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If we're talking about handwritten annotations, then I'm not sure if Epub even supports that. It's like trying to markup a webpage in manner that is portable, with all the challenges of no definite view given font style/size changes and varying screen sizes. It's not like PDF, where you can have a 100% author-intended view.
I really hope typed notes are supported. They can do something cute like a view with a post-it note stuck onto the page or something more practical like a paperclip at the top to designate a note. What would also be useful is highlighting, which is anchored from text position to text position and so can survive text style changes.
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