fix: resolve data directory persistence between Electron and Web modes

apps/server/src/index.ts

@@ -91,6 +91,9 @@ const PORT = parseInt(process.env.PORT || '3008', 10);
 const HOST = process.env.HOST || '0.0.0.0';
 const HOSTNAME = process.env.HOSTNAME || 'localhost';
 const DATA_DIR = process.env.DATA_DIR || './data';
+logger.info('[SERVER_STARTUP] process.env.DATA_DIR:', process.env.DATA_DIR);
+logger.info('[SERVER_STARTUP] Resolved DATA_DIR:', DATA_DIR);
+logger.info('[SERVER_STARTUP] process.cwd():', process.cwd());
 const ENABLE_REQUEST_LOGGING_DEFAULT = process.env.ENABLE_REQUEST_LOGGING !== 'false'; // Default to true
 
 // Runtime-configurable request logging flag (can be changed via settings)
@@ -175,14 +178,25 @@ app.use(
         return;
       }
 
-      // For local development, allow localhost origins
-      if (
-        origin.startsWith('http://localhost:') ||
-        origin.startsWith('http://127.0.0.1:') ||
-        origin.startsWith('http://[::1]:')
-      ) {
-        callback(null, origin);
-        return;
+      // For local development, allow all localhost/loopback origins (any port)
+      try {
+        const url = new URL(origin);
+        const hostname = url.hostname;
+
+        if (
+          hostname === 'localhost' ||
+          hostname === '127.0.0.1' ||
+          hostname === '::1' ||
+          hostname === '0.0.0.0' ||
+          hostname.startsWith('192.168.') ||
+          hostname.startsWith('10.') ||
+          hostname.startsWith('172.')
+        ) {
+          callback(null, origin);
+          return;
+        }
+      } catch (err) {
+        // Ignore URL parsing errors
       }
 
       // Reject other origins by default for security

apps/server/src/routes/settings/routes/update-global.ts

@@ -45,18 +45,24 @@ export function createUpdateGlobalHandler(settingsService: SettingsService) {
       }
 
       // Minimal debug logging to help diagnose accidental wipes.
-      if ('projects' in updates || 'theme' in updates || 'localStorageMigrated' in updates) {
-        const projectsLen = Array.isArray((updates as any).projects)
-          ? (updates as any).projects.length
-          : undefined;
-        logger.info(
-          `Update global settings request: projects=${projectsLen ?? 'n/a'}, theme=${
-            (updates as any).theme ?? 'n/a'
-          }, localStorageMigrated=${(updates as any).localStorageMigrated ?? 'n/a'}`
-        );
-      }
+      const projectsLen = Array.isArray((updates as any).projects)
+        ? (updates as any).projects.length
+        : undefined;
+      const trashedLen = Array.isArray((updates as any).trashedProjects)
+        ? (updates as any).trashedProjects.length
+        : undefined;
+      logger.info(
+        `[SERVER_SETTINGS_UPDATE] Request received: projects=${projectsLen ?? 'n/a'}, trashedProjects=${trashedLen ?? 'n/a'}, theme=${
+          (updates as any).theme ?? 'n/a'
+        }, localStorageMigrated=${(updates as any).localStorageMigrated ?? 'n/a'}`
+      );
 
+      logger.info('[SERVER_SETTINGS_UPDATE] Calling updateGlobalSettings...');
       const settings = await settingsService.updateGlobalSettings(updates);
+      logger.info(
+        '[SERVER_SETTINGS_UPDATE] Update complete, projects count:',
+        settings.projects?.length ?? 0
+      );
 
