Usually, the configuration in local is considered as modified by the user, and the default is the one shipped with the app, that will be overwritten next time an upgrade will be applied.
The distinction between default and local makes sense for apps upgrade and for precedence reasons. (local has higher precedence than default). But not so much for deployment because default and local are both pushed to the deployment-clients.
From an app development point of view. When you develop an app, you edit the local to test, using the webinterface, then when you are done, you can move the config to default and make it final.
So I would recommend to use the same approach and store your configuration on default .
Then you will be able to see in local the files modified by the system (usually the app.conf to enable the app)
