Remove all version history from the local Git repository, so the current contents of the repository appear as the only commit.
This is the hardcore way, check source for more info
Step 1: remove all history
rm -rf .git
Step 2: reconstruct the Git repo with only the current content do one at a time
git init
git add .
git commit -m "Initial commit"
Step 3: push to GitHub.
git remote add origin <github-uri>
git push -u --force origin master
source: http://stackoverflow.com/questions/9683279/make-the-current-commit-the-only-initial-commit-in-a-git-repository