I have two separate HTML documents -- the first with the body of the text and superscripted note numbers, the second with the actual notes, numbered sequentially. I am looking for a way to merge the notes into the main document so that they will appear as linked footnotes or endnotes.

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Could you be more specific? Are you trying to make the superscripts link to the footnotes? Do you need to do something to them beyond pasting the endnotes into the first document? – digitxp Aug 15 '10 at 21:33
What I need is for the notes in the second file to be pasted as linked footnotes in the first file. Currently the only way I can do this is by manually copying each note separately and linking it. I'm wondering if there's a way to do it all at once. – Dave Aug 16 '10 at 0:42
If you have some example files, that'll be great. Throw them up somewhere. – crazysim Aug 16 '10 at 1:53
The material is not really something I can put in the public domain. I have a feeling that this is going to be more trouble than it's worth... the simplest way might actually be to do it manually. – Dave Aug 16 '10 at 15:02
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