[How to remove a directory from git repository] (http://stackoverflow.com/questions/6313126/how-to-remove-a-directory-from-git-repository)
git rm -r one-of-the-directories
git commit -m "Remove duplicated directory"
git push origin <your-git-branch> (typically 'master', but not always)
what you usually want to do is remove this directory from git but not delete it entirely from the filesystem (local)
In that case use:
git rm -r --cached myFolder