md files that aren’t hundreds of columns wide. As a side benefit, you can drop the -wrap=preserve flag and end up with. Rmd files like me, all you need to do is add +footnotes to the end of of the variant: gfm line in your YAML header. If you’re running pandoc from the command line all you need to do is add -t gfm+footnotes to your pandoc command. Since standard markdown natively supports footnotes when used as an output format, I didn’t even think to look into manually enabling them for GitHub-Flavored Markdown. The documentation notes that you can add extensions to output formats they don’t normally support. Update: John MacFarlane helpfully pointed out that this is all incredibly unnecessary because pandoc makes it easy to add support for footnotes to GitHub-Flavored Markdown.
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