In performExport, if git commit succeeded but push failed, the
finalizeExportMetadata() was never called because we returned early.
This meant metadata would not reflect the successful export+commit.
Now finalize is called:
- Right after syncBranchCommitAndPush succeeds
- Right after gitCommit succeeds (before push attempt)
- When no git changes exist (export still happened)
Push failure still returns early, but metadata is already updated.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Executed-By: beads/crew/dave
Rig: beads
Role: crew
This fixes the atomicity gap where exportToJSONL would update SQLite
metadata (clear dirty flags, update content hash, last_import_time)
BEFORE the git commit. If git commit failed, SQLite would incorrectly
indicate the sync succeeded.
Changes:
- Add ExportResult struct to capture export metadata for deferred finalization
- Add exportToJSONLDeferred() that exports without updating metadata
- Add finalizeExport() to update metadata after git commit succeeds
- Update daemon_sync.go sync flows to defer metadata updates
Now the sync flow is truly atomic: metadata only updates after git commit.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Executed-By: beads/crew/dave
Rig: beads
Role: crew
The sync.remote config was being set via `bd config set sync.remote <name>`
but `bd sync` was still using 'origin' for git pull/push operations.
Changes:
- Updated gitPull() and gitPush() in sync_git.go to accept a configuredRemote
parameter that takes precedence over git's branch tracking config
- Updated sync.go to read sync.remote config and pass it to gitPull/gitPush
- Updated daemon_sync.go to read sync.remote config for all daemon sync ops
- Added user-facing messages to show which remote is being used
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Executed-By: beads/crew/dave
Rig: beads
Role: crew
Strip (bd-xxx), (gt-xxx) suffixes from code comments and changelog
entries. The descriptions remain meaningful without the ephemeral
issue IDs.
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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
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Modernize sorting code to use Go 1.21+ slices package:
- Replace sort.Slice with slices.SortFunc across 16 files
- Use cmp.Compare for orderable types (strings, ints)
- Use time.Time.Compare for time comparisons
- Use cmp.Or for multi-field sorting
- Use slices.SortStableFunc where stability matters
Benefits: cleaner 3-way comparison, slightly better performance,
modern idiomatic Go.
Part of GH#692 refactoring epic.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* fix(daemon): include tombstones in exportToJSONLWithStore for sync propagation
The daemon's exportToJSONLWithStore() function was using an empty
IssueFilter which defaults to IncludeTombstones: false. This caused
deleted issues (tombstones) to be excluded from JSONL exports during
daemon sync cycles.
Bug scenario:
1. User runs `bd delete <issue>` with daemon active
2. Database correctly marks issue as tombstone
3. Main .beads/issues.jsonl correctly shows status:"tombstone"
4. But sync branch worktree JSONL still showed status:"open"
5. Other clones would not see the deletion
The fix adds IncludeTombstones: true to match the behavior of
exportToJSONL() in sync.go, ensuring tombstones propagate to other
clones and prevent resurrection of deleted issues.
Adds regression test TestExportToJSONLWithStore_IncludesTombstones
that verifies tombstones are included in daemon JSONL exports.
* fix: resolve all golangci-lint errors (cherry-pick from fix/linting-errors)
Cherry-picked linting fixes to ensure CI passes.
---------
Co-authored-by: Charles P. Cross <cpdata@users.noreply.github.com>
Add omitempty JSON tags to Issue struct fields (Description, Status,
Priority, IssueType) and SetDefaults method to apply proper defaults
when importing JSONL with omitted fields.
This reduces JSONL file size for minimal issues like notifications
by not exporting empty/default values.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
GH#464: Add safety guards to prevent deletion of open/in_progress issues during sync:
- Safety guard in git-history-backfill (importer.go)
- Safety guard in deletions manifest processing
- Warning when uncommitted changes detected before pull (daemon_sync.go)
- Enhanced repo ID mismatch error message
GH#545: Fix bd blocked to show status=blocked issues (sqlite/ready.go):
- Changed from INNER JOIN to LEFT JOIN to include issues without dependencies
- Added WHERE clause to include both status=blocked AND dependency-blocked issues
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Co-Authored-By: Claude Opus 4.5 <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
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
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
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Extract shared performSync implementation with skipGit parameter:
- createSyncFunc and createLocalSyncFunc now delegate to performSync
- Follows same pattern as performExport and performAutoImport
- Reduces ~80 lines of duplicated code
Generated with Claude Code
Co-Authored-By: Claude <noreply@anthropic.com>
Consolidate createSyncFunc and createLocalSyncFunc into a shared
performSync function, following the same pattern used for:
- performExport (used by createExportFunc and createLocalExportFunc)
- performAutoImport (used by createAutoImportFunc and createLocalAutoImportFunc)
The new performSync takes a skipGit bool parameter that skips all git
operations (commits, pulls, pushes) and 3-way merge when true.
