The last comment from the discussion over there:
I thought that there should be distinction between user and application data in your model that is currently lacking – e.g. a propriety application configuration file is less likely to be meaningful for other apps and doesn’t require sharing
I think that’s a good point, and as far as I know the little discussion we had about that did not yet lead to a satisfying conclusion. The current status is basically that you can do what you want (e.g. use a category named after the app or place a dotfile in a common on), which is obviously not as nice as agreeing on a common way of storing app configs and the like.
Maybe we should re-open the discussion somewhere (probably on the forums until we have implementation details to discuss).
Please continue this discussion at will.