Uniquify folders

I have one project that I work on where I need to track two folders that have the same name.  Say /foo/bar and /java/com/foo/bar.  It would be nice to have a way to make these unique.

One way to do this would be to do something like Emacs's uniquify.  I have it set up so that these two would be named bar/foo and bar/com.  Alternatively, you could just let me choose a display name for them (that wouldn't involve renaming the folder in the filesystem).