feat(storage): add --backend flag for Dolt backend selection

Phase 2 of Dolt integration - enables runtime backend selection:

- Add --backend flag to bd init (sqlite|dolt)
- Create storage factory for backend instantiation
- Update daemon and main.go to use factory with config detection
- Update database discovery to find Dolt backends via metadata.json
- Fix Dolt schema init to split statements for MySQL compatibility
- Add ReadOnly mode to skip schema init for read-only commands

Usage: bd init --backend dolt --prefix myproject

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/daemon.go

@@ -16,6 +16,7 @@ import (
 	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/daemon"
 	"github.com/steveyegge/beads/internal/rpc"
+	"github.com/steveyegge/beads/internal/storage/factory"
 	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/syncbranch"
 )
@@ -403,17 +404,22 @@ func runDaemonLoop(interval time.Duration, autoCommit, autoPush, autoPull, local
 		log.Warn("could not remove daemon-error file", "error", err)
 	}
 
-	store, err := sqlite.New(ctx, daemonDBPath)
+	store, err := factory.NewFromConfig(ctx, beadsDir)
 	if err != nil {
 		log.Error("cannot open database", "error", err)
 		return // Use return instead of os.Exit to allow defers to run
 	}
 	defer func() { _ = store.Close() }()
 
-	// Enable freshness checking to detect external database file modifications
+	// Enable freshness checking for SQLite backend to detect external database file modifications
 	// (e.g., when git merge replaces the database file)
-	store.EnableFreshnessChecking()
-	log.Info("database opened", "path", daemonDBPath, "freshness_checking", true)
+	// Dolt doesn't need this since it handles versioning natively.
+	if sqliteStore, ok := store.(*sqlite.SQLiteStorage); ok {
+		sqliteStore.EnableFreshnessChecking()
+		log.Info("database opened", "path", store.Path(), "backend", "sqlite", "freshness_checking", true)
+	} else {
+		log.Info("database opened", "path", store.Path(), "backend", "dolt")
+	}
 
 	// Auto-upgrade .beads/.gitignore if outdated
 	gitignoreCheck := doctor.CheckGitignore()
@@ -426,14 +432,16 @@ func runDaemonLoop(interval time.Duration, autoCommit, autoPush, autoPull, local
 		}
 	}
 
-	// Hydrate from multi-repo if configured
-	if results, err := store.HydrateFromMultiRepo(ctx); err != nil {
-		log.Error("multi-repo hydration failed", "error", err)
-		return // Use return instead of os.Exit to allow defers to run
-	} else if results != nil {
-		log.Info("multi-repo hydration complete")
-		for repo, count := range results {
-			log.Info("hydrated issues", "repo", repo, "count", count)
+	// Hydrate from multi-repo if configured (SQLite only)
+	if sqliteStore, ok := store.(*sqlite.SQLiteStorage); ok {
+		if results, err := sqliteStore.HydrateFromMultiRepo(ctx); err != nil {
+			log.Error("multi-repo hydration failed", "error", err)
+			return // Use return instead of os.Exit to allow defers to run
+		} else if results != nil {
+			log.Info("multi-repo hydration complete")
+			for repo, count := range results {
+				log.Info("hydrated issues", "repo", repo, "count", count)
+			}
 		}
 	}
 
@@ -618,13 +626,13 @@ func runDaemonLoop(interval time.Duration, autoCommit, autoPush, autoPull, local
 // Note: The individual auto-commit/auto-push settings are deprecated.
 // Use auto-sync for read/write mode, auto-pull for read-only mode.
 func loadDaemonAutoSettings(cmd *cobra.Command, autoCommit, autoPush, autoPull bool) (bool, bool, bool) {
-	dbPath := beads.FindDatabasePath()
-	if dbPath == "" {
+	beadsDir := beads.FindBeadsDir()
+	if beadsDir == "" {
 		return autoCommit, autoPush, autoPull
 	}
 
