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He is using a hack to store the GitHub pages. That this is even possible is due to the awesomeness of git. Since it is a hack, you have to be careful what you're doing. He should have done all the gh-pages stuff in a separate clone. The GitHub instructions where he pasted the branch creation commands from also tells you to do just that. Keep the pages branch in a clone of the repo inside the repo, just in a folder called 'docs'. You'll never have to mess with these branches, as you can generate docs, commit and push from a Makefile.