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If you have a decent ereader app or Kobo eink, reading and taking notes on epub is FAR better than PDF. Annotations plugin or Kobo Utilities can read Kobo annotations back.
Also you can edit the config on a Kobo so an extra context menu item is on epubs and then export a plain text file with date, location, highlight and note for each annotation.
PDFs are really just for publishing or printing or "book replicas" on a big screen.
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