You don’t have to lose your static config files! If you have something you’d like to stick around in the app image, just put it in the directory before issuing the af update or af push command. For example, if my app needs values stored in /settings.conf, just make sure you have a local copy of settings.conf in the root directory you are pushing the app from, do the af update/push, et voila! The file sticks around from boot to boot.
The same applies for WordPress plugin and theme directories. Just make sure the respective folder is in the app root when you send up the app and you’re good to go! I scratched my head a bit over this as it’s explained only subtly in the AppFog documentation. Persistent file storage is apparently a “top priority” but it’s been many months since they promised that.