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Originally Posted by kovidgoyal
There is nothing hidden about the footnotes page. It is the aside element that would need to be hidden. And in fact, even if calibre output epub 3, footnotes would not be put in aside elements as that is just less broadly compatible and offers no actual benefits.
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The current iBooks specs require footnotes as asides. The benefit: it easier to create and update footnotes when dealing with raw HTML.
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About the only thing that would change when outputting for epub3 is the footnotes would have the added epub 3 specific epub:type annotation -- which is really not required for any halfway decent epub reading software. Detecting footnotes using heuristics works great in most readers.
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Heuristic detection is not as reliable as semantic/valid code. And platforms like iBooks have strict requirements.
EPUB 3 is the new standard. I don't understand why you would resist making your software compatible with the modern specifications.