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I'm using PRSAnnots (thanks!) and I like it for PDF files, but I'd too appreciate something similar for EPUBs (even if it was just for highlights and typed annotations; I understand why handwritten ones would be a problem). The difference is not just flexibility in font sizes and such, but also the reader performance. Some time ago I annotated a novel-sized text (and a fat novel at that), converted the file to PDF for that purpose, but it grew awfully slow with each new annotation so that in the end I had to split it in two and still had to wait several seconds for page turns. Luckily I don't need to do this too often.
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