I recently began using two-factor authentication on GitHub, and I am now unable to use git over https on private repos in the usual way:
peter@computer:~$ git cl
If your repo have 2FA enabled. Highly suggest to use the app provided by github.com Here is the link: https://desktop.github.com/
After you downloaded it and installed it. Follow the withard, the app will ask you to provide the one time password for login. Once you filled in the one time password, you could see your repo/projects now.