- Replace in-memory ID counter with atomic database-backed counter
- Add issue_counters table for atomic, cross-process ID generation
- Add SyncAllCounters() and SyncCounterForPrefix() methods
- Preserve dirty_issues table and dirty tracking from main
- Both features (atomic counter + dirty tracking) now work together
- All tests passing

Closes bd-62

This commit addresses all critical follow-up issues identified in the
code review of PR #8 (atomic counter implementation).

## bd-64: Fix SyncAllCounters performance bottleneck (P0)
- Replace SyncAllCounters() on every CreateIssue with lazy initialization
- Add ensureCounterInitialized() that only scans prefix-specific issues on first use
- Performance improvement: O(n) full table scan → O(1) for subsequent creates
- Add comprehensive tests in lazy_init_test.go

## bd-65: Add migration for issue_counters table (P1)
- Add migrateIssueCountersTable() similar to migrateDirtyIssuesTable()
- Checks if table is empty and syncs from existing issues on first open
- Handles both fresh databases and migrations from old databases
- Add comprehensive tests in migration_test.go (3 scenarios)

## bd-66: Make import counter sync failure fatal (P1)
- Change SyncAllCounters() failure from warning to fatal error in import
- Prevents ID collisions when counter sync fails
- Data integrity > convenience

## bd-67: Update test comments (P2)
- Update TestMultiProcessIDGeneration comments to reflect fix is in place
- Change "With the bug, we expect errors" → "After the fix, all should succeed"

All tests pass. Atomic counter implementation is now production-ready.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Release notes:
- --deps flag for one-command issue creation (#18)
- External reference tracking for linking to external trackers
- Critical bug fixes (dep tree, auto-import, parallel creation)
- Windows build support and Go extension examples
- Community PRs merged (#8, #10, #12, #14, #15, #17)

See CHANGELOG.md for full details.

Security fixes from SECURITY_AUDIT.md:

1. JSONL file locking (#1 & steveyegge#3): Add flock-based shared/exclusive locking
   for JSONL reads (auto-import) and writes (export/flush) to prevent
   corruption when sync and daemon flush race.

2. Transaction tracking (steveyegge#2): Add atomic counter to track active
   transactions, ensuring reconnect waits for in-flight transactions.

3. Daemon crash lock cleanup (steveyegge#5): Use flock semantics instead of PID
   checking for stale lock detection. Add cleanup in panic handler.

4. Sync lock scope (steveyegge#6): Extend lock to cover entire sync operation
   including git pull/push, not just DB operations.

5. FlushManager shutdown timeout (steveyegge#7): Increase timeout from 30s to 120s
   for large databases. Add context-aware flush with progress logging.

6. WAL checkpoint error handling (steveyegge#8): Add 5-retry exponential backoff
   for checkpoint failures. Show user warning on persistent failure.

Also includes comprehensive race condition test suite covering:
- Concurrent export/import operations
- Daemon lifecycle and lock handling
- Sync/flush race scenarios
- SQLite store concurrency

Co-Authored-By: SageOx <[email protected]>

Increase FlushManager shutdown timeout from 30s to 120s to accommodate
large databases with 1000+ issues. Add WAL checkpoint retry logic with
exponential backoff to prevent data loss when concurrent readers hold locks.

Security fixes from SECURITY_AUDIT.md:
- Issue steveyegge#7: Shutdown timeout causing pending writes to be lost
- Issue steveyegge#8: WAL checkpoint failure silently losing data

Changes:
- Increase shutdownTimeout from 30s to 120s
- Add 5-retry exponential backoff for WAL checkpoint on close
- Warn user if checkpoint fails after retries
- Add flush_manager_race_test.go for concurrency testing
- Add wal_test.go for checkpoint with concurrent readers

Co-Authored-By: SageOx <[email protected]>

Add WAL checkpoint retry logic with exponential backoff to prevent data
loss when concurrent readers hold locks during database close.

Security fixes from SECURITY_AUDIT.md:
- Issue steveyegge#8: WAL checkpoint failure silently losing data

Changes:
- Add 5-retry exponential backoff for WAL checkpoint in Close()
- Warn user if checkpoint fails after retries (potential data loss)
- Add flush_manager_race_test.go for concurrency testing
- Add wal_test.go for checkpoint with concurrent readers

Co-Authored-By: SageOx <[email protected]>

Add --prefer-local, --prefer-gitlab, and --prefer-newer flags to bd gitlab sync:
- --prefer-local: Always keep local beads version on conflict
- --prefer-gitlab: Always use GitLab version on conflict
- --prefer-newer: Use most recently updated version (default)

Features:
- Unified resolveGitLabConflicts() function with strategy parameter
- Flag validation (only one conflict strategy allowed)
- Automatic conflict detection and resolution in bidirectional sync
- 7 new tests for conflict resolution

Co-Authored-By: Claude Opus 4.5 <[email protected]>

Add --prefer-local, --prefer-gitlab, and --prefer-newer flags to bd gitlab sync:
- --prefer-local: Always keep local beads version on conflict
- --prefer-gitlab: Always use GitLab version on conflict
- --prefer-newer: Use most recently updated version (default)

Features:
- Unified resolveGitLabConflicts() function with strategy parameter
- Flag validation (only one conflict strategy allowed)
- Automatic conflict detection and resolution in bidirectional sync
- 7 new tests for conflict resolution

Co-Authored-By: Claude Opus 4.5 <[email protected]>

Add --prefer-local, --prefer-gitlab, and --prefer-newer flags to bd gitlab sync:
- --prefer-local: Always keep local beads version on conflict
- --prefer-gitlab: Always use GitLab version on conflict
- --prefer-newer: Use most recently updated version (default)

Features:
- Unified resolveGitLabConflicts() function with strategy parameter
- Flag validation (only one conflict strategy allowed)
- Automatic conflict detection and resolution in bidirectional sync
- 7 new tests for conflict resolution

Co-Authored-By: Claude Opus 4.5 <[email protected]>

Executed-By: beads/crew/emma
Rig: beads
Role: crew

Add WAL checkpoint retry logic with exponential backoff to prevent data
loss when concurrent readers hold locks during database close.

Security fixes from SECURITY_AUDIT.md:
- Issue #8: WAL checkpoint failure silently losing data

Changes:
- Add 5-retry exponential backoff for WAL checkpoint in Close()
- Warn user if checkpoint fails after retries (potential data loss)
- Add flush_manager_race_test.go for concurrency testing
- Add wal_test.go for checkpoint with concurrent readers

Co-Authored-By: SageOx <[email protected]>