git Warning: remote HEAD refers to nonexistent ref, unable to checkout
I found out what was going wrong. The problem was that I wasn't paying attention to the warnings when I was pushing to my gitosis server so I didn't realize that I wasn't pushing a particular branch. I had assumed it would just push the current but that isn't the case until you set:
git config push.default current
One more possible cause for this warning might be that the master branch in the repository is missing (OR) the repository does NOT use a master branch. If this is the case, just don't worry about the Warning!, use
git checkout <some_existing_branch>The warning is because, by default, after the pull git tries to checkout into the master branch.