This reduces ~60 lines of duplicated code and provides a single
implementation to maintain.
Closes: bd-73u
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Co-Authored-By: Claude <noreply@anthropic.com>
Extract performExport() and performAutoImport() shared implementations:
- createExportFunc() and createLocalExportFunc() now use performExport()
with skipGit parameter
- createAutoImportFunc() and createLocalAutoImportFunc() now use performAutoImport()
with skipGit parameter
- createLocalSyncFunc() kept as-is (different flow from createSyncFunc)
Reduces daemon_sync.go by 89 lines (1003 -> 914) while maintaining
identical behavior and test coverage.
All existing tests pass. New shared functions use conditional logic
to skip git operations when skipGit=true, eliminating the need for
separate implementations.
* feat(daemon): add --local flag for git-free operation
Add --local mode to the daemon that allows it to run without a git
repository. This decouples the daemon's core functionality (auto-flush
to JSONL, auto-import from JSONL) from git synchronization.
Changes:
- Add --local flag to daemon command
- Skip git repo check when --local is set
- Add validation that --auto-commit and --auto-push cannot be used with --local
- Create local-only sync functions that skip git operations:
- createLocalSyncFunc: export-only for polling mode
- createLocalExportFunc: export without git commit/push
- createLocalAutoImportFunc: import without git pull
- Update startup message to indicate LOCAL mode
- Update event loop to use local functions when in local mode
This enables use cases like:
- Single-machine issue tracking without git
- Auto-flush to JSONL for backup purposes
- Running daemon in environments without git access
Multi-machine sync still requires git (as expected).
* fix(daemon): skip fingerprint validation in local mode
validateDatabaseFingerprint() calls beads.ComputeRepoID() which
executes git commands. This fails in non-git directories even
with --local flag.
Skip fingerprint validation entirely when running in local mode
since there's no git repository to validate against.
* test(daemon): add comprehensive test coverage for --local mode
Add tests for:
- Flag validation (--local incompatible with --auto-commit/--auto-push)
- Git check skip logic in local mode
- createLocalSyncFunc, createLocalExportFunc, createLocalAutoImportFunc
- Fingerprint validation skip in local mode
- Full integration test in non-git directory
- Export/import round-trip test
---------
Co-authored-by: Claude <noreply@anthropic.com>
Root cause: bd sync exports DB to JSONL BEFORE pulling from remote.
If the local DB is stale (fewer issues than JSONL), the stale data gets
exported and committed, potentially corrupting the remote when pushed.
The existing ZFC (Zero-Fill Check) only detected when DB had MORE issues
than JSONL, missing the dangerous reverse case.
Fix: Added "reverse ZFC" check in sync.go that detects when JSONL has
significantly more issues than DB (>20% divergence or empty DB).
When detected, it imports JSONL first to sync the database before
any export occurs.
This prevents stale/fresh clones from exporting their incomplete
database state over a well-populated JSONL file.
Version bump: 0.26.0 -> 0.26.1
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Co-Authored-By: Claude <noreply@anthropic.com>
The metadata key 'last_import_hash' was misleading because it's updated on
both import AND export. Renamed to 'jsonl_content_hash' which more accurately
describes its purpose - tracking the content hash of the JSONL file.
Added migration support: read operations try new key first, then fall back
to old key for backwards compatibility with existing databases.
Files modified:
- cmd/bd/integrity.go: Update key name with migration support
- cmd/bd/import.go: Update key name
- cmd/bd/sync.go: Update key name
- cmd/bd/autoflush.go: Update key name with migration support
- cmd/bd/daemon_sync.go: Update key name
- cmd/bd/daemon_event_loop.go: Update key name with migration support
- internal/autoimport/autoimport.go: Update key name with migration support
- Updated all related tests
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Co-Authored-By: Claude <noreply@anthropic.com>
The sync validation was incorrectly triggering 'data loss detected' when
issue count decreased after import, even for legitimate deletions recorded
in deletions.jsonl.
Changes:
- Modified validatePostImport to accept jsonlPath and check deletions manifest
- When issue count decreases, check if decrease is within recorded deletions
- Updated all call sites in sync.go and daemon_sync.go
- Added comprehensive tests for deletion-aware validation
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Co-Authored-By: Claude <noreply@anthropic.com>
After sync completion, orphan .base.jsonl and .left.jsonl files were
remaining in .beads/ directory. These are merge artifacts that should be
cleaned up after successful sync.
