fix(daemon): add cross-process locking to registry (bd-5bj)

The global daemon registry (~/.beads/registry.json) could be corrupted
when multiple daemons from different workspaces wrote simultaneously.

Changes:
- Add file locking (flock) for cross-process synchronization
- Use atomic writes (temp file + rename) to prevent partial writes
- Keep entire read-modify-write cycle under single lock
- Add FlockExclusiveBlocking and FlockUnlock to lockfile package

This prevents race conditions that caused JSON corruption like `]]`.

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

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

internal/daemon/registry.go

@@ -7,6 +7,8 @@ import (
 	"path/filepath"
 	"sync"
 	"time"
+
+	"github.com/steveyegge/beads/internal/lockfile"
 )
 
 // RegistryEntry represents a daemon entry in the registry
@@ -21,8 +23,9 @@ type RegistryEntry struct {
 
 // Registry manages the global daemon registry file
 type Registry struct {
-	path string
-	mu   sync.Mutex
+	path     string
+	lockPath string
+	mu       sync.Mutex // in-process mutex (cross-process uses file lock)
 }
 
 // NewRegistry creates a new registry instance
@@ -39,14 +42,36 @@ func NewRegistry() (*Registry, error) {
 	}
 
 	registryPath := filepath.Join(beadsDir, "registry.json")
-	return &Registry{path: registryPath}, nil
+	lockPath := filepath.Join(beadsDir, "registry.lock")
+	return &Registry{path: registryPath, lockPath: lockPath}, nil
 }
 
-// readEntries reads all entries from the registry file
-func (r *Registry) readEntries() ([]RegistryEntry, error) {
+// withFileLock executes fn while holding an exclusive file lock on the registry.
+// This provides cross-process synchronization for read-modify-write operations.
+func (r *Registry) withFileLock(fn func() error) error {
 	r.mu.Lock()
 	defer r.mu.Unlock()
 
+	// Open or create lock file
+	// nolint:gosec // G304: controlled path from config
+	lockFile, err := os.OpenFile(r.lockPath, os.O_CREATE|os.O_RDWR, 0644)
+	if err != nil {
+		return fmt.Errorf("failed to open lock file: %w", err)
+	}
+	defer func() { _ = lockFile.Close() }()
+
+	// Acquire exclusive lock (blocking)
+	if err := lockfile.FlockExclusiveBlocking(lockFile); err != nil {
+		return fmt.Errorf("failed to acquire lock: %w", err)
+	}
+	defer func() { _ = lockfile.FlockUnlock(lockFile) }()
+
+	return fn()
+}
+
+// readEntriesLocked reads all entries from the registry file.
+// Caller must hold the file lock.
+func (r *Registry) readEntriesLocked() ([]RegistryEntry, error) {
 	data, err := os.ReadFile(r.path)
 	if err != nil {
 		if os.IsNotExist(err) {
@@ -63,11 +88,9 @@ func (r *Registry) readEntries() ([]RegistryEntry, error) {
 	return entries, nil
 }
 
-// writeEntries writes all entries to the registry file
-func (r *Registry) writeEntries(entries []RegistryEntry) error {
-	r.mu.Lock()
-	defer r.mu.Unlock()
-
+// writeEntriesLocked writes all entries to the registry file atomically.
+// Caller must hold the file lock.
+func (r *Registry) writeEntriesLocked(entries []RegistryEntry) error {
 	// Ensure we always write an array, never null
 	if entries == nil {
 		entries = []RegistryEntry{}
@@ -78,98 +101,153 @@ func (r *Registry) writeEntries(entries []RegistryEntry) error {
 		return fmt.Errorf("failed to marshal registry: %w", err)
 	}
 
-	// nolint:gosec // G306: Registry file needs to be readable for daemon discovery
-	if err := os.WriteFile(r.path, data, 0644); err != nil {
-		return fmt.Errorf("failed to write registry: %w", err)
+	// Write atomically: write to temp file, then rename
+	dir := filepath.Dir(r.path)
+	tmpFile, err := os.CreateTemp(dir, "registry-*.json.tmp")
+	if err != nil {
+		return fmt.Errorf("failed to create temp file: %w", err)
+	}
+	tmpPath := tmpFile.Name()
+
+	// Write data to temp file
+	if _, err := tmpFile.Write(data); err != nil {
+		_ = tmpFile.Close()
+		_ = os.Remove(tmpPath)
+		return fmt.Errorf("failed to write temp file: %w", err)
+	}
+
+	// Sync to disk before rename
+	if err := tmpFile.Sync(); err != nil {
+		_ = tmpFile.Close()
+		_ = os.Remove(tmpPath)
+		return fmt.Errorf("failed to sync temp file: %w", err)
+	}
+
+	if err := tmpFile.Close(); err != nil {
+		_ = os.Remove(tmpPath)
+		return fmt.Errorf("failed to close temp file: %w", err)
+	}
+
+	// Atomic rename
+	if err := os.Rename(tmpPath, r.path); err != nil {
+		_ = os.Remove(tmpPath)
+		return fmt.Errorf("failed to rename temp file: %w", err)
 	}
 
