[zeveb]

Interestingly (and IMHO unsurprisingly) org-mode does this correctly[0]. Footnotes are identified by 'fn:' and a unique token (of course, numbers are unique tokens); they can be easily inserted with C-c C-x f, and can also be renumbered — including normalisation.

I reminded of this discussion from a week and a half ago: https://news.ycombinator.com/item?id=15321850

IMHO org-mode is, as the original author puts it, 'one of the most reasonable markup languages to use for text.' I suggest that rather than trying to improve Markdown, folks just use org-mode instead.

[0] http://orgmode.org/manual/Footnotes.html

[thomastjeffery]

I still think that org-mode and Markdown have quite different targets.

org-mode seeks to be organized and manipulable, whereas Markdown seeks to be readable, and parsable.