Is there a specific reason why this is creating problems for you. As it is a not so uncommon approach to use a hidden directory in the root to store some information. You probably also have a .settings folder there and maybe more.
As far as I know, this information is also just temporarily generated, as you're allowed to delete it. Adding it to the process definition sounds like a bad idea to me But maybe we should just look at whether it is possible to live without them.
If this is an issue for you, could you open up a JIRA issue for this and log as much information as possible why, so we (and others) can follow up?