I use git professionally on a daily basis and I agree with learning the command line version. If nothing else, just to test out the theory that it is the GitHub application that is the issue here. Git is a true distributed source control system and does not lock or checkout files, those concepts are just not part of git at all. I suspect you have something else locking those files. Git also does not mark files as changed if you have not changed them, since it actually uses lstat and SHA1 hashes to make those comparisons when you are checking status or committing. If git thinks a file has been changed, it really has been changed; the odds of a false positive are very low.