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I have had (setq org-footnote-auto-label 'plain) in my init.el to get footnote labels of the form[1]. But after updating to version 9, I see this option is no longer supported? Does this really mean that there is no longer any way to get plain footnotes?? (Surely there is no reason to prefer[fn:1] in documents that have no chance of containing false positives? which is true of all my documents.)

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It's true, that style of footnote no longer works. ORG-NEWS says:

Footnotes

[1]-like constructs are not valid footnotes

Using [1] as a footnote was already discouraged in the manual, since it introduced too many false-positives in many Org documents. These constructs are now unsupported.

If you used [N] in some of your documents, consider turning them into [fn:N].

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