Why the focus on GitHub?
This article is quite poorly worded - if you only use GitHub you're safe as they've put protection in at the server side (though obviously upgrading anyway would still be recommended), the issue is if you use git (which while it is the client software you use with GitHub, it is not 'their' client software - GitHub came around about 2-3 years later as a collection of repositories with a nice web UI etc) on other untrusted repositories on case insensitive systems where your .git directory can get overwritten...