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On the page you refer to, there is also a link to a plugin for calibre. As I did never use it, I cannot say anything about it (the same goes for the python script). As for annotations in kepub.epubs, I am having problems if there are several chapters in one (x)html. The TOC also only works correctly for those chapters that start at the beginning of a (x)html. But I did not yet much systematic testing, so I might be wrong.
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