[MODULES-166] add patching overlay module roots

This is what we have been using for patching for now - which seems to be the sanest way to do this. I don't really think adding more information about patching to modules itself makes more sense. Also if we decide to only have a single overlay directory per layer or similar - we would not need to change modules. So if you are alright with this, i'd like to get this into upstream so that we can start adding some tests for this. Thanks