 	ctx := context.Background()
-	store, err := sqlite.New(ctx, dbPath)
+	store, err := factory.NewFromConfig(ctx, beadsDir)
 	if err != nil {
 		return autoCommit, autoPush, autoPull
 	}

cmd/bd/init.go

@@ -15,6 +15,8 @@ import (
 	"github.com/steveyegge/beads/internal/config"
 	"github.com/steveyegge/beads/internal/configfile"
 	"github.com/steveyegge/beads/internal/git"
+	"github.com/steveyegge/beads/internal/storage"
+	"github.com/steveyegge/beads/internal/storage/dolt"
 	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/syncbranch"
 	"github.com/steveyegge/beads/internal/types"
@@ -43,6 +45,7 @@ With --stealth: configures per-repository git settings for invisible beads usage
 		prefix, _ := cmd.Flags().GetString("prefix")
 		quiet, _ := cmd.Flags().GetBool("quiet")
 		branch, _ := cmd.Flags().GetString("branch")
+		backend, _ := cmd.Flags().GetString("backend")
 		contributor, _ := cmd.Flags().GetBool("contributor")
 		team, _ := cmd.Flags().GetBool("team")
 		stealth, _ := cmd.Flags().GetBool("stealth")
@@ -51,6 +54,15 @@ With --stealth: configures per-repository git settings for invisible beads usage
 		force, _ := cmd.Flags().GetBool("force")
 		fromJSONL, _ := cmd.Flags().GetBool("from-jsonl")
 
+		// Validate backend flag
+		if backend != "" && backend != configfile.BackendSQLite && backend != configfile.BackendDolt {
+			fmt.Fprintf(os.Stderr, "Error: invalid backend '%s' (must be 'sqlite' or 'dolt')\n", backend)
+			os.Exit(1)
+		}
+		if backend == "" {
+			backend = configfile.BackendSQLite // Default to SQLite
+		}
+
 		// Initialize config (PersistentPreRun doesn't run for init command)
 		if err := config.Initialize(); err != nil {
 			fmt.Fprintf(os.Stderr, "Warning: failed to initialize config: %v\n", err)
@@ -280,9 +292,20 @@ With --stealth: configures per-repository git settings for invisible beads usage
 		}
 
 		ctx := rootCtx
-		store, err := sqlite.New(ctx, initDBPath)
+
+		// Create storage backend based on --backend flag
+		var storagePath string
+		var store storage.Storage
+		if backend == configfile.BackendDolt {
+			// Dolt uses a directory, not a file
+			storagePath = filepath.Join(beadsDir, "dolt")
+			store, err = dolt.New(ctx, &dolt.Config{Path: storagePath})
+		} else {
+			storagePath = initDBPath
+			store, err = sqlite.New(ctx, storagePath)
+		}
 		if err != nil {
-			fmt.Fprintf(os.Stderr, "Error: failed to create database: %v\n", err)
+			fmt.Fprintf(os.Stderr, "Error: failed to create %s database: %v\n", backend, err)
 			os.Exit(1)
 		}
 
@@ -361,6 +384,12 @@ With --stealth: configures per-repository git settings for invisible beads usage
 					}
 				}
 			}
+
+			// Save backend choice (only store if non-default to keep metadata.json clean)
+			if backend != configfile.BackendSQLite {
+				cfg.Backend = backend
+			}
+
 			if err := cfg.Save(beadsDir); err != nil {
 				fmt.Fprintf(os.Stderr, "Warning: failed to create metadata.json: %v\n", err)
 				// Non-fatal - continue anyway
@@ -508,7 +537,8 @@ With --stealth: configures per-repository git settings for invisible beads usage
 		}
 
