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/doctor/fix/validation_test.go

@@ -0,0 +1,37 @@
+package fix
+
+import (
+	"testing"
+)
+
+// TestFixFunctions_RequireBeadsDir verifies all fix functions properly validate
+// that a .beads directory exists before attempting fixes.
+// This replaces 10+ individual "missing .beads directory" subtests.
+func TestFixFunctions_RequireBeadsDir(t *testing.T) {
+	funcs := []struct {
+		name string
+		fn   func(string) error
+	}{
+		{"GitHooks", GitHooks},
+		{"MergeDriver", MergeDriver},
+		{"Daemon", Daemon},
+		{"DBJSONLSync", DBJSONLSync},
+		{"DatabaseVersion", DatabaseVersion},
+		{"SchemaCompatibility", SchemaCompatibility},
+		{"SyncBranchConfig", SyncBranchConfig},
+		{"SyncBranchHealth", func(dir string) error { return SyncBranchHealth(dir, "beads-sync") }},
+		{"UntrackedJSONL", UntrackedJSONL},
+		{"MigrateTombstones", MigrateTombstones},
+	}
+
+	for _, tc := range funcs {
+		t.Run(tc.name, func(t *testing.T) {
+			// Use a temp directory without .beads
+			dir := t.TempDir()
+			err := tc.fn(dir)
+			if err == nil {
+				t.Errorf("%s should return error for missing .beads directory", tc.name)
+			}
+		})
+	}
+}