Fix critical race conditions in auto-flush feature

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>

.beads/issues.jsonl

@@ -23,6 +23,10 @@
 {"id":"bd-3","title":"Document git workflow in README","description":"Add Git Workflow section to README explaining binary vs text approaches","status":"closed","priority":1,"issue_type":"chore","created_at":"2025-10-12T00:43:03.461615-07:00","updated_at":"2025-10-12T16:19:11.970753-07:00","closed_at":"2025-10-12T00:43:30.283178-07:00"}
 {"id":"bd-30","title":"Remove unused issueMap in scoreCollisions","description":"scoreCollisions() creates issueMap and populates it (lines 135-138) but never uses it. Either remove it or add a TODO comment explaining future use. Located in collision.go:135-138. Cosmetic cleanup.","status":"open","priority":4,"issue_type":"chore","created_at":"2025-10-12T16:39:40.101611-07:00","updated_at":"2025-10-12T16:39:40.101611-07:00"}
 {"id":"bd-31","title":"Test issue for design field","description":"Testing the new update flags","design":"## Design Plan\\n- Add flags to update command\\n- Test thoroughly\\n- Document changes","acceptance_criteria":"- All three fields (design, notes, acceptance-criteria) can be updated\\n- Changes persist in database\\n- bd show displays the fields correctly","notes":"Implementation complete. All tests passing.","status":"closed","priority":3,"issue_type":"task","created_at":"2025-10-12T17:09:22.147446-07:00","updated_at":"2025-10-12T17:10:32.828906-07:00","closed_at":"2025-10-12T17:10:32.828906-07:00"}
+{"id":"bd-32","title":"bd should auto-detect .beads/*.db in current directory","description":"When bd is run without --db flag, it defaults to beads' own database instead of looking for a .beads/*.db file in the current working directory. This causes confusion when working on other projects that use beads for issue tracking (like vc).\n\nExpected behavior: bd should search for .beads/*.db in cwd and use that if found, before falling back to default beads database.\n\nExample: Running 'bd ready' in /Users/stevey/src/vc/vc/ should automatically find and use .beads/vc.db without requiring --db flag every time.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-10-13T21:15:16.866255-07:00","updated_at":"2025-10-13T21:30:47.456341-07:00","closed_at":"2025-10-13T21:30:47.456341-07:00"}
+{"id":"bd-33","title":"Document or automate JSONL sync workflow for git collaboration","description":"When using beads across multiple machines/environments via git, there's a workflow gap:\n\n1. Machine A: Create issues → stored in .beads/project.db\n2. Machine A: bd export -o .beads/issues.jsonl\n3. Machine A: git add .beads/issues.jsonl \u0026\u0026 git commit \u0026\u0026 git push\n4. Machine B: git pull\n5. Machine B: ??? issues.jsonl exists but project.db is empty/stale\n\nThe missing step is: bd import --db .beads/project.db -i .beads/issues.jsonl\n\nThis needs to be either:\na) Documented clearly in workflow docs\nb) Automated (e.g., git hook, or bd auto-imports if jsonl is newer than db)\nc) Both\n\nReal-world impact: User had Claude Code on GCP VM create vc issues from BOOTSTRAP.md. They were exported to issues.jsonl and committed. But on local machine, vc.db was empty until manual import was run.","status":"open","priority":1,"issue_type":"task","created_at":"2025-10-13T21:15:30.271236-07:00","updated_at":"2025-10-13T21:15:30.271236-07:00"}
+{"id":"bd-34","title":"Implement reserved database name _.db","description":"Auto-detection now skips .beads/_.db to prevent pollution when beads dogfoods itself. This allows beads to use its own issue tracker without interfering with other projects using beads in the same directory tree. Implementation includes filtering in findDatabase(), stopping directory walk when .beads/ is found, and documentation in README.md and CLAUDE.md.","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-10-13T21:46:15.189582-07:00","updated_at":"2025-10-13T21:54:26.388271-07:00","closed_at":"2025-10-13T21:54:26.388271-07:00"}
+{"id":"bd-35","title":"Auto-flush JSONL on CRUD operations with 5-second debounce","description":"Implemented automatic write-through from SQLite to JSONL with 5-second debouncing. After any CRUD operation (create, update, close, dep add/remove), changes are scheduled to flush to JSONL after 5 seconds of inactivity. On process exit, any pending changes are flushed immediately. This prevents .db and .jsonl from getting out of sync, solving the workflow gap where agents forget to run 'bd export'. Can be disabled with --no-auto-flush flag. Addresses bd-33.","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-10-13T22:21:13.94705-07:00","updated_at":"2025-10-13T22:22:38.359968-07:00","closed_at":"2025-10-13T22:22:38.359968-07:00"}
 {"id":"bd-4","title":"Add demo GIF/video showing bd quickstart in action","description":"Record asciinema or create animated GIF showing the full workflow","status":"open","priority":2,"issue_type":"feature","created_at":"2025-10-12T10:50:49.500051-07:00","updated_at":"2025-10-12T16:19:11.97083-07:00","dependencies":[{"issue_id":"bd-4","depends_on_id":"bd-8","type":"parent-child","created_at":"2025-10-12T10:51:08.399915-07:00","created_by":"stevey"}]}
 {"id":"bd-5","title":"Implement MCP server for Claude Desktop","description":"Complete the claude-desktop-mcp example with working TypeScript implementation","status":"open","priority":1,"issue_type":"feature","created_at":"2025-10-12T10:50:50.942964-07:00","updated_at":"2025-10-12T16:19:11.970913-07:00","dependencies":[{"issue_id":"bd-5","depends_on_id":"bd-8","type":"parent-child","created_at":"2025-10-12T10:51:08.404381-07:00","created_by":"stevey"}]}
 {"id":"bd-6","title":"Add migration scripts for GitHub Issues","description":"Create scripts to import from GitHub Issues API or exported JSON","status":"open","priority":2,"issue_type":"feature","created_at":"2025-10-12T10:50:52.140018-07:00","updated_at":"2025-10-12T16:19:11.97099-07:00","dependencies":[{"issue_id":"bd-6","depends_on_id":"bd-8","type":"parent-child","created_at":"2025-10-12T10:51:08.40857-07:00","created_by":"stevey"}]}