The fix adds SnapshotManager.Cleanup() call to createSyncFunc in
daemon_sync.go after successful import, matching the behavior of the CLI
sync command. Supports both single-repo and multi-repo modes.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Auto-import was allowing git history backfill to run, which could
incorrectly purge issues. The fix adds NoGitHistory=true to all
auto-import code paths:
- autoimport.go (importFromGit)
- autoflush.go (autoImportIfNewer)
- daemon_sync.go (importToJSONLWithStore)
Git history backfill is designed to detect deletions that happened
after a local DB was created. During auto-import, there is no local
work to protect - we are importing from the authoritative JSONL source.
Also adds comprehensive tests for NoGitHistory behavior.
Generated with Claude Code
Co-Authored-By: Claude <noreply@anthropic.com>
The staleness check compares last_import_time against JSONL file mtime.
File mtime has nanosecond precision, but last_import_time was stored with
only second precision (RFC3339). This caused a race condition where the
stored time could be slightly earlier than the file mtime, triggering
false "Database out of sync" errors - particularly in git worktrees.
Changed all 6 locations that set last_import_time to use RFC3339Nano.
The CheckStaleness parser already handles both formats, so this is
backward compatible.
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Co-Authored-By: Claude <noreply@anthropic.com>
Windows test fixes (bd-web8):
- Add sanitizeMetadataKey() to replace colons with underscores
- Windows absolute paths (e.g., C:\...) contain colons that conflict with
metadata key separator ':'
- Update tests to use sanitized keys when checking metadata
- Tests now pass on Windows by auto-sanitizing path-based keys
Nix flake fixes (bd-8y1a):
- Update vendorHash in default.nix to match current Go module dependencies
- Hash mismatch was causing Nix build failures in CI
Test improvements:
- Rename TestUpdateExportMetadataInvalidKeySuffix to reflect new behavior
- Test now verifies sanitization instead of rejection
- All tests pass locally
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Co-Authored-By: Claude <noreply@anthropic.com>
This commit addresses critical code review findings from bd-dvd and bd-ymj fixes:
## Completed Tasks
### bd-ar2.1: Extract duplicated metadata update code
- Created `updateExportMetadata()` helper function
- Eliminated 22-line duplication between createExportFunc and createSyncFunc
- Single source of truth for metadata updates
### bd-ar2.2: Add multi-repo support to export metadata updates
- Added per-repo metadata key tracking with keySuffix parameter
- Both export and sync functions now update metadata for all repos
### bd-ar2.3: Fix tests to use actual daemon functions
- TestExportUpdatesMetadata now calls updateExportMetadata() directly
- Added TestUpdateExportMetadataMultiRepo() for multi-repo testing
- Fixed export_mtime_test.go tests to call updateExportMetadata()
### bd-ar2.9: Fix variable shadowing in GetNextChildID
- Changed `err` to `resurrectErr` to avoid shadowing
- Improves code clarity and passes linter checks
### bd-ar2.10: Fix hasJSONLChanged to support per-repo keys
- Updated hasJSONLChanged() to accept keySuffix parameter
- Reads metadata with correct per-repo keys
- All callers updated (validatePreExport, daemon import, sync command)
### bd-ar2.11: Use stable repo identifiers instead of paths
- Added getRepoKeyForPath() helper function
- Uses stable identifiers like ".", "../frontend" instead of absolute paths
- Metadata keys now portable across machines and clones
- Prevents orphaned metadata when repos are moved
## Files Changed
- cmd/bd/daemon_sync.go: Helper functions, metadata updates
- cmd/bd/integrity.go: hasJSONLChanged() with keySuffix support
- cmd/bd/sync.go: Updated to use getRepoKeyForPath()
- cmd/bd/*_test.go: Tests updated for new signatures
- internal/storage/sqlite/hash_ids.go: Fixed variable shadowing
## Testing
All export, sync, and integrity tests pass.
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Co-Authored-By: Claude <noreply@anthropic.com>
Bug 1 (bd-dvd): GetNextChildID now attempts parent resurrection from JSONL
before failing. Added TryResurrectParent call to match CreateIssue behavior.
Bug 2 (bd-ymj): Export now updates last_import_hash metadata to prevent
'JSONL content has changed' errors on subsequent exports.
Files changed:
- internal/storage/sqlite/hash_ids.go: Add resurrection attempt
- cmd/bd/daemon_sync.go: Add metadata updates after export
- Tests added for both fixes
- Fixed pre-existing bug in integrity_content_test.go
Follow-up work tracked in epic bd-ar2 (9 issues for improvements).
Fixes GH #334
Replace mtime-based staleness detection with content-based (SHA256 hash) to prevent
git operations from resurrecting deleted issues.
**Problem:**
Auto-import used file modification time to detect if JSONL was "newer" than database.
Git operations (checkout, merge, pull) restore old files with recent mtimes, causing
auto-import to load stale data over current database state, resurrecting deleted issues.
