- Add closed_at field to Issue type with JSON marshaling
- Implement closed_at timestamp in SQLite storage layer
- Update import/export to handle closed_at field
- Add comprehensive tests for closed_at functionality
- Maintain backward compatibility with existing databases
Amp-Thread-ID: https://ampcode.com/threads/T-f3a7799b-f91e-4432-a690-aae0aed364b3
Co-authored-by: Amp <amp@ampcode.com>
- Added design documents (ULTRATHINK_BD222.md, ULTRATHINK_BD224.md)
- Created bd-224 epic with 6 child issues for status/closed_at invariant fix
- Created bd-222 epic with 7 child issues for batching API
- Set up dependencies: bd-224 blocks bd-222 (must fix invariant first)
- Dependencies enable max parallelism while ensuring correct order
Code review and fixes:
- Increased scanner buffer to 2MB for large JSON lines
- Added line numbers and snippets to parse error messages
- Made non-SQLite fallback conservative (skip import to prevent data loss)
- Improved collision warnings (concise, show first 10 IDs)
- Removed unused autoImportWithoutCollisionDetection function
Status/closed_at invariant enforcement:
- Auto-import now enforces invariant on all creates/updates
- Fixed CreateIssue to respect closed_at field (was ignoring it)
- Closed issues without closed_at get timestamp set automatically
Integration tests:
- TestAutoImportWithCollision: verifies local changes preserved
- TestAutoImportNoCollision: happy path with new issues
- TestAutoImportClosedAtInvariant: enforces invariant
Closes bd-226, bd-230, bd-231
Ran: UPDATE issues SET closed_at = updated_at WHERE status = 'closed' AND closed_at IS NULL
Result: 0 remaining inconsistencies (verified)
Database now ready for CHECK constraint migration
Findings:
- 86/93 closed issues (92%) are missing closed_at timestamps
- All inconsistencies are historical (old issues bd-1 through bd-93)
- No cases of non-closed issues with timestamps
Recommendation: Set closed_at = updated_at for affected issues
Next: Apply cleanup SQL and add constraint
Fixed UNIQUE constraint errors when creating multiple issues in parallel.
Root cause: The previous two-step approach used INSERT OR IGNORE to
pre-initialize counters, followed by an UPSERT to increment. Multiple
concurrent transactions could all execute the INSERT OR IGNORE with the
same initial value, causing them to generate duplicate IDs.
Solution: Replaced with a single atomic UPSERT that:
1. Initializes counter from MAX(existing IDs) if needed
2. Updates counter to MAX(current, max existing) + 1 on conflict
3. Returns the final incremented value
This ensures counters are correctly initialized from existing issues
(fixing lazy init tests) while preventing race conditions through the
BEGIN IMMEDIATE transaction serialization.
Tested with 10 parallel processes - all succeeded with unique IDs.
Also added comprehensive profiling test suite for import performance
investigation (bd-199).
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Co-Authored-By: Claude <noreply@anthropic.com>
Recovery investigation complete. Key findings documented in bd-229 notes.
No need for separate recovery doc - issue tracker has the details.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Successfully recovered 3 valuable issues from 22 total lost during auto-import bug:
- bd-222 → bd-232: Batching API feature request
- bd-223 → bd-233: Early context check optimization
- bd-221 context preserved in bd-89 notes
19 test fixtures identified but not recovered (no production value).
Auto-import collision detection fix (bd-228) prevents future data loss.
See LOST_ISSUES_RECOVERY.md for full investigation details.
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Co-Authored-By: Claude <noreply@anthropic.com>
CRITICAL FIX: Auto-import was silently overwriting local changes without any
collision detection or warning. This caused data loss in multi-developer workflows.
Changes:
- Auto-import now uses sqlite.DetectCollisions() before importing
- Colliding issues are skipped (preserves local changes)
- Warning printed with list of skipped issues and resolution instructions
- Added autoImportWithoutCollisionDetection() fallback for non-SQLite backends
- All tests pass
Impact:
- Local changes are now preserved during git pull
- Users are informed when collisions occur
- Can manually resolve with 'bd import --resolve-collisions'
- No more silent data corruption
Also:
- Removed critical warning banner from README
- Created bd-229 for data recovery investigation
- Closed bd-228 as fixed
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Co-Authored-By: Claude <noreply@anthropic.com>
CRITICAL: Auto-import silently overwrites local changes without collision detection.
