Fixing/removing/replacing the permissions checking code

There currently are a few open issues related to the permissions checking (e.g. https://github.com/commercialhaskell/stack/issues/2187, https://github.com/commercialhaskell/stack/issues/3076). I originally wrote that code and added the `--allow-different-user` flag but I don't really understand it so well and don't expect to be able to fix it soon.

I'm wondering if it would be better to remove that code and instead add a simple warning and/or [y/n] interaction when stack tries to write to directories that are owned by a different user. Maybe it should be possible to disable the warning with `permissions-check: false` or something similar.