fix: resolve data directory persistence between Electron and Web modes

This commit fixes bidirectional data synchronization between Electron and Web
modes by addressing multiple interconnected issues:

**Core Fixes:**

1. **Electron userData Path (main.ts)**
   - Explicitly set userData path in development using app.setPath()
   - Navigate from __dirname to project root instead of relying on process.cwd()
   - Ensures Electron reads from /data instead of ~/.config/Automaker

2. **Server DataDir Path (main.ts, start-automaker.sh)**
   - Fixed startServer() to use __dirname for reliable path calculation
   - Export DATA_DIR environment variable in start-automaker.sh
   - Server now consistently uses shared /data directory

3. **Settings Sync Protection (settings-service.ts)**
   - Modified wipe protection to distinguish legitimate removals from accidents
   - Allow empty projects array if trashedProjects has items
   - Prevent false-positive wipe detection when removing projects

4. **Diagnostics & Logging**
   - Enhanced cache loading logging in use-settings-migration.ts
   - Detailed migration decision logs for troubleshooting
   - Track project counts from both cache and server

**Impact:**
- Projects created in Electron now appear in Web mode after restart
- Projects removed in Web mode stay removed in Electron after restart
- Settings changes sync bidirectionally across mode switches
- No more data loss or project duplication issues

**Testing:**
- Verified Electron uses /home/dhanush/Projects/automaker/data
- Confirmed server startup logs show correct DATA_DIR
- Tested project persistence across mode restarts
- Validated no writes to ~/.config/Automaker in dev mode

Fixes: Data persistence between Electron and Web modes

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

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');