 		fmt.Printf("\n%s bd initialized successfully!\n\n", ui.RenderPass("✓"))
-		fmt.Printf("  Database: %s\n", ui.RenderAccent(initDBPath))
+		fmt.Printf("  Backend: %s\n", ui.RenderAccent(backend))
+		fmt.Printf("  Database: %s\n", ui.RenderAccent(storagePath))
 		fmt.Printf("  Issue prefix: %s\n", ui.RenderAccent(prefix))
 		fmt.Printf("  Issues will be named: %s\n\n", ui.RenderAccent(prefix+"-<hash> (e.g., "+prefix+"-a3f2dd)"))
 		fmt.Printf("Run %s to get started.\n\n", ui.RenderAccent("bd quickstart"))
@@ -540,6 +570,7 @@ func init() {
 	initCmd.Flags().StringP("prefix", "p", "", "Issue prefix (default: current directory name)")
 	initCmd.Flags().BoolP("quiet", "q", false, "Suppress output (quiet mode)")
 	initCmd.Flags().StringP("branch", "b", "", "Git branch for beads commits (default: current branch)")
+	initCmd.Flags().String("backend", "", "Storage backend: sqlite (default) or dolt (version-controlled)")
 	initCmd.Flags().Bool("contributor", false, "Run OSS contributor setup wizard")
 	initCmd.Flags().Bool("team", false, "Run team workflow setup wizard")
 	initCmd.Flags().Bool("stealth", false, "Enable stealth mode: global gitattributes and gitignore, no local repo tracking")

cmd/bd/main.go

@@ -18,13 +18,14 @@ import (
 	"github.com/spf13/cobra"
 	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/config"
+	"github.com/steveyegge/beads/internal/configfile"
 	"github.com/steveyegge/beads/internal/debug"
 	"github.com/steveyegge/beads/internal/hooks"
 	"github.com/steveyegge/beads/internal/molecules"
 	"github.com/steveyegge/beads/internal/rpc"
 	"github.com/steveyegge/beads/internal/storage"
+	"github.com/steveyegge/beads/internal/storage/factory"
 	"github.com/steveyegge/beads/internal/storage/memory"
-	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/utils"
 )
 
@@ -753,22 +754,36 @@ var rootCmd = &cobra.Command{
 		// Fall back to direct storage access
 		var err error
 		var needsBootstrap bool // Track if DB needs initial import (GH#b09)
-		if useReadOnly {
-			// Read-only mode: prevents file modifications (GH#804)
-			store, err = sqlite.NewReadOnlyWithTimeout(rootCtx, dbPath, lockTimeout)
-			if err != nil {
+		beadsDir := filepath.Dir(dbPath)
+
+		// Detect backend from metadata.json
+		backend := factory.GetBackendFromConfig(beadsDir)
+
+		// Create storage with appropriate options
+		opts := factory.Options{
+			ReadOnly:    useReadOnly,
+			LockTimeout: lockTimeout,
+		}
+
+		if backend == configfile.BackendDolt {
+			// For Dolt, use the dolt subdirectory
+			doltPath := filepath.Join(beadsDir, "dolt")
+			store, err = factory.NewWithOptions(rootCtx, backend, doltPath, opts)
+		} else {
+			// SQLite backend
+			store, err = factory.NewWithOptions(rootCtx, backend, dbPath, opts)
+			if err != nil && useReadOnly {
 				// If read-only fails (e.g., DB doesn't exist), fall back to read-write
 				// This handles the case where user runs "bd list" before "bd init"
 				debug.Logf("read-only open failed, falling back to read-write: %v", err)
-				store, err = sqlite.NewWithTimeout(rootCtx, dbPath, lockTimeout)
+				opts.ReadOnly = false
+				store, err = factory.NewWithOptions(rootCtx, backend, dbPath, opts)
 				needsBootstrap = true // New DB needs auto-import (GH#b09)
 			}
-		} else {
-			store, err = sqlite.NewWithTimeout(rootCtx, dbPath, lockTimeout)
 		}
+
 		if err != nil {
 			// Check for fresh clone scenario
-			beadsDir := filepath.Dir(dbPath)
 			if handleFreshCloneError(err, beadsDir) {
 				os.Exit(1)
 			}

