I made a fresh Ext JS application with Ext JS 4.1.1a and latest cmd v3.0.0.190. Out of the box everything works fine but when I add store to controller
stores: ['Bookings']
I get an error: Error: [Ext.Loader] Failed loading 'app/controller/BookingSearch.js/store/Bookings.js', please verify that the file exist.

As you can see the path for loading the store is prefixed with the controller's path for some reason.