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If you compose in Word, with its comprehensive footnote capabilities, a Calibre conversion to EPUB does a pretty good job of constructing functional links.
But foot/end notes are a blasted nuisance when reading an eBook. I try to confine them to academic references - necessary for completeness, but rarely actually read! Anything else that is worth reading can go in the text flow. We should design eBooks, not facsimiles of printed ones. (I understand perfectly that our customers may not agree :-)
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