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@cliotropic I think Pandoc template would allow you to do away with markdown environment altogether. Put everything now in the environment+
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@cliotropic Pandoc allows raw TeX in input, though it treats anything inside an environment as TeX johnmacfarlane.net/pandoc/README.html#raw-tex
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@cliotropic $body$ and then use that new LaTeX file as the template in a Pandoc command. May still need tweaks but that's the basic approach