We recently upgraded to Unity 4.2, however after following the upgrade notes regarding the Assets/Plugins/iOS folder, my custom UnityAppController.mm file is being copied to Libraries instead of Classes folder! Of course this causes duplicate symbol definitions in XCode 5.
We solved this problem using a different approach: we subclass UnityAppController and patch main.mm to use our own class. Unity 4.2 makes this even simpler with the IMPL_APP_CONTROLLER_SUBCLASS macro.