First of all another question : How do I remove a runtime?
This the past there was some XML file I could edit but I don't see it anymore.

Having different runtimes instead of subfolders make things easy to install. I just drop the content of a zip-file into a runtime and it is done.
Sometimes packages contains empty folders. That may be the reson I have an hair folder in my V4 runtime even when there is nothing in it.