The title says it all. I have to say your unconventional directory layout (in particular, not using a theories folder) makes it more annoying than it would have to be to update your build system. ;)
If you tell me there's currently no branch somewhere that would break, I'd be happy to introduce a theories folder for you. That would mostly involve git mv coq/ra coq/theories as well as moving Makefile and _CoqProject one folder up, i.e., directly into coq/.