Hey,
depending on the complexity of your project( external dependencies, folder structure etc ) it should not be that difficult to have your app in a custom directory actually.
Take BasicApp for example, you could place it in a random directory in your filesystem and the only thing that would need to change in order for the app to build, would be the path to find the root directory of Cinder.
For projects that require finer control Cinder provides currently the ci_make_app macro. This macro is the entry point for applications that want to include directories, blocks and/or external libraries. You can see the argument it accepts here . The forum thread here is also a good resource regarding Cinder and CMake. That said, it would be great to have a proper documentation of the current CMake workflow and a guide is definitely on the todo list for when the time first allows. Until then you can always come back here if something is not clear or not working!
HTH,
Petros