I have followed these instructions below to upload a project.
Global setup:
Download and install Git
git config --global user.name \"Your Name\"
For me the problem was the execution of clone via sudo.
If you clone to a directory where you have user permission ( /home/user/git) it will work fine.
(Explanation: Running a command as superuser will not work with the same public key as running a command as user. Therefore Github refused the connection.)
This solution requires a SSH key already to be set up: https://help.github.com/articles/generating-ssh-keys