feat: update resumeFeature API to support optional useWorktrees parameter

- Modified the resumeFeature method across multiple files to accept an optional useWorktrees parameter, defaulting to false for improved control over worktree usage.
- Updated related hooks and service methods to ensure consistent handling of the new parameter.
- Enhanced server route logic to reflect the change, ensuring worktrees are only utilized when explicitly enabled.

apps/server/src/routes/auto-mode/routes/resume-feature.ts

@@ -29,8 +29,9 @@ export function createResumeFeatureHandler(autoModeService: AutoModeService) {
       }
 
       // Start resume in background
+      // Default to false - worktrees should only be used when explicitly enabled
       autoModeService
-        .resumeFeature(projectPath, featureId, useWorktrees ?? true)
+        .resumeFeature(projectPath, featureId, useWorktrees ?? false)
         .catch((error) => {
           logger.error(`[AutoMode] Resume feature ${featureId} error:`, error);
         });

apps/server/src/routes/auto-mode/routes/run-feature.ts

@@ -31,8 +31,9 @@ export function createRunFeatureHandler(autoModeService: AutoModeService) {
 
       // Start execution in background
       // If worktreePath is provided, use it directly; otherwise let the service decide
+      // Default to false - worktrees should only be used when explicitly enabled
       autoModeService
-        .executeFeature(projectPath, featureId, useWorktrees ?? true, false, worktreePath)
+        .executeFeature(projectPath, featureId, useWorktrees ?? false, false, worktreePath)
         .catch((error) => {
           logger.error(`[AutoMode] Feature ${featureId} error:`, error);
         });

apps/server/src/services/auto-mode-service.ts

@@ -193,7 +193,7 @@ export class AutoModeService {
   async executeFeature(
     projectPath: string,
     featureId: string,
-    useWorktrees = true,
+    useWorktrees = false,
     isAutoMode = false,
     providedWorktreePath?: string
   ): Promise<void> {
@@ -352,7 +352,7 @@ export class AutoModeService {
   async resumeFeature(
     projectPath: string,
     featureId: string,
-    useWorktrees = true
+    useWorktrees = false
   ): Promise<void> {
     // Check if context exists in .automaker directory
     const featureDir = getFeatureDir(projectPath, featureId);