fix(dolt): proper server mode support for routing and storage

- FindDatabasePath now handles Dolt server mode (no local dir required)
- main.go uses NewFromConfigWithOptions for Dolt to read server settings
- Routing uses factory via callback to respect backend configuration
- Handle Dolt "database exists" error (error 1007) gracefully

Previously, Dolt server mode failed because:
1. FindDatabasePath required a local directory to exist
2. main.go bypassed server mode config when creating Dolt storage
3. Routing always opened SQLite regardless of backend config

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

cmd/bd/direct_mode.go

@@ -7,7 +7,7 @@ import (
 
 	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/debug"
-	"github.com/steveyegge/beads/internal/storage/sqlite"
+	"github.com/steveyegge/beads/internal/storage/factory"
 )
 
 // ensureDirectMode makes sure the CLI is operating in direct-storage mode.
@@ -52,7 +52,8 @@ func disableDaemonForFallback(reason string) {
 	}
 }
 
-// ensureStoreActive guarantees that a local SQLite store is initialized and tracked.
+// ensureStoreActive guarantees that a storage backend is initialized and tracked.
+// Uses the factory to respect metadata.json backend configuration (SQLite, Dolt embedded, or Dolt server).
 func ensureStoreActive() error {
 	lockStore()
 	active := isStoreActive() && getStore() != nil
@@ -61,15 +62,15 @@ func ensureStoreActive() error {
 		return nil
 	}
 
-	path := getDBPath()
-	if path == "" {
-		if found := beads.FindDatabasePath(); found != "" {
-			setDBPath(found)
-			path = found
-		} else {
-			// Check if this is a JSONL-only project
+	// Find the .beads directory
 	beadsDir := beads.FindBeadsDir()
-			if beadsDir != "" {
+	if beadsDir == "" {
+		return fmt.Errorf("no beads database found.\n" +
+			"Hint: run 'bd init' to create a database in the current directory,\n" +
+			"      or use 'bd --no-db' for JSONL-only mode")
+	}
+
+	// Check if this is a JSONL-only project
 	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
 	if _, err := os.Stat(jsonlPath); err == nil {
 		// JSONL exists - check if no-db mode is configured
@@ -77,31 +78,28 @@ func ensureStoreActive() error {
 			return fmt.Errorf("this project uses JSONL-only mode (no SQLite database).\n" +
 				"Hint: use 'bd --no-db <command>' or set 'no-db: true' in config.yaml")
 		}
-					// JSONL exists but no-db not configured - fresh clone scenario
+	}
+
+	// Use factory to create the appropriate backend (SQLite, Dolt embedded, or Dolt server)
+	// based on metadata.json configuration
+	store, err := factory.NewFromConfig(getRootContext(), beadsDir)
+	if err != nil {
+		// Check for fresh clone scenario (JSONL exists but no database)
+		if _, statErr := os.Stat(jsonlPath); statErr == nil {
 			return fmt.Errorf("found JSONL file but no database: %s\n"+
 				"Hint: run 'bd init' to create the database and import issues,\n"+
 				"      or use 'bd --no-db' for JSONL-only mode", jsonlPath)
 		}
-			}
-			return fmt.Errorf("no beads database found.\n" +
-				"Hint: run 'bd init' to create a database in the current directory,\n" +
-				"      or use 'bd --no-db' for JSONL-only mode")
-		}
-	}
-
-	sqlStore, err := sqlite.New(getRootContext(), path)
-	if err != nil {
-		// Check for fresh clone scenario
-		if isFreshCloneError(err) {
-			beadsDir := filepath.Dir(path)
-			handleFreshCloneError(err, beadsDir)
-			return fmt.Errorf("database not initialized")
-		}
 		return fmt.Errorf("failed to open database: %w", err)
 	}
 
+	// Update the database path for compatibility with code that expects it
+	if dbPath := beads.FindDatabasePath(); dbPath != "" {
+		setDBPath(dbPath)
+	}
+
 	lockStore()
-	setStore(sqlStore)
+	setStore(store)
 	setStoreActive(true)
 	unlockStore()
 

cmd/bd/routed.go

@@ -6,6 +6,7 @@ import (
 
 	"github.com/steveyegge/beads/internal/routing"
 	"github.com/steveyegge/beads/internal/storage"
+	"github.com/steveyegge/beads/internal/storage/factory"
 	"github.com/steveyegge/beads/internal/types"
 	"github.com/steveyegge/beads/internal/utils"
 )
@@ -41,7 +42,8 @@ func resolveAndGetIssueWithRouting(ctx context.Context, localStore storage.Stora
 	}
 
