On an epub program I wrote a long time ago, I made it all automatic. The endnote was placed right in the text surrounded with ##endnote##, including any html markup. The endnotes were processed all in one go, after the book was finished. It numbered the notes, starting at 1 for each file, generated the forward and back id's, and separated the endnotes into files: "Notes for [title of file], created the files, added them to the manifest, etc., etc. It was about the only part of the program that worked consistently well, and was sure a timesaver if you had a lot of notes.
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