- Changed 'bd clean' to 'bd cleanup' (correct command name)
- Added cleanup step to remove backup files and temporary artifacts
- Ensures clean repository state at end of agent sessions
Ran bd cleanup --force to remove all closed issues, keeping only 48 open issues.
This significantly reduces the database size and makes it easier to work with.
Deleted:
- 490 closed issues
- 221 dependency links
- 54 labels
- 755 events
Orphaned issues (will need parent repair):
- bd-tne, bd-tru, bd-ktng, bd-c362, bd-98c4e1fa.1, bd-7e7ddffa.1, bd-o78
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Problem:
In direct mode, bd list was making a separate GetLabels() call for
each issue when displaying labels. With 538 issues, this resulted in
538 separate database queries.
While investigating the reported 5+ second slowness, discovered this
N+1 query issue that would impact performance with many issues.
Solution:
1. Added GetLabelsForIssues(issueIDs []string) to Storage interface
2. Implemented bulk fetch in SQLite (already existed, now exposed)
3. Implemented bulk fetch in MemoryStorage
4. Updated list.go to fetch all labels in single query
Changes:
- internal/storage/storage.go: Add GetLabelsForIssues to interface
- internal/storage/memory/memory.go: Implement GetLabelsForIssues
- cmd/bd/list.go: Use bulk fetching in all output modes
Impact:
Eliminates N queries for labels, replacing with 1 bulk query.
This optimization applies to direct mode only (daemon mode already
uses bulk operations via RPC).
Note: The reported 5s slowness was actually caused by daemon auto-start
timeout. Use --no-daemon flag or run 'bd migrate --update-repo-id' to
resolve the legacy database issue causing daemon startup failures.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Removed all closed beads (490 total, 497 including cascade deletions):
- Completed feature implementations
- Fixed bugs and resolved issues
- Test issues from development
- Deprecated/removed features
- Refactoring tasks
Database reduced from 538 to 48 beads (46 open, 2 other states)
All deleted beads preserved in git history for reference.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
This command cleans up temporary files created during git merges by reading
patterns directly from .beads/.gitignore (Merge artifacts section).
Files removed:
- 3-way merge snapshots (beads.base.jsonl, beads.left.jsonl, beads.right.jsonl)
- Merge metadata (*.meta.json)
- Git merge driver temp files (*.json[0-9], *.jsonl[0-9])
Files preserved:
- beads.jsonl (source of truth)
- beads.db (SQLite database)
- metadata.json, config.yaml
- All daemon files
Usage:
bd clean # Clean up temporary files
bd clean --dry-run # Preview what would be deleted
Implementation:
- Reads patterns from .beads/.gitignore instead of hardcoding them
- No --force flag needed - just runs by default
- Only cleans truly temporary merge artifacts, never the database
Also:
- Restored beads.jsonl to 538 issues from commit 6cd3a32
- Set issue-prefix to "bd" in config.yaml
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Revert migration to issues.jsonl (was causing data corruption)
- Backup issues.jsonl for reference
- Database and beads.jsonl now in sync (538 issues)
- Clean slate for stable operations
Add comprehensive detection and migration guidance for old beads integration
patterns. This helps users adopt the more efficient bd prime approach.
Changes:
- Enhanced CheckLegacyBeadsSlashCommands with detailed migration steps
and token efficiency benefits (99% reduction: ~10.5k → ~50 tokens)
- Added CheckAgentDocumentation to detect missing AGENTS.md/CLAUDE.md
and suggest bd onboard or bd setup claude
- Enhanced CheckClaude to recommend bd prime hooks for MCP-only setups
with clear token efficiency messaging
- Added comprehensive tests for all new checks
bd doctor now detects:
1. Old slash command patterns (/beads:*) and recommends bd prime hooks
2. Missing agent documentation and suggests creating it
3. MCP-only setups without hooks and shows token savings potential
4. Provides clear migration paths and benefits for all scenarios
Token efficiency messaging:
- MCP mode: ~50 tokens vs ~10.5k for full scan (99% reduction)
- CLI mode: ~1-2k tokens with automatic context recovery
- Hooks auto-refresh context on SessionStart and PreCompact
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Implements automatic fix capability for bd doctor with user confirmation
and security hardening.
Features:
- Organizes fix implementations under doctor/fix/ directory structure
- Shows all fixable issues and prompts for confirmation (Y/n) before applying
- Provides clear output about what was fixed and any errors encountered
- Re-runs diagnostics after fixes to show updated state
- Each fix is idempotent and safe to run multiple times
Automatic fixes implemented:
- Git hooks (runs bd hooks install)
- Daemon health issues (runs bd daemons killall)
- DB-JSONL sync problems (runs bd sync --import-only)
- File permissions (fixes .beads/ and database permissions)
- Database version mismatches (runs bd migrate)
- Schema compatibility issues (runs bd migrate)
- Gitignore updates (writes canonical template)
Security improvements:
- Prevents command injection by using os.Executable() instead of PATH lookup
- Prevents path traversal attacks with workspace validation
- Fixes race conditions by using cmd.Dir instead of os.Chdir()
- Corrects file permission logic (proper bit masking)
- Validates all operations run in beads workspaces only
Files changed:
- cmd/bd/doctor.go: Enhanced applyFixes() with confirmation and better UX
- cmd/bd/doctor/gitignore.go: Fixed permissions (0600 → 0644)
- cmd/bd/doctor/fix/common.go: Security helpers (getBdBinary, validateBeadsWorkspace)
- cmd/bd/doctor/fix/hooks.go: Git hooks fix
- cmd/bd/doctor/fix/daemon.go: Daemon health fix
- cmd/bd/doctor/fix/sync.go: DB-JSONL sync fix
- cmd/bd/doctor/fix/permissions.go: File permissions fix
- cmd/bd/doctor/fix/migrate.go: Database migration fixes
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Ensures cache stays synchronized with dependency and status changes
by calling invalidateBlockedCache() at all mutation points (bd-5qim).
