You can use git. Simply use FolderIn and FolderOut plugins to write/load files to/from the repo. We do this with our User Guides for Sigil and PageEdit.
So the workflow is to use FolderIn to load the epub from a github repo. Make any changes you need in Sigil using its editors or OpenWith and your favourite editors and when ready use FolderOut to write the files to the repo and do you commits if you desire.
In addition, Sigil's Checkpoint feature already creates a github repo to store files in in case reversions are needed. That internal github repo is stored in the Sigil Preferences directory. It can be accessed and manipulated like any git repo. Making a Checkpoint creates a tagged commit to this internal github repo.
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