Good conversation, and sorry I was on vacation for it. 
Here is something I wrote before which relates to this: Managing App Definitions and Extensions in OpenMRS
Since we built the refapp, Bahmni has taken what I think is a better philosophical approach to the way these apps are set up, and I think we should draw inspiration from what they have done.
My quick thought about this is:
- Upon first installation, we write the built-in app definitions to a config folder in the filesystem (like Bahmni does) or the database
- Users are able to edit these just like any other apps