Fix auto-sync service not stopping when disabled

- Use global auto-sync service instance instead of creating new instances
- This ensures stopAutoSync() is called on the actual running service
- Fix .env file parsing to handle comments and empty lines properly
- Update both TRPC and REST API endpoints to use global instance
- Auto-sync service will now properly stop when disabled in settings

src/app/api/settings/auto-sync/route.ts

@@ -160,8 +160,14 @@ export async function POST(request: NextRequest) {
 
     // Reschedule auto-sync service with new settings
     try {
-      const { AutoSyncService } = await import('../../../../server/services/autoSyncService.js');
-      const autoSyncService = new AutoSyncService();
+      const { getAutoSyncService } = await import('../../../../server/lib/autoSyncInit.js');
+      let autoSyncService = getAutoSyncService();
+      
+      // If no global instance exists, create one
+      if (!autoSyncService) {
+        const { AutoSyncService } = await import('../../../../server/services/autoSyncService.js');
+        autoSyncService = new AutoSyncService();
+      }
       
       if (settings.autoSyncEnabled) {
         autoSyncService.scheduleAutoSync();

src/server/api/routers/scripts.ts

@@ -503,7 +503,16 @@ export const scriptsRouter = createTRPCRouter({
     }))
     .mutation(async ({ input }) => {
       try {
-        const autoSyncService = new AutoSyncService();
+        // Use the global auto-sync service instance
+        const { getAutoSyncService } = await import('~/server/lib/autoSyncInit');
+        let autoSyncService = getAutoSyncService();
+        
+        // If no global instance exists, create one
+        if (!autoSyncService) {
+          const { AutoSyncService } = await import('~/server/services/autoSyncService');
+          autoSyncService = new AutoSyncService();
+        }
+        
         autoSyncService.saveSettings(input);
         
         // Reschedule auto-sync if enabled

src/server/services/autoSyncService.js

@@ -155,13 +155,28 @@ export class AutoSyncService {
       const existingKeys = new Set();
       
       for (const line of lines) {
-        const [key] = line.split('=');
-        const trimmedKey = key?.trim();
-        if (trimmedKey && trimmedKey in settingsMap) {
-          // @ts-ignore - Dynamic key access is safe here
-          newLines.push(`${trimmedKey}=${settingsMap[trimmedKey]}`);
-          existingKeys.add(trimmedKey);
-        } else if (trimmedKey && !(trimmedKey in settingsMap)) {
+        const trimmedLine = line.trim();
+        
+        // Skip empty lines and comments
+        if (!trimmedLine || trimmedLine.startsWith('#')) {
+          newLines.push(line);
+          continue;
+        }
+        
+        const equalIndex = trimmedLine.indexOf('=');
+        if (equalIndex === -1) {
+          // Line doesn't contain '=', keep as is
+          newLines.push(line);
+          continue;
+        }
+        
+        const key = trimmedLine.substring(0, equalIndex).trim();
+        if (key && key in settingsMap) {
+          // Replace existing setting
+          newLines.push(`${key}=${settingsMap[key]}`);
+          existingKeys.add(key);
+        } else {
+          // Keep other settings as is
           newLines.push(line);
         }
       }