 	return nil
 }
 
+// readEntries reads all entries from the registry file (with locking).
+func (r *Registry) readEntries() ([]RegistryEntry, error) {
+	var entries []RegistryEntry
+	err := r.withFileLock(func() error {
+		var readErr error
+		entries, readErr = r.readEntriesLocked()
+		return readErr
+	})
+	return entries, err
+}
+
+// writeEntries writes all entries to the registry file (with locking).
+func (r *Registry) writeEntries(entries []RegistryEntry) error {
+	return r.withFileLock(func() error {
+		return r.writeEntriesLocked(entries)
+	})
+}
+
 // Register adds a daemon to the registry
 func (r *Registry) Register(entry RegistryEntry) error {
-	entries, err := r.readEntries()
-	if err != nil {
-		return err
-	}
-
-	// Remove any existing entry for this workspace or PID
-	filtered := []RegistryEntry{}
-	for _, e := range entries {
-		if e.WorkspacePath != entry.WorkspacePath && e.PID != entry.PID {
-			filtered = append(filtered, e)
+	return r.withFileLock(func() error {
+		entries, err := r.readEntriesLocked()
+		if err != nil {
+			return err
 		}
-	}
 
-	// Add new entry
-	filtered = append(filtered, entry)
+		// Remove any existing entry for this workspace or PID
+		filtered := []RegistryEntry{}
+		for _, e := range entries {
+			if e.WorkspacePath != entry.WorkspacePath && e.PID != entry.PID {
+				filtered = append(filtered, e)
+			}
+		}
 
-	return r.writeEntries(filtered)
+		// Add new entry
+		filtered = append(filtered, entry)
+
+		return r.writeEntriesLocked(filtered)
+	})
 }
 
 // Unregister removes a daemon from the registry
 func (r *Registry) Unregister(workspacePath string, pid int) error {
-	entries, err := r.readEntries()
-	if err != nil {
-		return err
-	}
-
-	// Filter out entries matching workspace or PID
-	filtered := []RegistryEntry{}
-	for _, e := range entries {
-		if e.WorkspacePath != workspacePath && e.PID != pid {
-			filtered = append(filtered, e)
+	return r.withFileLock(func() error {
+		entries, err := r.readEntriesLocked()
+		if err != nil {
+			return err
 		}
-	}
 
-	return r.writeEntries(filtered)
+		// Filter out entries matching workspace or PID
+		filtered := []RegistryEntry{}
+		for _, e := range entries {
+			if e.WorkspacePath != workspacePath && e.PID != pid {
+				filtered = append(filtered, e)
+			}
+		}
+
+		return r.writeEntriesLocked(filtered)
+	})
 }
 
 // List returns all daemons from the registry, automatically cleaning up stale entries
 func (r *Registry) List() ([]DaemonInfo, error) {
-	entries, err := r.readEntries()
-	if err != nil {
-		return nil, err
-	}
-
 	var daemons []DaemonInfo
-	var aliveEntries []RegistryEntry
 
-	for _, entry := range entries {
-		// Check if process is still alive
-		if !isProcessAlive(entry.PID) {
-			// Stale entry - skip and don't add to alive list
-			continue
+	err := r.withFileLock(func() error {
+		entries, err := r.readEntriesLocked()
+		if err != nil {
+			return err
 		}
 
-		// Process is alive, add to both lists
-		aliveEntries = append(aliveEntries, entry)
+		var aliveEntries []RegistryEntry
 
-		// Try to connect and get current status
-		daemon := discoverDaemon(entry.SocketPath)
-		
-		// If connection failed but process is alive, still include basic info
-		if !daemon.Alive {
-			daemon.Alive = true // Process exists, socket just might not be ready
-			daemon.WorkspacePath = entry.WorkspacePath
-			daemon.DatabasePath = entry.DatabasePath
-			daemon.SocketPath = entry.SocketPath
-			daemon.PID = entry.PID
-			daemon.Version = entry.Version
+		for _, entry := range entries {
+			// Check if process is still alive
+			if !isProcessAlive(entry.PID) {
+				// Stale entry - skip and don't add to alive list
+				continue
+			}
+
+			// Process is alive, add to both lists
+			aliveEntries = append(aliveEntries, entry)
+
+			// Try to connect and get current status
+			daemon := discoverDaemon(entry.SocketPath)
+
+			// If connection failed but process is alive, still include basic info
+			if !daemon.Alive {
+				daemon.Alive = true // Process exists, socket just might not be ready
+				daemon.WorkspacePath = entry.WorkspacePath
+				daemon.DatabasePath = entry.DatabasePath
+				daemon.SocketPath = entry.SocketPath
+				daemon.PID = entry.PID
+				daemon.Version = entry.Version
+			}
+
+			daemons = append(daemons, daemon)
 		}
 
-		daemons = append(daemons, daemon)
-	}
-
-	// Clean up stale entries from registry
-	if len(aliveEntries) != len(entries) {
-		if err := r.writeEntries(aliveEntries); err != nil {
-			// Log warning but don't fail - we still have the daemon list
-			fmt.Fprintf(os.Stderr, "Warning: failed to cleanup stale registry entries: %v\n", err)
+		// Clean up stale entries from registry
+		if len(aliveEntries) != len(entries) {
+			if err := r.writeEntriesLocked(aliveEntries); err != nil {
+				// Log warning but don't fail - we still have the daemon list
+				fmt.Fprintf(os.Stderr, "Warning: failed to cleanup stale registry entries: %v\n", err)
+			}
 		}
-	}
 
-	return daemons, nil
+		return nil
+	})
+
+	return daemons, err
 }
 
 // Clear removes all entries from the registry (for testing)