Setting up a new repos might involve lots of experimenting and backtracking. To clean the slate and do a proper initial commit it is useful to reset the git history.
Remove all version control info
rm -rf .git
Create a new repos
git add . git commit -m "Initial commit"
Push it to an existing github repos, overwriting the history.
git remote add origin https://github.com/username/repos git push -u --force origin master
After this commit and push changes as usual.