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
@@ -61,47 +62,44 @@ 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
-			beadsDir := beads.FindBeadsDir()
-			if beadsDir != "" {
-				jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
-				if _, err := os.Stat(jsonlPath); err == nil {
-					// JSONL exists - check if no-db mode is configured
-					if isNoDbModeConfigured(beadsDir) {
-						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
-					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")
+	// Find the .beads directory
+	beadsDir := beads.FindBeadsDir()
+	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
+		if isNoDbModeConfigured(beadsDir) {
+			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")
 		}
 	}
 
-	sqlStore, err := sqlite.New(getRootContext(), path)
+	// 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
-		if isFreshCloneError(err) {
-			beadsDir := filepath.Dir(path)
-			handleFreshCloneError(err, beadsDir)
-			return fmt.Errorf("database not initialized")
+		// 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("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()