I've recently been experimenting with drafting conference papers using markdown and converting them to latex with pandoc. For this to me worthwhile -- for me -- it's important that I can produce an almost-final version using only a conference-specific template file. Ideally, I'd like to be able to use "./confHelper.sh myMarkdown.txt myConferencePaper.pdf" to get a submission-ready result.

There are a few issues I can live with, namely lack of an obvious markdown replacement for the different flavors of \cite{} (e.g., \citeA, \citeNP) as well as the need to update table and figure number references by hand, but there is one blocker:

My papers tend to include tables, and conferences often use a two-column environment. I've tried a couple of workarounds, like using "\renewenvironment" in my template file to replace longtables with tables-in-tabulars, but that breaks my captions. Can anyone recommend a good solution?