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
🤖 Generated with [Claude Code](https://claude.com/claude-code)
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.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
