Pod folders in root don't get deleted when running `ember depodify` with podModulePrefix defined

[trabus]

If a project has pods on the app root, setting a podModulePrefix in config, then running ember depodify should delete the empty pod folders after conversion.
Also, if a project has pods on the app root with podModulePrefix defined, ember podify should move pods into podModulePrefix folder and delete the empty folders on the app root.