       // Apply server log level if it was updated
       if ('serverLogLevel' in updates && updates.serverLogLevel) {

apps/server/src/services/settings-service.ts

@@ -273,13 +273,39 @@ export class SettingsService {
     };
 
     const currentProjectsLen = Array.isArray(current.projects) ? current.projects.length : 0;
+    // Check if this is a legitimate project removal (moved to trash) vs accidental wipe
+    const newTrashedProjectsLen = Array.isArray(sanitizedUpdates.trashedProjects)
+      ? sanitizedUpdates.trashedProjects.length
+      : Array.isArray(current.trashedProjects)
+        ? current.trashedProjects.length
+        : 0;
+
     if (
       Array.isArray(sanitizedUpdates.projects) &&
       sanitizedUpdates.projects.length === 0 &&
       currentProjectsLen > 0
     ) {
-      attemptedProjectWipe = true;
-      delete sanitizedUpdates.projects;
+      // Only treat as accidental wipe if trashedProjects is also empty
+      // (If projects are moved to trash, they appear in trashedProjects)
+      if (newTrashedProjectsLen === 0) {
+        logger.warn(
+          '[WIPE_PROTECTION] Attempted to set projects to empty array with no trash! Ignoring update.',
+          {
+            currentProjectsLen,
+            newProjectsLen: 0,
+            newTrashedProjectsLen,
+            currentProjects: current.projects?.map((p) => p.name),
+          }
+        );
+        attemptedProjectWipe = true;
+        delete sanitizedUpdates.projects;
+      } else {
+        logger.info('[LEGITIMATE_REMOVAL] Removing all projects to trash', {
+          currentProjectsLen,
+          newProjectsLen: 0,
+          movedToTrash: newTrashedProjectsLen,
+        });
+      }
     }
 
     ignoreEmptyArrayOverwrite('trashedProjects');

apps/ui/src/components/views/dashboard-view.tsx

@@ -124,6 +124,19 @@ export function DashboardView() {
         const initResult = await initializeProject(path);
 
         if (!initResult.success) {
+          // If the project directory doesn't exist, automatically remove it from the project list
+          if (initResult.error?.includes('does not exist')) {
+            const projectToRemove = projects.find((p) => p.path === path);
+            if (projectToRemove) {
+              logger.warn(`[Dashboard] Removing project with non-existent path: ${path}`);
+              moveProjectToTrash(projectToRemove.id);
+              toast.error('Project directory not found', {
+                description: `Removed ${name} from your projects list since the directory no longer exists.`,
+              });
+              return;
+            }
+          }
+
           toast.error('Failed to initialize project', {
             description: initResult.error || 'Unknown error occurred',
           });
@@ -151,7 +164,15 @@ export function DashboardView() {
         setIsOpening(false);
       }
     },
-    [trashedProjects, currentProject, globalTheme, upsertAndSetCurrentProject, navigate]
+    [
+      projects,
+      trashedProjects,
+      currentProject,
+      globalTheme,
+      upsertAndSetCurrentProject,
+      navigate,
+      moveProjectToTrash,
+    ]
   );
 
   const handleOpenProject = useCallback(async () => {

apps/ui/src/hooks/use-settings-migration.ts

@@ -111,9 +111,34 @@ export function resetMigrationState(): void {
 
 /**
  * Parse localStorage data into settings object
+ *
+ * Checks for settings in multiple locations:
+ * 1. automaker-settings-cache: Fresh server settings cached from last fetch
+ * 2. automaker-storage: Zustand-persisted app store state (legacy)
+ * 3. automaker-setup: Setup wizard state (legacy)
+ * 4. Standalone keys: worktree-panel-collapsed, file-browser-recent-folders, etc.
+ *
+ * @returns Merged settings object or null if no settings found
  */
 export function parseLocalStorageSettings(): Partial<GlobalSettings> | null {
   try {
+    // First, check for fresh server settings cache (updated whenever server settings are fetched)
+    // This prevents stale data when switching between modes
+    const settingsCache = getItem('automaker-settings-cache');
+    if (settingsCache) {
+      try {
+        const cached = JSON.parse(settingsCache) as GlobalSettings;
+        const cacheProjectCount = cached?.projects?.length ?? 0;
+        logger.info(`[CACHE_LOADED] projects=${cacheProjectCount}, theme=${cached?.theme}`);
+        return cached;
+      } catch (e) {
+        logger.warn('Failed to parse settings cache, falling back to old storage');
+      }
+    } else {
+      logger.info('[CACHE_EMPTY] No settings cache found in localStorage');
+    }
+
+    // Fall back to old Zustand persisted storage
     const automakerStorage = getItem('automaker-storage');
     if (!automakerStorage) {
       return null;
@@ -186,7 +211,14 @@ export function parseLocalStorageSettings(): Partial<GlobalSettings> | null {
 
