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/apps/helpers.js

@@ -17,7 +17,8 @@ const platformPaths = require('../../platform-paths');
  * @param {Object} deps.log - Logger instance
  * @returns {Object} Helper functions
  */
-module.exports = function({ docker, caddy, credentialManager, servicesStateManager, fetchT, log }) {
+module.exports = function(ctx) {
+  const { docker, caddy, credentialManager, servicesStateManager, fetchT, log } = ctx;
 
   async function checkPortConflicts(ports, excludeContainerName = null) {
     const conflicts = [];