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Foliate supports exports in various formats, one of those being Markdown. A less sophisticated method could be manually exporting the annotations for each e-book and run HPI on the markdown exports ?
https://johnfactotum.github.io/foliate/
Seems like a nice app for reading epubs, apparently epub annotation feature is hard to find
https://github.com/johnfactotum/foliate/wiki#how-are-notes-and-bookmarks-stored
/cc @bepolymathe
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