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The limit cited by Toxaris is also something to take into consideration as you place any footnotes, or links whose destination might either within the file or in another one.
Especially for the millions of machines already out there, repeated jumps out of the open file can take time, time which might be annoying to the reader and ameliorated to some extent by linking within the file whenever it makes sense. For instance, footnotes that link to a section at the end of the chapter instead of another file at the end of the book.
This may pose other issues, such as how do you skip over them easily, etc. But it is worthy of some thought nonetheless.
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