It's smarts in the calibre e-book reader. The release notes when this was added to calibre are:
Quote:
Now when you click on a link to a footnote/endnote, the corresponding note is shown in a separate popup window, for convenient reference. Footnote links are recognized using the EPUB 3 footnote markup as well as some heuristics. Any superscript or subscript links are assumed to be footnote links. Any link that links to another file which in turn links back to the original link, is assumed to be an endnote.
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I don't know if it is worthwhile adding the epub3 markup as I don't know if any other ereader app that will use them.