fix(routes): restore ctx access in 15 route files broken by Phase 2.1 refactor

The modular refactor changed function signatures to destructured deps but
left internal ctx.* references intact, causing "ctx is not defined" errors
on /api/config, /api/logo, and many other endpoints. Also implements
loadTotpConfig and saveTotpConfig which were left as stubs.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

dashcaddy-api/routes/arr/smart-connect.js

@@ -12,7 +12,8 @@ const { APP_PORTS } = require('../../constants');
  * @param {Object} deps.helpers - Arr helpers module
  * @returns {express.Router}
  */
-module.exports = function({ credentialManager, fetchT, asyncHandler, errorResponse, log, helpers }) {
+module.exports = function(ctx) {
+  const { credentialManager, fetchT, asyncHandler, errorResponse, log, helpers } = ctx;
   const router = express.Router();
 
   // Smart Connect: Unified orchestration endpoint