This caught me out.
I enabled Two-Factor Authentication on my GitHub account the other day, it works quite well with other services I use and I’ve had no problem with the Android App. Anyway, I promptly forgot about doing this and a week later I was struggling to clone a repository – whilst the URI was working fine the username and password pair returned a “not authorized” error.
Eclipse needs a way past the new level of security.
This can be achieved by using a GitHub access token, which works in the same way as an OAuth token.
Once the token is created (don’t forget to copy it from the success screen, you won’t see it again) it can be used straight away in place of your account password.
That’s 30 minutes of my life I’ll never get back!