internal/beads/beads.go

@@ -215,7 +215,9 @@ func findLocalBeadsDir() string {
 
 // findDatabaseInBeadsDir searches for a database file within a .beads directory.
 // It implements the standard search order:
-// 1. Check config.json first (single source of truth)
+// 1. Check metadata.json first (single source of truth)
+//    - For SQLite backend: returns path to .db file
+//    - For Dolt backend: returns path to dolt/ directory
 // 2. Fall back to canonical beads.db
 // 3. Search for *.db files, filtering out backups and vc.db
 //
@@ -225,11 +227,21 @@ func findLocalBeadsDir() string {
 //
 // Returns empty string if no database is found.
 func findDatabaseInBeadsDir(beadsDir string, warnOnIssues bool) string {
-	// Check for config.json first (single source of truth)
+	// Check for metadata.json first (single source of truth)
 	if cfg, err := configfile.Load(beadsDir); err == nil && cfg != nil {
-		dbPath := cfg.DatabasePath(beadsDir)
-		if _, err := os.Stat(dbPath); err == nil {
-			return dbPath
+		backend := cfg.GetBackend()
+		if backend == configfile.BackendDolt {
+			// For Dolt, check if the dolt directory exists
+			doltPath := filepath.Join(beadsDir, "dolt")
+			if info, err := os.Stat(doltPath); err == nil && info.IsDir() {
+				return doltPath
+			}
+		} else {
+			// For SQLite, check if the .db file exists
+			dbPath := cfg.DatabasePath(beadsDir)
+			if _, err := os.Stat(dbPath); err == nil {
+				return dbPath
+			}
 		}
 	}
 

internal/configfile/configfile.go

@@ -12,6 +12,7 @@ const ConfigFileName = "metadata.json"
 type Config struct {
 	Database    string `json:"database"`
 	JSONLExport string `json:"jsonl_export,omitempty"`
+	Backend     string `json:"backend,omitempty"` // "sqlite" (default) or "dolt"
 
 	// Deletions configuration
 	DeletionsRetentionDays int `json:"deletions_retention_days,omitempty"` // 0 means use default (3 days)
@@ -113,3 +114,17 @@ func (c *Config) GetDeletionsRetentionDays() int {
 	}
 	return c.DeletionsRetentionDays
 }
+
+// Backend constants
+const (
+	BackendSQLite = "sqlite"
+	BackendDolt   = "dolt"
+)
+
+// GetBackend returns the configured backend type, defaulting to SQLite.
+func (c *Config) GetBackend() string {
+	if c.Backend == "" {
+		return BackendSQLite
+	}
+	return c.Backend
+}

internal/storage/dolt/store.go

@@ -21,6 +21,7 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"strings"
 	"sync"
 	"sync/atomic"
 	"time"
@@ -52,6 +53,7 @@ type Config struct {
 	CommitterEmail string // Git-style committer email
 	Remote         string // Default remote name (e.g., "origin")
 	Database       string // Database name within Dolt (default: "beads")
+	ReadOnly       bool   // Open in read-only mode (skip schema init)
 }
 
 // New creates a new Dolt storage backend
@@ -85,8 +87,25 @@ func New(ctx context.Context, cfg *Config) (*DoltStore, error) {
 		return nil, fmt.Errorf("failed to create database directory: %w", err)
 	}
 
-	// Build Dolt connection string
-	// Format: file:///path/to/db?commitname=Name&commitemail=email&database=dbname
+	// First, connect without specifying a database to create it if needed
+	initConnStr := fmt.Sprintf(
+		"file://%s?commitname=%s&commitemail=%s",
+		cfg.Path, cfg.CommitterName, cfg.CommitterEmail)
+
+	initDB, err := sql.Open("dolt", initConnStr)
+	if err != nil {
+		return nil, fmt.Errorf("failed to open Dolt for initialization: %w", err)
+	}
+
+	// Create the database if it doesn't exist
+	_, err = initDB.ExecContext(ctx, fmt.Sprintf("CREATE DATABASE IF NOT EXISTS %s", cfg.Database))
+	if err != nil {
+		initDB.Close()
+		return nil, fmt.Errorf("failed to create database: %w", err)
+	}
+	initDB.Close()
+
+	// Now connect with the database specified
 	connStr := fmt.Sprintf(
 		"file://%s?commitname=%s&commitemail=%s&database=%s",
 		cfg.Path, cfg.CommitterName, cfg.CommitterEmail, cfg.Database)
@@ -121,11 +140,14 @@ func New(ctx context.Context, cfg *Config) (*DoltStore, error) {
 		committerEmail: cfg.CommitterEmail,
 		remote:         cfg.Remote,
 		branch:         "main",
+		readOnly:       cfg.ReadOnly,
 	}
 