Changes:
- Added prominent warning banner at top of README
- Documents data corruption risk for multi-developer workflows
- Provides --no-auto-import workaround
- References bd-228 for tracking and updates
This affects anyone using bd with multiple developers or agent swarms.
Local updates/closes can be silently reverted by auto-import after git pull.
Also includes:
- ULTRATHINK_BD224.md analysis document (bd-224, bd-225)
- Updated issues.jsonl with bd-224, bd-225, bd-226, bd-227, bd-228
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Deleted stale beads.db (last modified Oct 14, 20KB)
- bd.db is the active database (2MB, 208 issues)
- Filed bd-199 to investigate import timeout with 208 issues
- Import should handle 100k+ issues, currently times out at 208
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Co-Authored-By: Claude <noreply@anthropic.com>
Created bd-198: Add label management commands to CLI
- Add bd label add/remove/list subcommands
- Extend bd list with --label filter
- Enable organizing issues into streams/categories
- Support parallel workflow coordination
Closes mistakenly created GitHub issue #39 (should use beads itself).
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Use IMMEDIATE transactions with dedicated connections to fix race condition
where multiple processes creating issues concurrently caused "UNIQUE constraint
failed: issues.id" errors.
Key changes:
- Use BEGIN IMMEDIATE to acquire RESERVED lock early
- Use dedicated connection (sql.Conn) for transaction to ensure all operations
happen on same connection
- Increase busy_timeout from 10s to 30s for better parallel write handling
- Use context.Background() for ROLLBACK to ensure cleanup even if ctx cancelled
Added regression test TestParallelIssueCreation that creates 20 issues in
parallel and verifies no ID collisions occur.
Fixes#6🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Add idx_dependencies_depends_on_type index on (depends_on_id, type)
- Optimize queries filtering by both target issue and dependency type
- Improve performance for dep tree and relationship queries
- Update plugin version to 0.9.5
- Sync issue database
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Remove TESTING_NEXT.md (content tracked in bd-64)
- Remove .beads/bd-9-design.md (designs belong in issue design field)
- Update DESIGN.md: replace Implementation Roadmap with pointer to bd list
- All work tracking now in beads database, not markdown files
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Fixes Claude Code marketplace plugin installation failure (bd-183).
Problem: The plugin.json manifest included an engines field (borrowed from npm)
to specify minimum bd CLI version requirements. However, Claude Code's plugin
manifest schema doesn't recognize this field, causing validation errors when
installing via /plugin marketplace add.
Solution:
1. Remove the engines field from plugin.json
2. Add runtime version checking in the MCP server startup
3. Update documentation to reflect automatic version checking
Changes:
- .claude-plugin/plugin.json: Remove unsupported engines field
- integrations/beads-mcp/src/beads_mcp/bd_client.py:
- Add BdVersionError exception class
- Add _check_version() method to validate bd CLI >= 0.9.0
- Use bd version command (not bd --version)
- integrations/beads-mcp/src/beads_mcp/tools.py:
- Make _get_client() async to support version checking
- Update all tool functions to await _get_client()
- Add version check on first MCP server use
- .claude-plugin/commands/bd-version.md: Update to mention automatic checking
- PLUGIN.md: Document automatic version validation at startup
Benefits:
- Plugin installs successfully via Claude Code marketplace
- Clear error messages if bd CLI version is too old
- Version check happens once per MCP server lifetime (not per command)
- Users get actionable update instructions in error messages
Closes bd-183
During git pull --rebase, we resolved a JSONL conflict by accepting the remote's
cleaned version with --theirs. This accidentally deleted 3 legitimate issues that
were created locally:
- bd-180: Investigate vector/semantic search for issue discovery
- bd-181: Implement storage driver interface for pluggable backends
- bd-182: Investigate auto-export debounce not triggering
Recovered these from git history (HEAD~3) and re-imported them.
Stats: 72 → 75 issues (3 recovered)
**CI Improvements:**
- Fix Go version: 1.25 → 1.23 (matches go.mod)
- Add coverage threshold check (fail <50%, warn <55%)
- Coverage check runs after tests, before codecov upload
**Issue Cleanup:**
- Close bd-1: Stale test issue from early development
- Close bd-2: Auto-export verified working
- Close bd-9: Collision resolution complete (all subtasks done)
- Close bd-69: Coverage threshold implemented
**New Issues:**
- bd-69: CI coverage threshold (completed this session)
- bd-70: Test coverage improvements for auto-flush/import
Addresses review findings. System is now clean and ready for plugin testing (bd-64).
