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I love pandoc too, and there are three things that would make me absolutely giddy if they were added:

1) Proper reference support. In LaTeX you can use things like \ref{fig:foo} to insert autonumbers for things like Figure X and Table Y. (Which is awesome, because if you move a figure, you don't have to change all of your numbers around.) There's no Pandoc markdown equivalent, so this gets lost if I convert to e.g. HTML. I have to work around this with a script that looks for this LaTeX snippet and does the counters before passing to Pandoc.

2) Better footnote output for LaTeX. Right now, if you use a [^foo] footnote mark twice, you will get two \footnote{}'s in your LaTeX (and therefore a repeated footnote message in your output) instead of a \footnotemark for the second one.

3) Better metadata. Both Jekyll and MMD are so much more flexible about the metadata you add at the top of a document; Pandoc seems to think the only items I'll ever need are author, title, and date. If I could only add things like addresses, enclosures, salutation lines, and extra variables my templates could adjust to, I could produce more sensible templates for formats like business letters.

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