-	// Initialize schema
-	if err := store.initSchema(ctx); err != nil {
-		return nil, fmt.Errorf("failed to initialize schema: %w", err)
+	// Initialize schema (skip for read-only mode)
+	if !cfg.ReadOnly {
+		if err := store.initSchema(ctx); err != nil {
+			return nil, fmt.Errorf("failed to initialize schema: %w", err)
+		}
 	}
 
 	return store, nil
@@ -133,14 +155,34 @@ func New(ctx context.Context, cfg *Config) (*DoltStore, error) {
 
 // initSchema creates all tables if they don't exist
 func (s *DoltStore) initSchema(ctx context.Context) error {
-	// Execute schema creation
-	if _, err := s.db.ExecContext(ctx, schema); err != nil {
-		return fmt.Errorf("failed to create schema: %w", err)
+	// Execute schema creation - split into individual statements
+	// because MySQL/Dolt doesn't support multiple statements in one Exec
+	for _, stmt := range splitStatements(schema) {
+		stmt = strings.TrimSpace(stmt)
+		if stmt == "" {
+			continue
+		}
+		// Skip pure comment-only statements, but execute statements that start with comments
+		if isOnlyComments(stmt) {
+			continue
+		}
+		if _, err := s.db.ExecContext(ctx, stmt); err != nil {
+			return fmt.Errorf("failed to create schema: %w\nStatement: %s", err, truncateForError(stmt))
+		}
 	}
 
 	// Insert default config values
-	if _, err := s.db.ExecContext(ctx, defaultConfig); err != nil {
-		return fmt.Errorf("failed to insert default config: %w", err)
+	for _, stmt := range splitStatements(defaultConfig) {
+		stmt = strings.TrimSpace(stmt)
+		if stmt == "" {
+			continue
+		}
+		if isOnlyComments(stmt) {
+			continue
+		}
+		if _, err := s.db.ExecContext(ctx, stmt); err != nil {
+			return fmt.Errorf("failed to insert default config: %w", err)
+		}
 	}
 
 	// Create views
@@ -154,6 +196,74 @@ func (s *DoltStore) initSchema(ctx context.Context) error {
 	return nil
 }
 
+// splitStatements splits a SQL script into individual statements
+func splitStatements(script string) []string {
+	var statements []string
+	var current strings.Builder
+	inString := false
+	stringChar := byte(0)
+
+	for i := 0; i < len(script); i++ {
+		c := script[i]
+
+		if inString {
+			current.WriteByte(c)
+			if c == stringChar && (i == 0 || script[i-1] != '\\') {
+				inString = false
+			}
+			continue
+		}
+
+		if c == '\'' || c == '"' || c == '`' {
+			inString = true
+			stringChar = c
+			current.WriteByte(c)
+			continue
+		}
+
+		if c == ';' {
+			stmt := strings.TrimSpace(current.String())
+			if stmt != "" {
+				statements = append(statements, stmt)
+			}
+			current.Reset()
+			continue
+		}
+
+		current.WriteByte(c)
+	}
+
+	// Handle last statement without semicolon
+	stmt := strings.TrimSpace(current.String())
+	if stmt != "" {
+		statements = append(statements, stmt)
+	}
+
+	return statements
+}
+
+// truncateForError truncates a string for use in error messages
+func truncateForError(s string) string {
+	if len(s) > 100 {
+		return s[:100] + "..."
+	}
+	return s
+}
+
+// isOnlyComments returns true if the statement contains only SQL comments
+func isOnlyComments(stmt string) bool {
+	lines := strings.Split(stmt, "\n")
+	for _, line := range lines {
+		line = strings.TrimSpace(line)
+		if line == "" || strings.HasPrefix(line, "--") {
+			continue
+		}
+		// Found a non-comment, non-empty line
+		return false
+	}
+	return true
+}
+
 // Close closes the database connection
 func (s *DoltStore) Close() error {
 	s.closed.Store(true)

