Fix bd-73: Add git worktree detection and warnings

- Implement robust worktree detection using git-dir vs git-common-dir comparison
- Add prominent warning when daemon mode is active in a worktree
- Warn in 3 places: initial connection, auto-start, and daemon start command
- Show shared database path and clarify BEADS_AUTO_START_DAEMON behavior
- Document limitations and solutions in README.md and AGENTS.md
- Add comprehensive tests for detection and path truncation

Fixes #55

Amp-Thread-ID: https://ampcode.com/threads/T-254eb9e3-1a42-42d7-afdf-b7ca2d2dcb8b
Co-authored-by: Amp <amp@ampcode.com>

.beads/beads.jsonl

@@ -67,5 +67,7 @@
 {"id":"bd-7","title":"Write tests for merge functionality","description":"Unit tests: validation, merge logic, data integrity. Integration tests: end-to-end workflow, export/import. Edge case tests: chains, circular refs, epics.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-21T23:53:44.31362-07:00","updated_at":"2025-10-22T21:23:20.836984-07:00","closed_at":"2025-10-22T01:07:04.72062-07:00"}
 {"id":"bd-70","title":"Fix bd sync prefix mismatch error message suggesting non-existent flag","description":"GH #103: bd sync suggests using --rename-on-import flag that doesn't exist. Need to either implement the flag or fix the error message to suggest the correct workflow.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-10-22T17:54:24.473508-07:00","updated_at":"2025-10-22T21:23:20.837249-07:00","closed_at":"2025-10-22T17:57:46.973029-07:00"}
 {"id":"bd-71","title":"Fix MCP close tool method signature error","description":"GH #107: MCP close() tool fails with \"BdDaemonClient.close() takes 1 positional argument but 2 were given\". Need to fix method signature in beads-mcp server.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-10-22T19:17:05.429429-07:00","updated_at":"2025-10-22T21:23:20.837473-07:00","closed_at":"2025-10-22T19:19:54.601153-07:00"}
+{"id":"bd-72","title":"Update Claude Code marketplace plugin","description":"Update the beads plugin in the Claude Code marketplace to the latest version. This may help resolve some of the open GitHub issues related to marketplace installation and compatibility (#54, #112).\n\nShould include:\n- Latest beads version\n- Updated documentation\n- Any new features or bug fixes","status":"open","priority":2,"issue_type":"task","created_at":"2025-10-22T22:29:11.293161-07:00","updated_at":"2025-10-22T22:29:11.293161-07:00"}
+{"id":"bd-73","title":"Git worktree support - ensure --no-daemon works correctly","description":"Users working with git worktrees report that beads MCP commits to the wrong branch (main instead of worktree branch). \n\n**Root cause:** Git worktrees share the same .beads directory, so the daemon/MCP server doesn't know which branch the worktree has checked out.\n\n**Current state:**\n- Daemon mode: Cannot work properly with worktrees (fundamental limitation - shared .beads, unknown branch)\n- CLI with --no-daemon: Should work but needs verification\n\n**Action items:**\n1. Test and verify --no-daemon works correctly in worktrees\n2. Document the limitation in README/AGENTS.md\n3. Add clear error/warning when using daemon with worktrees\n4. Consider if MCP server can detect worktree usage and auto-disable daemon\n\n**Workaround for users:**\nUse --no-daemon flag when working in worktrees, or set BEADS_AUTO_DAEMON=false\n\n**Related:** GH issue #55","notes":"**Implementation completed with oracle review improvements:**\n\n1. **Robust detection** - Changed from substring check to canonical git-dir vs git-common-dir comparison\n2. **Correct warning gate** - Now only checks isGitWorktree() and only called when daemon is actually connected\n3. **Complete coverage** - Added warning to `bd daemon` command start path\n4. **Better UX** - Shows shared database path and clarifies BEADS_AUTO_START_DAEMON behavior\n5. **Improved tests** - Validates canonical detection method and path truncation\n\n**Files changed:**\n- cmd/bd/worktree.go - Improved detection and warning\n- cmd/bd/worktree_test.go - Better test coverage\n- cmd/bd/main.go - Warning after daemon connection (2 places)\n- cmd/bd/daemon.go - Warning when starting daemon\n- README.md \u0026 AGENTS.md - Documented limitations and solutions","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-10-22T22:38:52.438601-07:00","updated_at":"2025-10-22T22:58:00.306114-07:00","closed_at":"2025-10-22T22:51:45.464598-07:00"}
 {"id":"bd-8","title":"Improve error handling in dependency removal during remapping","description":"In updateDependencyReferences(), RemoveDependency errors are caught and ignored with continue (line 392). Comment says 'if dependency doesn't exist' but this catches ALL errors including real failures. Should check error type with errors.Is(err, ErrDependencyNotFound) and only ignore not-found errors, returning other errors properly.","status":"closed","priority":3,"issue_type":"bug","created_at":"2025-10-21T23:53:44.31362-07:00","updated_at":"2025-10-22T21:23:20.837687-07:00","closed_at":"2025-10-18T09:41:18.209717-07:00"}
 {"id":"bd-9","title":"Test issue 2","description":"","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-21T23:53:44.31362-07:00","updated_at":"2025-10-22T21:23:20.8379-07:00","closed_at":"2025-10-21T22:06:41.257019-07:00","labels":["test-label"]}