tufte-markdown
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Markdown content in html block tags is not converted
By convention markdown syntax inside block elements is not processed. And remark respects those conventions (see rehypejs/rehype-raw#8).
A number of items such as <footer> inside blockquotes, epigraphs etc. do not work as expected when they contain markdown (for some reason beyond my understanding markdown inside <figure> tag works).
Even in your own tests some items are not being rendered correctly. See for example, output for section.md in tests:
> [It is] notable that the Feynman lectures (3 volumes) write about all of
> physics in 1800 pages, using only 2 levels of hierarchical headings: chapters
> and A-level heads in the text. It also uses the methodology of
> <em>sentences</em> which then cumulate sequentially into <em>paragraphs</em>,
> rather than the grunts of bullet points. Undergraduate Caltech physics is very
> complicated material, but it didn't require an elaborate hierarchy to
> organize.
>
> <footer>
> [Edward Tufte, forum post, 'Book design: advice and examples' thread][quote-cite]
> </footer>
[quote-cite]: http://www.edwardtufte.com/bboard/q-and-a-fetch-msg?msg_id=0000hB
is rendered as:
<blockquote>
<p>[It is] notable that the Feynman lectures (3 volumes) write about all of
physics in 1800 pages, using only 2 levels of hierarchical headings: chapters
and A-level heads in the text. It also uses the methodology of
<em>sentences</em> which then cumulate sequentially into <em>paragraphs</em>,
rather than the grunts of bullet points. Undergraduate Caltech physics is very
complicated material, but it didn’t require an elaborate hierarchy to
organize.</p>
<footer>
[Edward Tufte, forum post, 'Book design: advice and examples' thread][quote-cite]
</footer>
</blockquote>
Notice that the footer remains unprocessed!
We either need to change conventions in conversation with @jez or hope that remark supports non-standard syntax through a plugin.