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I believe that direct-to-PDF conversion will internally use --standalone. It looks like any header-includes get duplicated when the output uses --standalone (even for markdown to markdown or markdown to latex). This can also happen under some conditions just using pandoc:
According to jgm/pandoc#4311, pandoc is performing as expected (even if it seems counterintuitive at times), so this will have to be handled within codebraid.
…or Pandoc Markdown to Pandoc Markdown conversions--this prevents includes from being included prematurely and makes roundtrip conversions behave as expected (#20)
I get an error when I try to convert from markdown to pdf with latex commands defined in header-includes in font matter.
File
test.md
Command run
Error
I don't get any error if I try to convert from markdown to markdown with codebraid or when I convert from markdown to pdf directly with pandoc :
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