My repo: https://shadyabhi@github.com/shadyabhi/learnajax.git
shadyabhi@archlinux-N210 ~/github/learnajax $ cat .git/config
[core]
repositoryformatversi
As I understand it, github.token (and github.user) aren't used by git HTTP transport - they're only there for other tools that use GitHub's API, such as GitX and GitNub.
I think the "Authentication failed" error must be due to you entering the wrong password. (This should be your GitHub password rather than the password to your SSH private key.)