feat: enhance global settings update with data loss prevention

- Added safeguards to prevent overwriting non-empty arrays with empty arrays during global settings updates, specifically for the 'projects' field.
- Implemented logging for updates to assist in diagnosing accidental wipes of critical settings.
- Updated tests to verify that projects are preserved during logout transitions and that theme changes are ignored if a project wipe is attempted.
- Enhanced the settings synchronization logic to ensure safe handling during authentication state changes.

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

@@ -11,7 +11,7 @@
 import type { Request, Response } from 'express';
 import type { SettingsService } from '../../../services/settings-service.js';
 import type { GlobalSettings } from '../../../types/settings.js';
-import { getErrorMessage, logError } from '../common.js';
+import { getErrorMessage, logError, logger } from '../common.js';
 
 /**
  * Create handler factory for PUT /api/settings/global
@@ -32,6 +32,18 @@ export function createUpdateGlobalHandler(settingsService: SettingsService) {
         return;
       }
 
+      // 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 settings = await settingsService.updateGlobalSettings(updates);
 
       res.json({

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

@@ -266,25 +266,80 @@ export class SettingsService {
     const settingsPath = getGlobalSettingsPath(this.dataDir);
 
     const current = await this.getGlobalSettings();
+
+    // Guard against destructive "empty array/object" overwrites.
+    // During auth transitions, the UI can briefly have default/empty state and accidentally
+    // sync it, wiping persisted settings (especially `projects`).
+    const sanitizedUpdates: Partial<GlobalSettings> = { ...updates };
+    let attemptedProjectWipe = false;
+
+    const ignoreEmptyArrayOverwrite = <K extends keyof GlobalSettings>(key: K): void => {
+      const nextVal = sanitizedUpdates[key] as unknown;
+      const curVal = current[key] as unknown;
+      if (
+        Array.isArray(nextVal) &&
+        nextVal.length === 0 &&
+        Array.isArray(curVal) &&
+        curVal.length > 0
+      ) {
+        delete sanitizedUpdates[key];
+      }
+    };
+
+    const currentProjectsLen = Array.isArray(current.projects) ? current.projects.length : 0;
+    if (
+      Array.isArray(sanitizedUpdates.projects) &&
+      sanitizedUpdates.projects.length === 0 &&
+      currentProjectsLen > 0
+    ) {
+      attemptedProjectWipe = true;
+      delete sanitizedUpdates.projects;
+    }
+
+    ignoreEmptyArrayOverwrite('trashedProjects');
+    ignoreEmptyArrayOverwrite('projectHistory');
+    ignoreEmptyArrayOverwrite('recentFolders');
+    ignoreEmptyArrayOverwrite('aiProfiles');
+    ignoreEmptyArrayOverwrite('mcpServers');
+    ignoreEmptyArrayOverwrite('enabledCursorModels');
+    ignoreEmptyArrayOverwrite('enabledCodexModels');
+
+    // Empty object overwrite guard
+    if (
+      sanitizedUpdates.lastSelectedSessionByProject &&
+      typeof sanitizedUpdates.lastSelectedSessionByProject === 'object' &&
+      !Array.isArray(sanitizedUpdates.lastSelectedSessionByProject) &&
+      Object.keys(sanitizedUpdates.lastSelectedSessionByProject).length === 0 &&
+      current.lastSelectedSessionByProject &&
+      Object.keys(current.lastSelectedSessionByProject).length > 0
+    ) {
+      delete sanitizedUpdates.lastSelectedSessionByProject;
+    }
+
+    // If a request attempted to wipe projects, also ignore theme changes in that same request.
+    if (attemptedProjectWipe) {
+      delete sanitizedUpdates.theme;
+    }
+
     const updated: GlobalSettings = {
       ...current,
-      ...updates,
+      ...sanitizedUpdates,
       version: SETTINGS_VERSION,
     };
 
     // Deep merge keyboard shortcuts if provided
-    if (updates.keyboardShortcuts) {
+    if (sanitizedUpdates.keyboardShortcuts) {
       updated.keyboardShortcuts = {
         ...current.keyboardShortcuts,
-        ...updates.keyboardShortcuts,
+        ...sanitizedUpdates.keyboardShortcuts,
       };
     }
 
     // Deep merge phaseModels if provided
-    if (updates.phaseModels) {
+    if (sanitizedUpdates.phaseModels) {
       updated.phaseModels = {
         ...current.phaseModels,
-        ...updates.phaseModels,
+        ...sanitizedUpdates.phaseModels,
       };
     }
 

apps/server/tests/unit/services/settings-service.test.ts

@@ -144,6 +144,33 @@ describe('settings-service.ts', () => {
       expect(updated.keyboardShortcuts.agent).toBe(DEFAULT_GLOBAL_SETTINGS.keyboardShortcuts.agent);
     });
 
+    it('should not overwrite non-empty projects with an empty array (data loss guard)', async () => {
+      const initial: GlobalSettings = {
+        ...DEFAULT_GLOBAL_SETTINGS,
+        theme: 'solarized' as GlobalSettings['theme'],
+        projects: [
+          {
+            id: 'proj1',
+            name: 'Project 1',
+            path: '/tmp/project-1',
+            lastOpened: new Date().toISOString(),
+          },
+        ] as any,
+      };
+      const settingsPath = path.join(testDataDir, 'settings.json');
+      await fs.writeFile(settingsPath, JSON.stringify(initial, null, 2));
+
+      const updated = await settingsService.updateGlobalSettings({
+        projects: [],
+        theme: 'light',
+      } as any);
+
+      expect(updated.projects.length).toBe(1);
+      expect((updated.projects as any)[0]?.id).toBe('proj1');
+      // Theme should be preserved in the same request if it attempted to wipe projects
+      expect(updated.theme).toBe('solarized');
+    });
+
     it('should create data directory if it does not exist', async () => {
       const newDataDir = path.join(os.tmpdir(), `new-data-dir-${Date.now()}`);
       const newService = new SettingsService(newDataDir);