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Actually by your description it looks like that you push all your content to master branch while GitHub use an orphan branch named gh-pages to serve GitHub pages. Hey you can refer following blog post, It helped me just try it out, You'll also find it useful: Host Your Website using GitHub Pages


This would be about Git remotes. When you fork in GitHub, the "source" repo will be considered a remote for the new fork. When you clone to your machine, and push back to a new GitHub repo, although the commits (and hashes for them) will be the same, GitHub will not have that "remote" relationship, which means it won’t have the relationship to send a "pull ...

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