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 	// Auto-upgrade .beads/.gitignore if outdated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)
 			}