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Well, except LaTeX probably isn't the best base format to write in -- Pandoc's LaTeX parser isn't very good, it doesn't parse (from a quick check) any of the papers I've written. They've tried hard, but I think it's a losing battle, particularly once people start using a large range of packages.

That's not surprising -- it's basically impossible to "parse" LaTeX, as it's defined by execution.

iirc pandoc's markdown provides the set of functionality that one is capable of transforming back and forth. So as long as you stay within those formatting confines, you are set.

This works for everything except table notes a la ```threeparttable```

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