 /**
  * Check if localStorage has more complete data than server
- * Returns true if localStorage has projects but server doesn't
+ *
+ * Compares the completeness of data to determine if a migration is needed.
+ * Returns true if localStorage has projects but server doesn't, indicating
+ * the localStorage data should be merged with server settings.
+ *
+ * @param localSettings Settings loaded from localStorage
+ * @param serverSettings Settings loaded from server
+ * @returns true if localStorage has more data that should be preserved
  */
 export function localStorageHasMoreData(
   localSettings: Partial<GlobalSettings> | null,
@@ -209,7 +241,15 @@ export function localStorageHasMoreData(
 
 /**
  * Merge localStorage settings with server settings
- * Prefers server data, but uses localStorage for missing arrays/objects
+ *
+ * Intelligently combines settings from both sources:
+ * - Prefers server data as the base
+ * - Uses localStorage values when server has empty arrays/objects
+ * - Specific handling for: projects, trashedProjects, mcpServers, recentFolders, etc.
+ *
+ * @param serverSettings Settings from server API (base)
+ * @param localSettings Settings from localStorage (fallback)
+ * @returns Merged GlobalSettings object ready to hydrate the store
  */
 export function mergeSettings(
   serverSettings: GlobalSettings,
@@ -291,20 +331,33 @@ export function mergeSettings(
  * This is the core migration logic extracted for use outside of React hooks.
  * Call this from __root.tsx during app initialization.
  *
- * @param serverSettings - Settings fetched from the server API
- * @returns Promise resolving to the final settings to use (merged if migration needed)
+ * Flow:
+ * 1. If server has localStorageMigrated flag, skip migration (already done)
+ * 2. Check if localStorage has more data than server
+ * 3. If yes, merge them and sync merged state back to server
+ * 4. Set localStorageMigrated flag to prevent re-migration
+ *
+ * @param serverSettings Settings fetched from the server API
+ * @returns Promise resolving to {settings, migrated} - final settings and whether migration occurred
  */
 export async function performSettingsMigration(
   serverSettings: GlobalSettings
 ): Promise<{ settings: GlobalSettings; migrated: boolean }> {
   // Get localStorage data
   const localSettings = parseLocalStorageSettings();
-  logger.info(`localStorage has ${localSettings?.projects?.length ?? 0} projects`);
-  logger.info(`Server has ${serverSettings.projects?.length ?? 0} projects`);
+  const localProjects = localSettings?.projects?.length ?? 0;
+  const serverProjects = serverSettings.projects?.length ?? 0;
+
+  logger.info('[MIGRATION_CHECK]', {
+    localStorageProjects: localProjects,
+    serverProjects: serverProjects,
+    localStorageMigrated: serverSettings.localStorageMigrated,
+    dataSourceMismatch: localProjects !== serverProjects,
+  });
 
   // Check if migration has already been completed
   if (serverSettings.localStorageMigrated) {
-    logger.info('localStorage migration already completed, using server settings only');
+    logger.info('[MIGRATION_SKIP] Using server settings only (migration already completed)');
     return { settings: serverSettings, migrated: false };
   }
 
@@ -412,6 +465,15 @@ export function useSettingsMigration(): MigrationState {
           if (global.success && global.settings) {
             serverSettings = global.settings as unknown as GlobalSettings;
             logger.info(`Server has ${serverSettings.projects?.length ?? 0} projects`);
+
+            // Update localStorage with fresh server data to keep cache in sync
+            // This prevents stale localStorage data from being used when switching between modes
+            try {
+              setItem('automaker-settings-cache', JSON.stringify(serverSettings));
+              logger.debug('Updated localStorage with fresh server settings');
+            } catch (storageError) {
+              logger.warn('Failed to update localStorage cache:', storageError);
+            }
           }
         } catch (error) {
           logger.error('Failed to fetch server settings:', error);