You need to run aa-logprof as sudo (so 'sudo aa-logprof) or you won't be able to commit the changes.

home/*/.java/deployment/cache/** rm,

You can put that rule in there.

Are you on 32bit Ubuntu? That would explain the issues. My rules are for 64bit so I gave access to 64bit libraries. You're on 32bit so you need to give access to 32bit libraries.