We've moved all App Store modules to the 'Project' option in the Project Explorer. This is done automatically when a module is downloaded from the App Store.
App Cloud Services, Administration and Navigation Layouts are now AppStore based.
What you can do for existing projects is download (and overwrite the existing) these modules from the App store.
* Note: there are two versions of the Administration & Navigation Layout modules in the App store
A. a version to be used together with App Cloud Services
B. a version to be used when you don't use App Cloud Services in your project.