Cache invalidation points:
- AddDependency: when type is 'blocks' or 'parent-child'
- RemoveDependency: when removed dep was 'blocks' or 'parent-child'
- UpdateIssue: when status field changes
- CloseIssue: always (closed issues don't block)
The invalidation strategy is full cache rebuild on any change,
which is fast enough (<1ms for 10K issues) and keeps the logic simple.
Only 'blocks' and 'parent-child' dependency types affect blocking,
so 'relates-to' and other types skip invalidation.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Replaces expensive recursive CTE query with simple cache lookup,
achieving 96% performance improvement on 10K databases (bd-5qim).
Performance results:
- Before: ~752ms (recursive CTE on every call)
- After: ~29ms (cache lookup + filters)
- Target: <50ms ✓
The query now uses a simple NOT EXISTS check against the
blocked_issues_cache table instead of computing the full
blocked issue tree on every call.
Cache is maintained by invalidateBlockedCache() called on
dependency and status changes (added in next commit).
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Introduces a materialized cache table to store blocked issue IDs,
replacing the expensive recursive CTE computation that was causing
~752ms query times on 10K databases (bd-5qim).
The cache is maintained via invalidation on dependency and status
changes, reducing GetReadyWork from O(n²) recursive traversal to
O(1) cache lookup.
Technical details:
- New blocked_issues_cache table with single issue_id column
- ON DELETE CASCADE ensures automatic cleanup
- Migration populates cache using existing recursive CTE logic
- rebuildBlockedCache() fully rebuilds cache on invalidation
- execer interface allows both *sql.DB and *sql.Tx usage
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Type Safety Improvements:
- Change dict → dict[str, Any] throughout codebase for explicit typing
- Add PEP 561 py.typed marker file to export type information
- Add types-requests to dev dependencies
- Improve signal handler typing (FrameType | None)
- Improve decorator typing (Callable[..., Awaitable[T]])
- Add quickstart() abstract method to BdClientBase for interface completeness
Bug Fixes:
- Fix variable shadowing: beads_dir → local_beads_dir in bd_client.py
- Improve error handling in mail.py:_call_agent_mail() to prevent undefined error
- Make working_dir required (not Optional) in BdDaemonClient
- Remove unnecessary 'or' defaults for required Pydantic fields
Validation:
- mypy passes with no errors
- All unit tests passing
- Daemon quickstart returns helpful static text (RPC doesn't support this command)
Automatically creates a promotional README.md in the .beads directory
when bd init is run. The README explains what Beads is, provides
essential commands, highlights key benefits for AI-assisted workflows,
and encourages developers to try Beads in their own projects.
Changes:
- Added createReadme() function to generate compelling README content
- Integrated README creation in both regular and --no-db init modes
- README creation is idempotent (skips if already exists)
- Non-fatal warnings if README creation fails
The README is designed to get open source contributors excited about
using Beads for their AI-assisted development workflows.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Created internal/storage/sqlite/errors.go with:
- Sentinel errors: ErrNotFound, ErrInvalidID, ErrConflict, ErrCycle
- wrapDBError helpers that auto-convert sql.ErrNoRows to ErrNotFound
- Type-safe error checking with errors.Is() compatibility
Updated error handling across storage layer:
- dirty.go: Added context to error returns, converted sql.ErrNoRows checks
- util.go: Updated withTx to use wrapDBError
- batch_ops.go: Added context wrapping to batch operations
- dependencies.go: Wrapped errors from markIssuesDirtyTx calls
- ids.go: Added error wrapping for ID validation
Also restored sqlite.go that was accidentally deleted in previous commit.
All tests pass. Provides consistent error wrapping with operation context
for better debugging.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Created internal/validation package for centralized validation logic
- Created cmd/bd/flags.go for shared flag registration
- Updated create and update commands to use shared logic
- Added support for 'P1' style priority to update command
- Added tests for validation logic
Amp-Thread-ID: https://ampcode.com/threads/T-c8d369a3-32f0-42a0-96d1-fd589e89bd6b
Co-authored-by: Amp <amp@ampcode.com>
Fixes `isHashID` checks for hyphenated application names
When a user calls bd init inside an application that has a "-" for
example my-first-application without any options than ids will follow a
pattern of my-first-application-{ID}. When using SplitN on the "-"
separator it would result in the split parts returning as [my,
first-application-{ID}] which is incorrectly pulling out the {ID}
resulting in the `isHashID` returning false when it could be a hash id.
Instead of using SplitN, this changes to find the last index of the
separator resulting in the suffix becoming the actual {ID}.
