My two cents: GitHub has changed its authentication scheme recently. At least for me, I needed to setup a one-time password scheme with OAuth (you can use another service) to access my account in GitHub page. I also needed to create a hash-like token for write operations (e.g. git push). This token is then used as password in your git client. I don’t know whether you aready know this, but since you’re complaining about authentication issues, perhaps a step is missing to work with GitHub.