Seriously, your git repo has a rar archive of the source instead of individual files?
Viewing post in GolDetective jam comments
Strange. I never encountered such an issue with git, but then this may be something with github...
The best way to avoid it would have been to make several commits during the development progress, that would automatically spread the amount of files out. But that's possibly a moot point by now.
Just think about it for the next project. Setting up version control right at the start keeps you from getting headaches later..