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Kris - I think Moon+ does something a little different. It will use the EPUB3 extension if it's there but I think it also will use a heuristic on EPUB2 files.
If I had to guess, they probably look at links (a href=) and see if there is a link back within the same paragraph or div section of the linked text. If so, it assumes that's a footnote and displays the text (sans link) within a pop-up.
Seems like something that could be doable.
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