- Add bd cleanup --ephemeral flag for transient message cleanup (bd-kwro.9)
- Add Ephemeral filter to IssueFilter type
- Add ephemeral filtering to SQLite storage queries
Tests (bd-kwro.10):
- Add internal/hooks/hooks_test.go for hook system
- Add cmd/bd/mail_test.go for mail commands
- Add internal/storage/sqlite/graph_links_test.go for graph links
Documentation (bd-kwro.11):
- Add docs/messaging.md for full messaging reference
- Add docs/graph-links.md for graph link types
- Update AGENTS.md with inter-agent messaging section
- Update CHANGELOG.md with all bd-kwro features
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add TypeMessage issue type for inter-agent communication
- Add 6 new Issue fields: Sender, Ephemeral, RepliesTo, RelatesTo,
DuplicateOf, SupersededBy
- Add 4 new dependency types: replies-to, relates-to, duplicates, supersedes
- Create migration 019_messaging_fields with indexes
- Update all CRUD operations across storage layer
- Fix reset_test.go to use correct function names
- Fix redundant newline lint error in sync.go
Closes: bd-kwro.1
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When git merge replaces the .beads/beads.db file, the daemon's
SQLite connection becomes stale (still reading deleted inode).
This adds FreshnessChecker that detects file replacement via
inode/mtime comparison and triggers automatic reconnection.
Implementation:
- freshness.go: monitors db file for replacement
- store.go: adds EnableFreshnessChecking() and reconnect()
- queries.go: calls checkFreshness() on GetIssue/SearchIssues
- daemon.go: enables freshness checking at startup
- freshness_test.go: comprehensive tests including merge scenario
Code quality (per review):
- Extract configureConnectionPool() helper to reduce duplication
- Handle Close() error in reconnect() (log but continue)
- Use t.Cleanup() pattern in tests per project conventions
- Rename setupFreshnessTest() per naming conventions
Overhead: ~2.6μs per read op (~0.8% of total query time)
Signed-off-by: Alessandro De Blasis <alex@deblasis.net>
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The orphan detection was incorrectly flagging issues with dots in their
prefix (e.g., "my.project-abc123") as orphans because it was looking for
any dot in the ID, treating everything before the first dot as the
parent ID.
The fix:
- Add IsHierarchicalID() helper that correctly detects hierarchical IDs
by checking if the ID ends with .{digits} (e.g., "bd-abc.1")
- Update SQL query in orphan detection migration to use GLOB patterns
that only match IDs ending with numeric suffixes
- Update all Go code that checks for hierarchical IDs to use the new
helper function
Test cases added:
- Unit tests for IsHierarchicalID covering normal, dotted prefix, and
edge cases
- Integration test verifying dotted prefixes do not trigger false
positives
Fixes: #508
Fixes GH#523: older versions of bd could close issues without setting
the closed_at timestamp. When importing such issues, validation would
fail with "closed issues must have closed_at timestamp".
This fix adds defensive handling in all issue creation/validation paths:
- If status is "closed" and closed_at is nil, set closed_at to
max(created_at, updated_at) + 1 second
- Similarly for tombstones missing deleted_at
Applied to:
- batch_ops.go: validateBatchIssuesWithCustomStatuses (main import path)
- transaction.go: CreateIssue and CreateIssues
- queries.go: CreateIssue
- multirepo.go: upsertIssueInTx
Also adds comprehensive tests for the defensive fix.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
CloseIssue was storing the reason only in the events table, not in the
issues.close_reason column. This caused `bd show --json` to return an
empty close_reason even when one was provided.
- Update CloseIssue in queries.go and transaction.go to set close_reason
- Clear close_reason when reopening issues (in manageClosedAt)
- Add tests for close_reason in storage and CLI JSON output
- Document the dual-storage of close_reason (issues + events tables)
- Fix bd-tnsq: executeDelete now sets closed_at=NULL when creating
tombstones, satisfying the CHECK constraint that requires
closed_at IS NULL when status != 'closed'
- Fix bd-08ea: cleanup command now also prunes expired tombstones
(older than 30 days) after converting closed issues to tombstones
- Add regression test for batch deletion of closed issues
🤖 Generated with [Claude Code](https://claude.com/claude-code)
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
When CreateTombstone was called on a closed issue, the CHECK constraint
(status = closed) = (closed_at IS NOT NULL) was violated because
closed_at was not cleared. Now setting closed_at = NULL in the UPDATE.
Added regression test for creating tombstone from closed issue.
Fixes: bd-fi05
Generated with Claude Code
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The deleted_at column was defined as TEXT in the schema but code was
trying to scan into sql.NullTime. The ncruces/go-sqlite3 driver only
auto-converts TEXT to time.Time for columns declared as DATETIME/DATE/
TIME/TIMESTAMP. For TEXT columns, it returns raw strings which
sql.NullTime.Scan() cannot handle.
Added parseNullableTimeString() helper that manually parses time strings
and changed all deletedAt variables from sql.NullTime to sql.NullString.
Fixes import failure: "sql: Scan error on column index 22, name
deleted_at: unsupported Scan, storing driver.Value type string into
type *time.Time"
🤖 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>
After adding close_reason column to issues table, two functions still
called GetCloseReason() to fetch from events table after already
scanning the column. Removed the redundant code.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Add migration 017_close_reason_column.go to create the column
- Update all INSERT statements to include close_reason
- Update all SELECT statements to include close_reason
- Update doctor.go to check for close_reason in schema validation
- Remove workaround code that batch-loaded close reasons from events table
- Fix migrations_test.go to include close_reason in test table schema
This fixes sync loops where close_reason values were silently dropped
because the DB lacked the column despite the struct having the field.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Users can now define custom status states for multi-step pipelines using:
bd config set status.custom "awaiting_review,awaiting_testing,awaiting_docs"
Changes:
- Add Status.IsValidWithCustom() method for custom status validation
- Add Issue.ValidateWithCustomStatuses() method
- Add GetCustomStatuses() method to storage interface
- Update CreateIssue/UpdateIssue to support custom statuses
- Add comprehensive tests for custom status functionality
- Update config command help text with custom status documentation
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Add CloseReason field to Issue struct
- Add GetCloseReason and GetCloseReasonsForIssues queries
- Batch-load close reasons in scanIssues for efficiency
- Display close reason in bd show output
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Add exponential backoff retry for BEGIN IMMEDIATE transactions to handle
concurrent write load without spurious failures.
Changes:
- Add IsBusyError() helper to detect database locked errors
- Add beginImmediateWithRetry() with exponential backoff (10ms, 20ms, 40ms, 80ms, 160ms)
- Update CreateIssue and CreateIssuesInBatch to use retry logic
- Add comprehensive tests for error detection and retry behavior
- Handles context cancellation between retry attempts
- Fails fast on non-busy errors
This eliminates spurious SQLITE_BUSY failures under normal concurrent usage
while maintaining proper error handling for other failure modes.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Standardized error handling across the SQLite storage layer by
consistently using wrapDBError() helper functions that were already
defined in errors.go.
Changes:
- config.go: Applied wrapDBError to all config/metadata functions
- queries.go: Fixed bare 'return err' in CreateIssue, UpdateIssue, DeleteIssues
- store.go: Changed %v to %w for proper error chain preservation
- errors_test.go: Added comprehensive test coverage for error wrapping
All error paths now:
- Wrap errors with operation context using %w
- Convert sql.ErrNoRows to ErrNotFound consistently
- Preserve error chains for unwrapping and type checking
This improves debugging by maintaining operation context throughout
the error chain and enables type-safe error checking with sentinel
errors.
All tests passing ✓
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
