feat(doctor): add --dry-run flag and fix registry parsing (bd-qn5, bd-a5z)

- Add --dry-run flag to preview fixes without applying changes
- Handle corrupted/empty/null-byte registry files gracefully
- Treat corrupted registry as empty instead of failing

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

internal/daemon/registry.go

@@ -71,6 +71,7 @@ func (r *Registry) withFileLock(fn func() error) error {
 
 // readEntriesLocked reads all entries from the registry file.
 // Caller must hold the file lock.
+// bd-qn5: Handles missing, empty, or corrupted registry files gracefully.
 func (r *Registry) readEntriesLocked() ([]RegistryEntry, error) {
 	data, err := os.ReadFile(r.path)
 	if err != nil {
@@ -80,9 +81,23 @@ func (r *Registry) readEntriesLocked() ([]RegistryEntry, error) {
 		return nil, fmt.Errorf("failed to read registry: %w", err)
 	}
 
+	// bd-qn5: Handle empty file or file with only whitespace/null bytes
+	// This can happen if the file was created but never written to, or was corrupted
+	trimmed := make([]byte, 0, len(data))
+	for _, b := range data {
+		if b != 0 && b != ' ' && b != '\t' && b != '\n' && b != '\r' {
+			trimmed = append(trimmed, b)
+		}
+	}
+	if len(trimmed) == 0 {
+		return []RegistryEntry{}, nil
+	}
+
 	var entries []RegistryEntry
 	if err := json.Unmarshal(data, &entries); err != nil {
-		return nil, fmt.Errorf("failed to parse registry: %w", err)
+		// bd-qn5: If registry is corrupted, treat as empty rather than failing
+		// A corrupted registry just means we'll need to rediscover daemons
+		return []RegistryEntry{}, nil
 	}
 
 	return entries, nil

internal/daemon/registry_test.go

@@ -240,13 +240,46 @@ func TestRegistryCorruptedFile(t *testing.T) {
 	os.MkdirAll(filepath.Dir(registryPath), 0755)
 	os.WriteFile(registryPath, []byte("invalid json{{{"), 0644)
 
-	// Reading should return an error
+	// bd-qn5: Corrupted registry should be treated as empty, not an error
+	// This allows bd doctor to work gracefully when registry is corrupted
 	entries, err := registry.readEntries()
-	if err == nil {
-		t.Error("Expected error when reading corrupted registry")
+	if err != nil {
+		t.Errorf("Expected corrupted registry to be treated as empty, got error: %v", err)
 	}
-	if entries != nil {
-		t.Errorf("Expected nil entries on error, got %v", entries)
+	if len(entries) != 0 {
+		t.Errorf("Expected empty entries for corrupted registry, got %v", entries)
+	}
+}
+
+// bd-qn5: Test for the specific null bytes case that was reported
+func TestRegistryNullBytesFile(t *testing.T) {
+	tmpDir := t.TempDir()
+	registryPath := filepath.Join(tmpDir, ".beads", "registry.json")
+
+	homeEnv := "HOME"
+	if runtime.GOOS == "windows" {
+		homeEnv = "USERPROFILE"
+	}
+	oldHome := os.Getenv(homeEnv)
+	os.Setenv(homeEnv, tmpDir)
+	defer os.Setenv(homeEnv, oldHome)
+
+	registry, err := NewRegistry()
+	if err != nil {
+		t.Fatalf("Failed to create registry: %v", err)
+	}
+
+	// Create a file with null bytes (the reported error case)
+	os.MkdirAll(filepath.Dir(registryPath), 0755)
+	os.WriteFile(registryPath, []byte{0, 0, 0, 0}, 0644)
+
+	// Should treat as empty, not error
+	entries, err := registry.readEntries()
+	if err != nil {
+		t.Errorf("Expected null-byte registry to be treated as empty, got error: %v", err)
+	}
+	if len(entries) != 0 {
+		t.Errorf("Expected empty entries for null-byte registry, got %v", entries)
 	}
 }