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Org-capture appends its notes to the bottom of my notes.org file. But this places them below the * Footnotes headline, which is problematic. Is there some way to configure org-capture so new notes are sent above the * Footnotes headline?

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The best option here would be to configure your capture templates to add entries under a certain heading (e.g Tasks or Notes). That way the other content of the target file is not affected. See the examples in the Org manual:

("t" "Todo" entry (file+headline "~/org/gtd.org" "Tasks")
         "* TODO %?\n  %i\n  %a")

Another option would be to customize org-reverse-note-order so that new entries are added at the top of the file rather than the end.

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