internal/storage/factory/factory.go

@@ -0,0 +1,86 @@
+// Package factory provides functions for creating storage backends based on configuration.
+package factory
+
+import (
+	"context"
+	"fmt"
+	"path/filepath"
+	"time"
+
+	"github.com/steveyegge/beads/internal/configfile"
+	"github.com/steveyegge/beads/internal/storage"
+	"github.com/steveyegge/beads/internal/storage/dolt"
+	"github.com/steveyegge/beads/internal/storage/sqlite"
+)
+
+// Options configures how the storage backend is opened
+type Options struct {
+	ReadOnly    bool
+	LockTimeout time.Duration
+}
+
+// New creates a storage backend based on the backend type.
+// For SQLite, path should be the full path to the .db file.
+// For Dolt, path should be the directory containing the Dolt database.
+func New(ctx context.Context, backend, path string) (storage.Storage, error) {
+	return NewWithOptions(ctx, backend, path, Options{})
+}
+
+// NewWithOptions creates a storage backend with the specified options.
+func NewWithOptions(ctx context.Context, backend, path string, opts Options) (storage.Storage, error) {
+	switch backend {
+	case configfile.BackendSQLite, "":
+		if opts.ReadOnly {
+			if opts.LockTimeout > 0 {
+				return sqlite.NewReadOnlyWithTimeout(ctx, path, opts.LockTimeout)
+			}
+			return sqlite.NewReadOnly(ctx, path)
+		}
+		if opts.LockTimeout > 0 {
+			return sqlite.NewWithTimeout(ctx, path, opts.LockTimeout)
+		}
+		return sqlite.New(ctx, path)
+	case configfile.BackendDolt:
+		return dolt.New(ctx, &dolt.Config{Path: path, ReadOnly: opts.ReadOnly})
+	default:
+		return nil, fmt.Errorf("unknown storage backend: %s (supported: sqlite, dolt)", backend)
+	}
+}
+
+// NewFromConfig creates a storage backend based on the metadata.json configuration.
+// beadsDir is the path to the .beads directory.
+func NewFromConfig(ctx context.Context, beadsDir string) (storage.Storage, error) {
+	return NewFromConfigWithOptions(ctx, beadsDir, Options{})
+}
+
+// NewFromConfigWithOptions creates a storage backend with options from metadata.json.
+func NewFromConfigWithOptions(ctx context.Context, beadsDir string, opts Options) (storage.Storage, error) {
+	cfg, err := configfile.Load(beadsDir)
+	if err != nil {
+		return nil, fmt.Errorf("loading config: %w", err)
+	}
+	if cfg == nil {
+		cfg = configfile.DefaultConfig()
+	}
+
+	backend := cfg.GetBackend()
+	switch backend {
+	case configfile.BackendSQLite:
+		return NewWithOptions(ctx, backend, cfg.DatabasePath(beadsDir), opts)
+	case configfile.BackendDolt:
+		// For Dolt, use a subdirectory to store the Dolt database
+		doltPath := filepath.Join(beadsDir, "dolt")
+		return NewWithOptions(ctx, backend, doltPath, opts)
+	default:
+		return nil, fmt.Errorf("unknown storage backend in config: %s", backend)
+	}
+}
+
+// GetBackendFromConfig returns the backend type from metadata.json
+func GetBackendFromConfig(beadsDir string) string {
+	cfg, err := configfile.Load(beadsDir)
+	if err != nil || cfg == nil {
+		return configfile.BackendSQLite
+	}
+	return cfg.GetBackend()
+}