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>
Both findBeadsDir() and findGitRoot() now use filepath.EvalSymlinks()
to resolve to canonical paths before comparison. This fixes the issue
where filepath.Rel() fails on macOS because /var is a symlink to
/private/var, causing path mismatches.
Fixes: TestDatabaseReinitialization failures on macOS
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Phase 1 of tombstone migration: bd delete now creates tombstones instead
of hard-deleting issues.
Key changes:
- Add CreateTombstone() method to SQLiteStorage for soft-delete
- Modify executeDelete() to create tombstones instead of removing rows
- Add IsExpired() method with 30-day default TTL and clock skew grace
- Fix deleted_at schema from TEXT to DATETIME for proper time scanning
- Update delete.go to call CreateTombstone (single issue path)
- Still writes to deletions.jsonl for backward compatibility (dual-write)
- Dependencies are removed when creating tombstones
- Tombstones are excluded from normal searches (bd-1bu)
TTL constants:
- DefaultTombstoneTTL: 30 days
- MinTombstoneTTL: 7 days (safety floor)
- ClockSkewGrace: 1 hour
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Add partial index on deleted_at for efficient TTL queries
- Exclude tombstones from SearchIssues by default (new IncludeTombstones filter)
- Report tombstone count separately in GetStatistics
- Display tombstone count in bd stats output
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Small fixes from code review:
- Error message now shows actual gitRef instead of hardcoded HEAD
- Removed unused lineNum variable in readFirstIssueFromGit
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
When sync-branch is configured in config.yaml, bd init now reads from
that branch (origin/<branch> first, then local <branch>) instead of
HEAD. This ensures fresh clones correctly import issues from the sync
branch.
Key changes:
- checkGitForIssues() now returns gitRef (third return value)
- New getLocalSyncBranch() reads sync-branch directly from config.yaml
(not cached global config) to handle test environments where CWD changes
- importFromGit() accepts gitRef parameter to read from correct branch
- Added readFirstIssueFromGit() for prefix auto-detection from git
- Fixed macOS symlink issue: filepath.EvalSymlinks() ensures /var and
/private/var paths are normalized before filepath.Rel()
Part of GitHub issue #464 (beads deletes issues in multi-clone environments)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <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 copilotInstructionsContent in onboard.go contained content specific to
developing the beads project itself (Go tech stack, SQLite, Cobra, project
structure, release scripts, etc.). This content doesn't make sense when
running bd onboard in other repositories that use bd for issue tracking.
Removed:
- Tech Stack section (Go, SQLite, Cobra, etc.)
- Coding Guidelines section (beads development instructions)
- Project Structure section (beads directory tree)
- Scripts section (bump-version.sh, release.sh, etc.)
- Key Documentation section (beads-specific docs)
- Beads-specific rules (BEADS_DB testing, test issues in production DB)
Kept:
- All bd command examples and workflow (unchanged)
- Priorities and issue types
- MCP server instructions
- Generic rules applicable to any project using bd
The beads repo's own .github/copilot-instructions.md is manually maintained
and still contains the beads-specific development instructions.
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>
Replaces manual working directory save/restore patterns
with Go's built-in `t.Chdir()` helper across 23 test files.
The manual pattern involved calling `os.Getwd()` to save
the original directory, using `defer os.Chdir(origWd)` for
restoration, and manually handling errors during directory
changes. This boilerplate has been replaced with single
`t.Chdir(path)` calls that handle cleanup automatically.
The `t.Chdir()` method automatically restores the working
directory when the test completes, eliminating the need for
manual defer statements and error handling.
Total:
~75 instances replaced (assuming Claude's math is right)
Co-authored-by: Claude <noreply@anthropic.com>
Reduces the default retention period for deletion manifest entries.
Shorter TTL limits blast radius of stale deletions that can poison
beads installations when agents get out of sync.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Increase Windows test timeout from 20m to 30m
- Add -parallel=4 flag to allow concurrent test execution
- Add t.Parallel() to safe table-driven tests in validate_test.go,
autoimport_test.go, and sync_test.go
This should prevent the Windows CI timeout caused by the cumulative
runtime of cmd/bd tests exceeding 20 minutes.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Add a `--stealth` flag to `bd setup claude` that installs
Claude Code hooks using `bd prime --stealth` instead of
`bd prime`. This extends the stealth workflow introduced for
`bd prime` to the setup command, enabling workflows where git
operations should be deferred or handled separately from bd
database flushing.
When `--stealth` is specified, the installed hooks call
`bd prime --stealth`, which outputs only `bd sync --flush-only`
in the close protocol, omitting all git operations.
Update `RemoveClaude()` to remove both command variants
(`bd prime` and `bd prime --stealth`) for backwards
compatibility with existing installations. Update
`hasBeadsHooks()` to detect either variant as a valid
installation.
Add comprehensive test coverage for stealth mode: hook
installation with stealth command, removal of both variants,
detection of both variants, and idempotency with stealth mode.
Co-Authored-By: Claude <noreply@anthropic.com>
Add a `--stealth` flag to `bd prime` that outputs a simplified
workflow using only `bd sync --flush-only`, omitting all git
operations (commit, push, pull).
This addresses use cases where git operations need to be deferred
or handled separately from the bd workflow (e.g. bd init --stealth),
where committing files is may not desired as part of the Claude
conversation.
In stealth mode, the close protocol shows only the flush step.
Includes tests for current and existing functionality.
To make testing easier,
refactor output functions to accept `io.Writer` parameters
instead of writing directly to `os.Stdout`,
and convert `isEphemeralBranch` from a function to a
variable for stubbing.
Co-Authored-By: Claude <noreply@anthropic.com>
- Fix gosec G204/G304 warnings by adding exclusions for safe subprocess
launches and file reads in doctor.go, jira.go, migrate_sync.go, and
syncbranch/worktree.go
- Fix misspell: "cancelled" -> "canceled" in sync.go
- Fix unparam: mark unused ctx params in jira.go placeholder functions
- Fix errcheck: explicitly ignore fmt.Sscanf return in doctor.go and
use closure pattern for deferred os.RemoveAll in worktree.go
- Increase Windows test timeout from 10m to 20m to prevent CI timeouts
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
The estimated_minutes field existed in the Issue schema but wasn't exposed
via CLI. This adds:
- --estimate / -e flag to bd create (e.g., bd create "Task" --estimate 120)
- --estimate / -e flag to bd update (e.g., bd update bd-xyz --estimate 60)
- EstimatedMinutes field to RPC CreateArgs and UpdateArgs
- Server-side handling in handleCreate and updatesFromArgs
- Validation for non-negative values
The value is specified in minutes and is useful for planning and
prioritization. The vscode-beads extension already has an Estimate column
that can now be populated.
Fixes#443🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Update examples to show `bd close <id1> <id2> ...` for batch closing
- Add quick reference entry for closing multiple issues at once
- Add tip about using parallel subagents for creating multiple issues
- Add comment in example about running bd create in parallel
Cherry-picked from PR #452 (prime.go changes only)
Co-Authored-By: Ryan Snodgrass <rsnodgrass@gmail.com>
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
