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In the case of the stuff I have up on there, they're just all in one html files with baked in css in style tags and js in script tags. The repo for the actual sub-domain is completely public if you wanted to look at anything, there are almost certainly better examples for the host floating around in the form of manual sites etc. if you can find them.
Functionally github.io just presents whatever you throw into the repository as the root directory of a site, github themselves host a very good, basic outline of how to set up a site on github.io.