**Solution:**
- Added computeJSONLHash() to compute SHA256 of JSONL content
- Added hasJSONLChanged() with two-tier check:
1. Fast-path: Check mtime first (99% of checks are instant)
2. Slow-path: Compute hash only if mtime changed (catches git operations)
- Store metadata: last_import_hash, last_import_mtime, last_import_time
- Updated auto-import in daemon_sync.go to use content-based check
- Updated validatePreExport to use content-based check (bd-xwo)
- Graceful degradation: metadata failures are non-fatal warnings
**Changes:**
- cmd/bd/integrity.go: Add computeJSONLHash(), hasJSONLChanged()
- cmd/bd/integrity_test.go: Add comprehensive tests for new functions
- cmd/bd/import.go: Update metadata after import
- cmd/bd/sync.go: Use hasJSONLChanged() instead of isJSONLNewer()
- cmd/bd/daemon_sync.go: Use hasJSONLChanged() in auto-import
**Testing:**
- Unit tests pass (TestHasJSONLChanged with 7 scenarios)
- Integration test passes (test_bd_khnb_fix.sh)
- Verified git resurrection scenario prevented
Fixes: bd-khnb
Related: bd-3bg, bd-xwo, bd-39o, bd-56p, bd-m8t, bd-rfj, bd-t5o
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Co-Authored-By: Claude <noreply@anthropic.com>
Complete implementation of signal-aware context propagation for graceful
cancellation across all commands and storage operations.
Key changes:
1. Signal-aware contexts (bd-rtp):
- Added rootCtx/rootCancel in main.go using signal.NotifyContext()
- Set up in PersistentPreRun, cancelled in PersistentPostRun
- Daemon uses same pattern in runDaemonLoop()
- Handles SIGINT/SIGTERM for graceful shutdown
2. Context propagation (bd-yb8):
- All commands now use rootCtx instead of context.Background()
- sqlite.New() receives context for cancellable operations
- Database operations respect context cancellation
- Storage layer propagates context through all queries
3. Cancellation tests (bd-2o2):
- Added import_cancellation_test.go with comprehensive tests
- Added export cancellation test in export_test.go
- Tests verify database integrity after cancellation
- All cancellation tests passing
Fixes applied during review:
- Fixed rootCtx lifecycle (removed premature defer from PersistentPreRun)
- Fixed test context contamination (reset rootCtx in test cleanup)
- Fixed export tests missing context setup
Impact:
- Pressing Ctrl+C during import/export now cancels gracefully
- No database corruption or hanging transactions
- Clean shutdown of all operations
Tested:
- go build ./cmd/bd ✓
- go test ./cmd/bd -run TestImportCancellation ✓
- go test ./cmd/bd -run TestExportCommand ✓
- Manual Ctrl+C testing verified
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Co-Authored-By: Claude <noreply@anthropic.com>
After daemon auto-export, JSONL mtime could be newer than database mtime
due to SQLite WAL mode not updating beads.db until checkpoint. This caused
validatePreExport to incorrectly block subsequent exports with "JSONL is
newer than database" error, leading to daemon shutdown.
Solution: Call TouchDatabaseFile after all export operations to ensure
database mtime >= JSONL mtime. This prevents false positives in validation
- Call getMultiRepoJSONLPaths() once at sync start instead of 3 times
- Eliminates redundant config lookups and path constructions
- Performance optimization for multi-repo workflows
- Added getMultiRepoJSONLPaths() helper to enumerate all JSONL files
- Updated daemon_sync.go to capture/update snapshots for each repo
- Added TestMultiRepoDeletionTracking to verify fix
- Added TestMultiRepoSnapshotIsolation for isolation guarantees
Previously, deletion tracking only worked for single-repo mode because
snapshot operations were hardcoded to the primary JSONL path. This fix
ensures snapshots are managed per-repository in multi-repo mode.
- Add 3-way merge deletion tracking using snapshot files
- Create .beads/beads.base.jsonl and .beads/beads.left.jsonl snapshots
- Integrate into both sync.go and daemon_sync.go
- Add comprehensive test suite in deletion_tracking_test.go
- Update .gitignore to exclude snapshot files
This fixes the resurrection bug where deleted issues come back after
multi-workspace git sync. Uses the beads-merge 3-way merge logic to
detect and apply deletions correctly.
- Add #nosec directives with explanations for all gosec warnings in worktree operations
- Tighten directory permissions from 0755 to 0750 for better security
- Fix misspellings: archaeological -> archeological, cancelled -> canceled
- Remove unused jsonlPath parameter from syncBranchCommitAndPush
- Change branchExists to return bool instead of (bool, error) - error was never used
All changes maintain backward compatibility and improve code quality.
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Co-Authored-By: Claude <noreply@anthropic.com>
