fix(doctor): UX improvements for diagnostics and daemon (#687)

* fix(doctor): UX improvements for diagnostics and daemon

- Add Repo Fingerprint check to detect when database belongs to a
  different repository (copied .beads dir or git remote URL change)
- Add interactive fix for repo fingerprint with options: update repo ID,
  reinitialize database, or skip
- Add visible warning when daemon takes >5s to start, recommending
  'bd doctor' for diagnosis
- Detect install method (Homebrew vs script) and show only relevant
  upgrade command
- Improve WARNINGS section:
  - Add icons (⚠ or ✖) next to each item
  - Color numbers by severity (yellow for warnings, red for errors)
  - Render entire error lines in red
  - Sort by severity (errors first)
  - Fix alignment with checkmarks above
- Use heavier fail icon (✖) for better visibility
- Add integration and validation tests for doctor fixes

* fix(lint): address errcheck and gosec warnings

- mol_bond.go: explicitly ignore ephStore.Close() error
- beads.go: add nosec for .gitignore file permissions (0644 is standard)

cmd/bd/snapshot_manager.go

@@ -186,6 +186,8 @@ func (sm *SnapshotManager) Validate() error {
 }
 
 // Cleanup removes all snapshot files and metadata
+//
+//nolint:unparam // error return kept for API consistency with other methods
 func (sm *SnapshotManager) Cleanup() error {
 	basePath, leftPath := sm.getSnapshotPaths()
 	baseMetaPath, leftMetaPath := sm.getSnapshotMetadataPaths()