I got this message when updating new files from remote and index got out of whack. Tried to fix the index, but resolving via Xcode 4.5, GitHub.app (103), and GitX.app (0.7.1) failed. So, I did this:
git commit -a -m "your commit message here"
which worked in bypassing the git index.
Two blog posts that helped me understand about Git and Xcode are: