GitHub - initialize from existing directory

git-init-repo-from-dir

Create the remote repository, and get the URL such as 

git@github.com:/youruser/somename.git or https://github.com/youruser/somename.git

If your local GIT repo is already set up, skips steps 2 and 3

Locally, at the root directory of your source, git init

Locally, add and commit what you want in your initial repo 
(for everything, 
git add . 
git commit -m 'initial commit comment'

to attach your remote repo with the name 'origin' (like cloning would do)
git remote add origin [URL From Step 1]

Execute git pull origin master to pull the remote branch so that they are in sync.
to push up your master branch (change master to something else for a different branch):
git push origin master

Nice, helpful, thanks.
Note to anyone who find this:
If you allowed initialize a README.md when you create the remote repo, you may have problems with git push origin master
I was able to git (ha! see what I did there?) around this with
git push --force origin master
(standard warnings that --force is highly destructive if you don't know what you're doing. I knew what I wanted this time.)

also, pro tip: if your git add . adds stuff you don't want, optionally use git rm to remove it.

Thanks for this, solved my problem. git push --force origin master is a good one to remember.

This is helpful. But on one occasion git pull origin master had refused with fatal: refusing to merge unrelated histories.

This explanation from StackOverflow helped with the problem. I have just used git pull origin master --allow-unrelated-histories to make it work.