 	beadsDir := filepath.Dir(dbPath)
-	routedStorage, err := routing.GetRoutedStorageForID(ctx, id, beadsDir)
+	// Use factory.NewFromConfig as the storage opener to respect backend configuration
+	routedStorage, err := routing.GetRoutedStorageWithOpener(ctx, id, beadsDir, factory.NewFromConfig)
 	if err != nil {
 		return nil, err
 	}

internal/beads/beads.go

@@ -232,7 +232,11 @@ func findDatabaseInBeadsDir(beadsDir string, warnOnIssues bool) string {
 	if cfg, err := configfile.Load(beadsDir); err == nil && cfg != nil {
 		backend := cfg.GetBackend()
 		if backend == configfile.BackendDolt {
-			// For Dolt, check if the configured database directory exists
+			// For Dolt server mode, database is on the server - no local directory required
+			if cfg.IsDoltServerMode() {
+				return cfg.DatabasePath(beadsDir)
+			}
+			// For embedded Dolt, check if the configured database directory exists
 			doltPath := cfg.DatabasePath(beadsDir)
 			if info, err := os.Stat(doltPath); err == nil && info.IsDir() {
 				return doltPath

internal/routing/routes.go

@@ -425,12 +425,27 @@ func (rs *RoutedStorage) Close() error {
 	return nil
 }
 
+// StorageOpener is a function that opens storage for a given beads directory.
+// This allows callers to provide custom storage opening logic (e.g., using factory).
+type StorageOpener func(ctx context.Context, beadsDir string) (storage.Storage, error)
+
 // GetRoutedStorageForID returns a storage connection for the given issue ID.
+// If the ID matches a route, it opens a connection to the routed database using SQLite.
+// Otherwise, it returns nil (caller should use their existing storage).
+//
+// DEPRECATED: Use GetRoutedStorageWithOpener for proper backend support.
+// The caller is responsible for closing the returned RoutedStorage.
+func GetRoutedStorageForID(ctx context.Context, id, currentBeadsDir string) (*RoutedStorage, error) {
+	return GetRoutedStorageWithOpener(ctx, id, currentBeadsDir, nil)
+}
+
+// GetRoutedStorageWithOpener returns a storage connection for the given issue ID.
 // If the ID matches a route, it opens a connection to the routed database.
+// The opener function is used to create storage; if nil, defaults to SQLite.
 // Otherwise, it returns nil (caller should use their existing storage).
 //
 // The caller is responsible for closing the returned RoutedStorage.
-func GetRoutedStorageForID(ctx context.Context, id, currentBeadsDir string) (*RoutedStorage, error) {
+func GetRoutedStorageWithOpener(ctx context.Context, id, currentBeadsDir string, opener StorageOpener) (*RoutedStorage, error) {
 	beadsDir, routed, err := ResolveBeadsDirForID(ctx, id, currentBeadsDir)
 	if err != nil {
 		return nil, err
@@ -441,8 +456,14 @@ func GetRoutedStorageForID(ctx context.Context, id, currentBeadsDir string) (*Ro
 	}
 
 	// Open storage for the routed directory
+	var store storage.Storage
+	if opener != nil {
+		store, err = opener(ctx, beadsDir)
+	} else {
+		// Default to SQLite for backward compatibility
 		dbPath := filepath.Join(beadsDir, "beads.db")
-	store, err := sqlite.New(ctx, dbPath)
+		store, err = sqlite.New(ctx, dbPath)
+	}
 	if err != nil {
 		return nil, err
 	}

internal/storage/dolt/store.go

@@ -312,9 +312,14 @@ func openServerConnection(ctx context.Context, cfg *Config) (*sql.DB, string, er
 
 	_, err = initDB.ExecContext(ctx, fmt.Sprintf("CREATE DATABASE IF NOT EXISTS %s", cfg.Database))
 	if err != nil {
+		// Dolt may return error 1007 even with IF NOT EXISTS - ignore if database already exists
+		errLower := strings.ToLower(err.Error())
+		if !strings.Contains(errLower, "database exists") && !strings.Contains(errLower, "1007") {
 			_ = db.Close()
 			return nil, "", fmt.Errorf("failed to create database: %w", err)
 		}
+		// Database already exists - that's fine, continue
+	}
 
 	return db, connStr, nil
 }