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/mol_bond.go

@@ -89,7 +89,7 @@ func runMolBond(cmd *cobra.Command, args []string) {
 			fmt.Fprintf(os.Stderr, "Error: failed to open wisp storage: %v\n", err)
 			os.Exit(1)
 		}
-		defer wispStore.Close()
+		defer func() { _ = wispStore.Close() }()
 		targetStore = wispStore
 
 		// Ensure wisp directory is gitignored