I was recently playing with putting source code on an encrypted drive. I cloned my GIT directory (on the command line) onto an encrypted drive, and when I open the directory with Rubymine, it opens everything just fine, but doesn't recognize that this is a GIT directory, and the GIT commands are not there. It seems to think that it isn't a GIT directory at all (ie, the "GIT Init...." command is there under the "Version Control" menu)
I used a drive encryped with TruCrypt, then one encrypted with the Apple Disk Util.
I created a drive that is a couple Gigs big.