The easiest way is to set the Packages/ directory as the base for your repository, since all settings (except for the license), Package Management plugins, themes, etc. are in subfolders. I have a license in my inbox, so I can find it anywhere.
As a warning, just make sure that you do not have any confidential information in any of your settings, such as server passwords, etc., because if you have not paid for a private Github repository, any user can see your settings.
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