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Maybe some way to search for scribbles/highlights? Their locations are noted in the accompanying XML file, right? You wouldn't be able to search for content (more's the pity), but you could at least skip ahead to the next annotation.
Actually, maybe a highlight mechanism could allow you to search for markups, if the highlighting feature worked less like a scribble and more like text selection (on text-based PDFs). Sort of "bookmarks-lite", storing the marks in the associated XML document, to avoid having to rebuild the PDF every time. Could that be built into ipdf application?
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