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>>My partner is writing her PhD thesis [...] in Markdown.

Is she though? Markdown doesn't even have image captions or like support for citations.

I think you if you use something like pandoc it allows to at markups for centering and citation refs, which I'm guessing was used for .md => .tex to .pdf. But they will be rendered plain text in makrdown preview

MD => .tex to .pdf works with citations, but when I last used it I still had to write the tables in pure latex. With any even vaguely complex figures or subfigures, I had to resort to latex. The bulk of the text could be in MD, but I had to write non-trivial portions in latex.

[something interesting][JoBloggs1996]

[JoBloggs1996]: ISBN:12356789 “Whatever you want to be the title text of the link here”

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