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phossler - I do notes, citations, index etc in Word, which has tools to do all that. IIRC OO Writer has similar facilities to Word. Jutoh has some too. Calibre does a pretty good job of converting a DOCX and maintaining all the links etc.
Its hard to keep track of chapter (foot) and endnote numbering manually and a multilevel index is even harder. In a book with lots of notes, references and a solid index there's often almost as much markup as there is text
BR