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If you're trying to do some custom auto-editing on your epubs then there's nothing to stop you continuing to use the 'old Tweak' method which is still an available option under the new name of 'Unpack Book'.
Alternatively, as you know Python, you could create your own plugin utilising calibre's EpubContainer class to do the unpacking and packing (plus other useful utilities) with your own code sitting in the middle.
Edit: Damn, too slow with the Unpack suggestion!
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