for stale startlock before waiting 5 seconds
When a previous daemon startup left behind a bd.sock.startlock file
(e.g., from a crashed process), the code was waiting 5 seconds before
checking if the lock was stale. This caused unnecessary delays on
every bd command when the daemon wasn't running.
Now checks if the PID in the startlock file is alive BEFORE waiting.
If the PID is dead or unreadable, the stale lock is cleaned up
immediately and lock acquisition is retried.
Fixes ~5s delay when startlock file exists from crashed process.
* perf: add benchmarks for large descriptions, bulk operations, and sync merge
Added three new performance benchmarks to identify bottlenecks in common operations:
1. BenchmarkLargeDescription - Tests handling of 100KB+ issue descriptions
- Measures string allocation/parsing overhead
- Result: 3.3ms/op, 874KB/op allocation
2. BenchmarkBulkCloseIssues - Tests closing 100 issues sequentially
- Measures batch write performance
- Result: 1.9s total, shows write amplification
3. BenchmarkSyncMerge - Tests JSONL merge cycle with creates/updates
- Simulates real sync operations (10 creates + 10 updates per iteration)
- Result: 29ms/op, identifies sync bottlenecks
Added BENCHMARKS.md documentation describing:
- How to run benchmarks with various options
- All available benchmark categories
- Performance targets on M2 Pro hardware
- Dataset caching strategy
- CPU profiling integration
- Optimization workflow
This completes performance testing coverage for previously unmeasured scenarios.
* docs: clarify daemon lock acquisition logic in comments
Improve comments to clarify that acquireStartLock does both:
1. Immediately check for stale locks from crashed processes (avoids 5s delay)
2. If PID is alive, properly wait for legitimate daemon startup (5s timeout)
No code changes - only clarified comment documentation for maintainability.
---------
Co-authored-by: Steve Yegge <steve.yegge@gmail.com>
After bd sync completes with sync.branch mode, the daemon or next CLI
command could see a hash mismatch between the restored JSONL file and
the DB metadata, triggering auto-import which then schedules re-export,
dirtying the working directory.
Two fixes:
1. sync.go: Update jsonl_content_hash after restoreBeadsDirFromBranch
to match the restored file hash
2. daemon_sync.go: Update jsonl_content_hash after performAutoImport
succeeds (was missing, unlike CLI import path)
Fixes: bd-lw0x, bd-hxou
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* feat(config): add no-install-hooks config to disable git hook installation
Add `no-install-hooks` boolean config that prevents git hook installation
during `bd init`. This can be set via:
- Environment variable: BD_NO_INSTALL_HOOKS=1
- Global config: ~/.config/bd/config.yaml with `no-install-hooks: true`
- Local config: .beads/config.yaml with `no-install-hooks: true`
The existing `--skip-hooks` flag continues to work and takes precedence.
Default behavior unchanged: hooks install by default.
* docs: add no-install-hooks to configuration documentation
- Add no-install-hooks to Supported Settings table in CONFIG.md
- Add example in config file section
- Add "Disabling Hook Installation" section to GIT_INTEGRATION.md
with examples for flag, env var, and config file methods
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>
- Update Makefile install target to extract and pass git commit/branch via ldflags
- Add -X main.Commit and -X main.Branch to all build configurations in .goreleaser.yml
- Create scripts/install.sh helper for explicit version control during installation
- Add comprehensive tests for commit/branch resolution and output formatting
Fixes github #503: 'bd version' now reports as-built commit hash and branch
information regardless of installation method (make install, go install, or
released binaries from goreleaser).
Implements the bd reset command for GitHub issue #479:
- CLI command with flags: --hard, --force, --backup, --dry-run, --skip-init, --verbose
- Impact summary showing issues/tombstones to be deleted
- Confirmation prompt (skippable with --force)
- Colored output for better UX
- Unit tests for reset.go and git.go
- Fix: use --force flag in git rm to handle staged files
Part of epic bd-aydr.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The Claude Code allowedTools pattern uses prefix matching with space separator,
not colon. "Bash(bd *)" matches "bd ready", "bd create", etc.
Follow-up to 3d48458.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Users with workflows that don't need sync-branch (e.g., Graphite PR
stacking, single-clone setups) were seeing confusing warnings.
Changes:
- Remove checkSyncBranchQuick() - no longer warn on every bd command
- Change bd doctor from warning to OK status for missing sync-branch
- Update message to "Not configured (optional)"
Fixes#498🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add bd to Claude Code allowedTools when running `bd setup claude` so
that all bd commands (create, update, close, etc.) can run without
requiring per-command approval.
Changes:
- Add addAllowedTool() and removeAllowedTool() helper functions
- InstallClaude() now adds "Bash(bd:*)" to allowedTools
- RemoveClaude() cleans up the allowedTools entry
- Add tests for new functionality
Users who have already run `bd setup claude` can run it again to add
the missing allowedTools entry while keeping their existing hooks.
Fixes#511🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Tests were hardcoding '.git' paths directly, which fails in git worktrees
where .git is a file (not a directory) containing a pointer to the actual
git directory.
