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for the footnotes / endnotes problem, i've found that for reasonably short footnotes the solution i prefer is to place them immediately after the paragraph which references them, in the flow of the text, setting them apart with a smaller font size, italics, indent, etc.
i find this less disruptive to my reading flow, more like footnotes available in the same page (which i also prefer to endnotes in paper books), than having to jump all the way to the end of the text for each note. if you don't want to read the notes you can easily skip over them, especially if they are properly formatted to be easy to identify.
it also has the advantage of being very easy to implement regardless of the format, and completely reflowable.
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