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/daemon_autostart.go

@@ -12,6 +12,7 @@ import (
 	"github.com/steveyegge/beads/internal/config"
 	"github.com/steveyegge/beads/internal/debug"
 	"github.com/steveyegge/beads/internal/rpc"
+	"github.com/steveyegge/beads/internal/ui"
 )
 
 // Daemon start failure tracking for exponential backoff
@@ -135,6 +136,8 @@ func restartDaemonForVersionMismatch() bool {
 	}
 
 	debug.Logf("new daemon failed to become ready")
+	fmt.Fprintf(os.Stderr, "%s Daemon restart timed out (>5s). Running in direct mode.\n", ui.RenderWarn("Warning:"))
+	fmt.Fprintf(os.Stderr, "  %s Run 'bd doctor' to diagnose daemon issues\n", ui.RenderMuted("Hint:"))
 	return false
 }
 
@@ -286,6 +289,9 @@ func startDaemonProcess(socketPath string) bool {
 
 	recordDaemonStartFailure()
 	debugLog("daemon socket not ready after 5 seconds")
+	// Emit visible warning so user understands why command was slow
+	fmt.Fprintf(os.Stderr, "%s Daemon took too long to start (>5s). Running in direct mode.\n", ui.RenderWarn("Warning:"))
+	fmt.Fprintf(os.Stderr, "  %s Run 'bd doctor' to diagnose daemon issues\n", ui.RenderMuted("Hint:"))
 	return false
 }