diff --git a/.beads/beads.jsonl b/.beads/beads.jsonl
index 072f7673..678ac3b5 100644
--- a/.beads/beads.jsonl
+++ b/.beads/beads.jsonl
@@ -33,6 +33,7 @@
 {"id":"bd-3e9ddc31","content_hash":"4e03660281dbe2c069617fc8d723d546d6e5eb386142c0359b862747867a1b90","title":"Replace getStorageForRequest with Direct Access","description":"Replace all getStorageForRequest(req) calls with s.storage","acceptance_criteria":"- No references to getStorageForRequest() in codebase (except in deleted file)\n- All handlers use s.storage directly\n- Code compiles without errors\n\nFiles to update:\n- internal/rpc/server_issues_epics.go (~8 calls)\n- internal/rpc/server_labels_deps_comments.go (~4 calls)\n- internal/rpc/server_compact.go (~2 calls)\n- internal/rpc/server_export_import_auto.go (~2 calls)\n- internal/rpc/server_routing_validation_diagnostics.go (~1 call)\n\nPattern: store, err := s.getStorageForRequest(req) → store := s.storage","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-27T23:20:10.393759-07:00","updated_at":"2025-10-30T17:12:58.21613-07:00","closed_at":"2025-10-28T14:08:38.06721-07:00"}
 {"id":"bd-3ee2c7e9","content_hash":"a1a26c30e2d2d791d3dd5b3fe3a917304cb001b1d024e4627e46fd93c98bcf86","title":"Add \"bd daemons\" command for multi-daemon management","description":"Add a new \"bd daemons\" command with subcommands to manage daemon processes across all beads repositories/worktrees. Should show all running daemons with metadata (version, workspace, uptime, last sync), allow stopping/restarting individual daemons, auto-clean stale processes, view logs, and show exclusive lock status.","design":"Subcommands:\n- list: Show all running daemons with metadata (workspace, PID, version, socket path, uptime, last activity, exclusive lock status)\n- stop \u003cpath|pid\u003e: Gracefully stop a specific daemon\n- restart \u003cpath|pid\u003e: Stop and restart daemon\n- killall: Emergency stop all daemons\n- health: Verify each daemon responds to ping\n- logs \u003cpath\u003e: View daemon logs\n\nFeatures:\n- Auto-clean stale sockets/dead processes\n- Discovery: Scan for .beads/bd.sock files + running processes\n- Communication: Use existing socket protocol, add GET /status endpoint for metadata","status":"open","priority":1,"issue_type":"epic","created_at":"2025-10-26T16:53:40.970042-07:00","updated_at":"2025-10-31T20:41:33.915811-07:00"}
 {"id":"bd-3f80d9e0","title":"Improve internal/daemon test coverage (currently 22.5%)","description":"Daemon functionality needs better coverage:\n- Auto-start behavior\n- Lock file management\n- Discovery mechanisms\n- Connection handling\n- Error recovery","status":"open","priority":2,"issue_type":"task","created_at":"2025-10-29T14:06:30.832728-07:00","updated_at":"2025-10-30T17:12:58.186077-07:00"}
+{"id":"bd-40a0","content_hash":"44ac6f2956fce0d7f1fa4d6f4e09b93b14bdd914c1199ed68dedf9c85fbdf4cf","title":"bd doctor should check for multiple DBs, multiple JSONLs, daemon health","description":"","design":"\nCurrently bd doctor only checks:\n- .beads/ directory exists\n- Database version vs CLI version  \n- ID format (hash vs sequential)\n- CLI version vs latest GitHub release\n\nIt should ALSO check for operational issues that cause silent failures:\n\n1. **Multiple database files** (*.db excluding backups and vc.db)\n   - Warn if multiple *.db files found (ambiguous which to use)\n   - Suggest running 'bd migrate' or manually removing old DBs\n\n2. **Multiple JSONL files** \n   - Check for both issues.jsonl and beads.jsonl\n   - Warn about ambiguity, suggest standardizing on one\n\n3. **Daemon health** (integrate bd daemons health)\n   - Check if daemon running for this workspace\n   - Detect version mismatches between daemon and CLI\n   - Detect zombie daemons (running but unresponsive)\n   - Detect stale daemon.pid files\n\n4. **Database-JSONL sync issues**\n   - Check if JSONL is newer than last import\n   - Warn if they're out of sync\n\n5. **Permissions issues**\n   - Check if .beads/ directory is writable\n   - Check if database file is readable/writable\n\nImplementation approach:\n- Add new check functions to doctor.go\n- Reuse logic from bd daemons health\n- Keep checks fast (\u003c 1 second total)\n- Output actionable fixes for each issue\n","status":"open","priority":1,"issue_type":"feature","created_at":"2025-10-31T21:16:47.042913-07:00","updated_at":"2025-10-31T21:16:47.042913-07:00"}
 {"id":"bd-46381404","content_hash":"1963d7e754c6eaafba9cbefc6d9f38cc4d872386d9d100ecbba7d7f24cbbcea3","title":"Test database naming","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-10-27T18:27:28.309676-07:00","updated_at":"2025-10-31T12:00:43.185201-07:00","closed_at":"2025-10-31T12:00:43.185201-07:00"}
 {"id":"bd-47c59dd4","content_hash":"24b00d276bd245aec3e6dfb6378457e785ac6a01538eba05450dd65dba993178","title":"Audit Current Cache Usage","description":"Understand exactly what code depends on the storage cache","acceptance_criteria":"- Document showing all cache dependencies\n- Confirmation that removing cache won't break MCP\n- List of tests that need updating\n\nFiles to examine:\n- internal/rpc/server_cache_storage.go (cache implementation)\n- internal/rpc/client.go (how req.Cwd is set)\n- internal/rpc/server_*.go (all getStorageForRequest calls)\n- integrations/beads-mcp/ (MCP multi-repo logic)\n\nTasks:\n- Document all callers of getStorageForRequest()\n- Verify req.Cwd is only set by RPC client for database discovery\n- Confirm MCP server doesn't rely on multi-repo cache behavior\n- Check if any tests assume multi-repo routing\n- Review environment variables: BEADS_DAEMON_MAX_CACHE_SIZE, BEADS_DAEMON_CACHE_TTL, BEADS_DAEMON_MEMORY_THRESHOLD_MB","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-27T23:20:10.393143-07:00","updated_at":"2025-10-30T17:12:58.215671-07:00","closed_at":"2025-10-28T10:47:37.875005-07:00"}
 {"id":"bd-4aeed709","content_hash":"3ab290915c117ec902bda1761e8c27850512f3fd4b494a93546c44b397d573a3","title":"bd resolve-conflicts - Git merge conflict resolver","description":"Automatically resolve JSONL merge conflicts.\n\nModes:\n- Mechanical: ID remapping (no AI)\n- AI-assisted: Smart merge/keep decisions\n- Interactive: Review each conflict\n\nHandles \u003c\u003c\u003c\u003c\u003c\u003c\u003c conflict markers in .beads/beads.jsonl\n\nFiles: cmd/bd/resolve_conflicts.go (new)","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-28T14:48:17.457619-07:00","updated_at":"2025-10-30T17:12:58.218109-07:00","closed_at":"2025-10-28T15:47:33.037021-07:00"}