Hi Eric,
Sigil's now internal python 3 plugin system makes all of these points moot as it allows programmed access to all files in the epub.
In fact, creating a "commit" output plugin, would enable files to be added for a revision control system quite easily as well. And using an "update" plugin, you could easily load in any changes made outside of Sigil via some other means.
So all and all, everything you want to do can be done by writing your own python 3 plugins and need not impact current Sigil at all.
Hope this helps,
KevinH
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