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
The codebase had two identical JSONL files (bd.jsonl and issues.jsonl).
The code defaults to issues.jsonl but FindJSONLPath() would pick bd.jsonl
alphabetically. Removed the duplicate to use only the standard filename.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Close completed test issues (bd-5, bd-51)
- Add versioning strategy task (bd-65)
- Add version sync bug (bd-66)
- Update CLAUDE.md to reflect MCP server implementation status
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Implement `bd create -f file.md` to parse markdown files and create
multiple issues in one command. This enables drafting features in
markdown and converting them to tracked issues.
Features:
- Parse markdown H2 headers (##) as issue titles
- Support all issue fields via H3 sections (### Priority, ### Type, etc.)
- Handle multiple issues per file
- Comprehensive validation and error handling
- Full test coverage with 5 test cases
Closes bd-91 (GH-9)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Fixed bug where PersistentPostRun was clearing isDirty flag before
calling flushToJSONL(), causing the flush to abort immediately.
The fix ensures flushToJSONL() handles the isDirty flag itself,
allowing the JSONL export to complete successfully.
Also added Arch Linux AUR installation instructions to README.
Changes:
- cmd/bd/main.go: Fixed PersistentPostRun flush logic
- README.md: Added Arch Linux (AUR) installation section
- .beads/bd.jsonl: Auto-exported issue bd-169 (init -q flag bug)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Created internal tracking issues for all open GitHub Issues:
- bd-85 (gh-1): Fix dep tree graph display issues [P1]
- bd-86 (gh-2): Evaluate Turso backend RFC [P3]
- bd-87 (gh-3): Debug zsh killed error [P1]
- bd-88 (gh-4): System-wide/multi-repo usage [P3]
- bd-89 (gh-6): Fix parallel creation race condition [P0]
- bd-90 (gh-7): AUR package tracking [P4]
- bd-91 (gh-9): Markdown file input support [P2]
- bd-92 (gh-11): Docker/hosted instance support [P2]
- bd-93 (gh-18): Add --deps flag to create [P2]
All issues use the new external_ref field to link to their GitHub
counterparts (gh-N). This establishes proper bidirectional tracking
between our internal beads workflow and public GitHub Issues.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Auto-sync export after implementing the external_ref field feature.
All existing issues remain unchanged (field not populated yet).
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Optimize auto-flush by tracking which issues have changed instead of
exporting the entire database on every flush. For large projects with
1000+ issues, this provides significant performance improvements.
Changes:
- Add dirty_issues table to schema with issue_id and marked_at columns
- Implement dirty tracking functions in new dirty.go file:
* MarkIssueDirty() - Mark single issue as needing export
* MarkIssuesDirty() - Batch mark multiple issues efficiently
* GetDirtyIssues() - Query which issues need export
* ClearDirtyIssues() - Clear tracking after successful export
* GetDirtyIssueCount() - Monitor dirty issue count
- Update all CRUD operations to mark affected issues as dirty:
* CreateIssue, UpdateIssue, DeleteIssue
* AddDependency, RemoveDependency (marks both issues)
* AddLabel, RemoveLabel, AddEvent
- Modify export to support incremental mode:
* Add --incremental flag to export only dirty issues
* Used by auto-flush for performance
* Full export still available without flag
- Add Storage interface methods for dirty tracking
Performance impact: With incremental export, large databases only write
changed issues instead of regenerating entire JSONL file on every
auto-flush.
Closes bd-39
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Implements bd-42: Add test coverage for auto-flush feature
Created cmd/bd/main_test.go with 11 comprehensive test functions:
- TestAutoFlushDirtyMarking: Verifies markDirtyAndScheduleFlush() marks DB as dirty
- TestAutoFlushDisabled: Tests --no-auto-flush flag disables feature
- TestAutoFlushDebounce: Tests rapid operations result in single flush
- TestAutoFlushClearState: Tests clearAutoFlushState() resets state
- TestAutoFlushOnExit: Tests flush happens on program exit
- TestAutoFlushConcurrency: Tests concurrent operations don't cause races
- TestAutoFlushStoreInactive: Tests flush skips when store is inactive
- TestAutoFlushJSONLContent: Tests flushed JSONL has correct content
- TestAutoFlushErrorHandling: Tests error scenarios (permissions, etc.)