Changes:
- Replace hardcoded '.git' paths with getGitDir() calls in all hook tests
- Add os.MkdirAll() calls to ensure hooks directory exists before writing
Fixes test failures in:
- TestInstallHooks, TestInstallHooksBackup, TestInstallHooksForce,
TestUninstallHooks, TestInstallHooksShared (hooks_test.go)
- TestDetectExistingHooks, TestInstallGitHooks_NoExistingHooks,
TestInstallGitHooks_ExistingHookBackup (init_hooks_test.go)
Cherry-picked from PR #472
Co-Authored-By: matt wilkie <maphew@gmail.com>
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Fix sync bug where newly created issues were incorrectly tombstoned during bd sync.
The root cause was git-history-backfill finding issues in local commits on the sync branch, then tombstoning them when they weren't in the merged JSONL. The fix protects issues from the left snapshot (local export) from git-history-backfill.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Enable daemon RPC support for delete operations to trigger auto-sync.
This PR adds delete operation support to the RPC daemon, ensuring that delete operations emit mutation events and trigger auto-sync like other mutating operations.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
The TestSyncBranchCommitAndPush_WithPreCommitHook test needed fixes
to run correctly in isolation:
1. Set global dbPath variable so findJSONLPath() can locate the JSONL
file during sync operations. Without this, the test failed with
"JSONL path not found".
2. Add dummy git remote so hasGitRemote() returns true. The
syncBranchCommitAndPush function skips sync branch operations
when no remote is configured (local-only mode support).
3. Relax commit count assertion to check for "multiple commits"
rather than exact count of 4, since sync branch initialization
may add an extra commit depending on timing.
These changes ensure the regression test properly validates that
--no-verify bypasses pre-commit hooks in worktree commits.
Test verified:
- FAILS without --no-verify fix (confirms bug detection)
- PASSES with --no-verify fix (confirms fix works)
The integration tests were failing to compile due to several issues
introduced by API changes that weren't reflected in the test files:
1. daemon_test.go:
- getPIDFilePath() signature changed: removed boolean parameter
- getLogFilePath() signature changed: removed boolean parameter
- Removed duplicate windowsOS constant (already in test_helpers_test.go)
2. daemon_parent_test.go:
- Removed duplicate runGitCmd() function (already in git_sync_test.go
with more functionality including date env vars)
- Removed unused os/exec import
These fixes allow `go test -tags integration ./cmd/bd` to compile
successfully. The test suite can now be run to verify daemon and
sync branch functionality.
No behavioral changes - only fixing test compilation issues.
When pre-commit hooks are installed (via "bd hooks install"), daemon auto-sync
to sync branches fails with "git commit failed in worktree: exit status 1".
Root cause:
- gitCommitInWorktree() was missing --no-verify flag
- Pre-commit hook runs "bd sync --flush-only" which fails in worktree context
- Worktree has .beads directory, triggering hook execution
- Hook fails because bd cannot find proper database in worktree path
The fix adds --no-verify to git commit in gitCommitInWorktree(), matching
the existing implementation in internal/syncbranch/worktree.go line 684.
This is correct because:
- Worktree commits are internal to bd sync operations
- Running pre-commit hooks in worktree context is semantically wrong
- The library function already skips hooks for this reason
Includes regression test that:
- Creates a repo with sync branch configured
- Installs a failing pre-commit hook (simulating bd hook behavior)
- Verifies commits succeed because --no-verify bypasses the hook
- Tests multiple consecutive commits to ensure consistent behavior
Tested manually by:
1. Creating issue with "bd create" (triggers mutation event)
2. Verifying daemon logs show successful commit to sync branch
3. Confirming push to remote sync branch completes
- Add bd migrate-tombstones command (bd-8f9) to convert legacy
deletions.jsonl entries to inline tombstones in issues.jsonl
- Supports --dry-run to preview changes
- Supports --verbose for detailed progress
- Archives deletions.jsonl with .migrated suffix after migration
- Update bd compact to prune expired tombstones (bd-okh)
- All compact modes now prune tombstones older than 30-day TTL
- Reports count of pruned tombstones in output
- Add resurrection merge test (bd-bob)
- Tests scenario where base is tombstone but both left/right resurrect
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Verify that tombstones are properly included when exporting issues
to JSONL format, including all tombstone-specific fields like
DeletedAt, DeletedBy, DeleteReason, and OriginalType.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Replace fragile strings.Contains("no-db: true") with proper YAML parsing
to avoid false matches in comments or nested keys.
Changes:
- Add NoDb field to localConfig struct
- Add isNoDbModeConfigured() helper function
- Update main.go and doctor.go to use the helper
- Add 8 test cases for isNoDbModeConfigured
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Close bd-6y5 (getLocalSyncBranch tests)
- Include tombstone export logic fix (bd-81x6)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Replace fragile line-by-line parsing with yaml.Unmarshal to handle:
- Indented sync-branch values
- Comments containing sync-branch
- Multi-line values
- Values with special characters
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Update import/export to handle tombstones for deletion sync propagation:
Exporter:
- Include tombstones in JSONL output by setting IncludeTombstones: true
- Both single-repo and multi-repo exports now include tombstones
Importer:
- Tombstones from JSONL are imported as-is (they're issues with status=tombstone)
- Legacy deletions.jsonl entries are converted to tombstones via convertDeletionToTombstone()
- Non-tombstone issues in deletions manifest are still skipped (backward compat)
- purgeDeletedIssues() now creates tombstones instead of hard-deleting
This is Phase 2 of the tombstone implementation (bd-dli design), enabling
inline soft-delete tracking for cross-clone deletion synchronization.
🤖 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>
Add unit tests verifying the --output flag registration and
exportDiagnostics function for saving doctor results to JSON files.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
