[chaoxu]

Have you tried Quarto? It should tick everything in your box (except MathML, but hey that might work too since Quarto is built on pandoc)

[countrymile]

+1 for quarto, i wrote my thesis in rmarkdown which flipped easily between latex and html output, with a bibtex referencing system. It also allowed you to inline latex for more complex outputs. And inlining calculated tables and charts meant i could keep my writing and code together. Quarto is the successor.

[periheli0n]

Thanks for the pointer, that looks interesting. Especially because it is open source!

I see it supports Jupyter notebook. Math support in those isn’t too bad at all, so it might just work for many cases.