- TestAutoImportIfNewer: Tests auto-import when JSONL is newer than DB
- TestAutoImportDisabled: Tests --no-auto-import flag disables auto-import
Coverage results:
- markDirtyAndScheduleFlush: 100%
- clearAutoFlushState: 100%
- flushToJSONL: 67.6%
- autoImportIfNewer: 66.1% (up from 0%)
All tests pass. Auto-flush feature is now thoroughly tested.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Three improvements to beads:
1. ID space partitioning (closes bd-24)
- Add --id flag to 'bd create' for explicit ID assignment
- Validates format: prefix-number (e.g., worker1-100)
- Enables parallel agents to partition ID space and avoid conflicts
- Storage layer already supported this, just wired up CLI
2. Auto-flush failure tracking (closes bd-38)
- Track consecutive flush failures with counter and last error
- Show prominent red warning after 3+ consecutive failures
- Reset counter on successful flush
- Users get clear guidance to run manual export if needed
3. Manual export cancels auto-flush timer
- Add clearAutoFlushState() helper function
- bd export now cancels pending auto-flush and clears dirty flag
- Prevents redundant exports when user manually exports
- Also resets failure counter on successful manual export
Documentation updated in README.md and CLAUDE.md with --id flag examples.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Downgraded bd-25 to P4 and closed as won't-fix for 1.0:
- Transaction support is premature optimization
- SQLite already provides ACID guarantees per-operation
- Collision resolution works reliably without multi-operation transactions
- Would add significant complexity for theoretical benefit
Will revisit if actual issues arise in production use.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Added os.MkdirAll(dbDir, 0755) to ensure the .beads directory exists
before attempting to glob for JSONL files. This fixes a bug where
findJSONLPath() would fail silently if the directory doesn't exist yet,
which can happen during new database initialization.
The fix:
- Creates the directory with 0755 permissions if it doesn't exist
- Handles errors gracefully by returning the default path
- Subsequent write operations will still fail with clear errors if
directory creation fails
Closes bd-36
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Adds auto-import feature to complement bd-35's auto-export, completing
the automatic sync workflow for git collaboration.
**Implementation:**
- Auto-import checks if JSONL is newer than DB on command startup
- Silently imports JSONL when modification time is newer
- Skips import command itself to avoid recursion
- Can be disabled with --no-auto-import flag
**Documentation updates:**
- Updated README.md git workflow section
- Updated CLAUDE.md workflow and pro tips
- Updated bd quickstart with auto-sync section
- Updated git hooks README to clarify they're now optional
**Testing:**
- Tested auto-import by touching JSONL and running commands
- Tested auto-export with create/close operations
- Complete workflow verified working
Closes bd-33
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Fixed three critical issues identified in code review:
1. Race condition with store access: Added storeMutex and storeActive
flag to prevent background flush goroutine from accessing closed
store. Background timer now safely checks if store is active before
attempting flush operations.
2. Missing auto-flush in import: Added markDirtyAndScheduleFlush()
call after import completes, ensuring imported issues sync to JSONL.
3. Timer cleanup: Explicitly set flushTimer to nil after Stop() to
prevent resource leaks.
Testing confirmed all fixes working:
- Debounced flush triggers after 5 seconds of inactivity
- Immediate flush on process exit works correctly
- Import operations now trigger auto-flush
- No race conditions detected
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Implements --resolve-collisions flag for import command to safely handle ID
collisions during branch merges. When enabled, colliding issues are remapped
to new IDs and all text references and dependencies are automatically updated.
Also adds comprehensive tests, branch-merge example, and documentation.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Add reference scoring to prioritize which colliding issues should be
renumbered during collision resolution. Issues with fewer references
are renumbered first to minimize total update work.
Changes to collision.go:
- Add ReferenceScore field to CollisionDetail
- scoreCollisions() calculates scores and sorts collisions ascending
- countReferences() counts text mentions + dependency references
- Uses word-boundary regex (\b) to match exact IDs (bd-10 not bd-100)
New tests in collision_test.go:
- TestCountReferences: validates reference counting logic
- TestScoreCollisions: verifies scoring and sorting behavior
- TestCountReferencesWordBoundary: ensures exact ID matching
Reference score = text mentions (desc/design/notes/criteria) + deps
Sort order: fewest references first (minimizes renumbering impact)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Enable external orchestrators to control issue ID assignment via --id flag
on bd create and optional next_id config. Keeps beads simple while allowing
orchestrators to implement ID partitioning strategies to minimize merge
conflicts. Complementary to bd-9 collision resolution work.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
