`apply_patch` only works with non-bare repositories

[dometto]

It looks like the apply_patch method (which we will have to rework into a revert method) currently only works with non-bare repositories, since RJGit just wraps jgit's porcelain ApplyCommand, which reads files from the worktree.

Looks like working around this will require us to somehow re-implement ApplyCommand#apply in such a way that it will operate on a string or input stream that's not on-disk.

[bartkamphorst]

When I run the apply tests with a bare repository it works fine. Closing for now.