Update local copy from github.com
git fetch origin
Update your local branch with origin/master, then replay your changes
git rebase origin/master
Overwrite local files
git checkout .
Commit changes
git commit -m "First import"
Send your commits to github.com
git push origin
On Ubuntu use GCT for commits
sudo apt-get install commit-tool
On OSX GITX INSTEAD
Mark all changes for commit
git add .
Commit your changes locally
git commit