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Thanks to @concentrateddon for this tutorial!
Create an SSH key on your server. Instructions at https://help.github.com/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/.
Add the SSH key to your GitHub account (which can access the private repo). https://help.github.com/articles/adding-a-new-ssh-key-to-your-github-account/
Change to your repo folder.
Run git remote add origin git@github.com:repouser/reponame to add the repo.
Run an initial git pull origin master and git push origin master.
Ensure origin is added as the repo in the jingo config YAML.