Footnotes/Endnotes to ePub

The basic problem here is that EPUB is extremely dependent on the reader. There is no "fixed" way to render pages, much less details like footnotes and endnotes and their links; each reader applies its own (developer's) notions, with little standardization. The best you can do is use a vanilla, standards-compliant reader like Calibre and work around the more general constrictions of the format.

End notes are a perpetual headache, often broken or breaking EPUB export from ID. This problem is multiplied if the source, with endnotes, was originally imported from Word, as it often is. But let's leave endnotes out of it, as they are not really a good alternate solution to footnotes.

The way footnotes are handled is, again, more dependent on the reader capabilities and settings than anything else. Footnoter are just a bit of linked text; how the reader chooses to handle the link and presentation of that 'detached' text is up to its design and settings.

The problem is that without pages, you don't have page footers, and without page footers, you don't have any place to put footnotes. (Reflowable EPUB has no pages — that is, it has one page of book length — and the "pagination" you see is purely an arbitrary artifact of how the reader chooses to present the content. In theory, readers could render footnotes in a print-like manner, as separated text at the bottom of a virtual page, but for some reason that's considered too complicated and few if any readers offer that options. So the "solution" is to group footnotes somewhere, at the end of each section or at the end of the book, and use hyperllinks to either jump to them or back, or use the "popup" method, which is clumsy at best.

My solution, until better technology comes along, is to simply embed the footnotes in the running text flow. Nothing fancy, no links, no jumps, no pop-ups, no irritating link formatting that can't be overridden... just put the note after the source paragraph. If you format it correctly, it' s no more obtrusive than notes at the bottom of a printed page:

It's imperfect, but then, even after twenty years, so are e-books as a whole. 😛