I wanted to do something like

>! \begin{align}
    >! x &= 42
    >! \end{align}

(Unfortunately even this code block is badly formated! Why is it indented this way?)

but the result is just poor

! \begin{align} >! x &= 42 >! \end{align}

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A work around is to put all the math on one "line".

>! \begin{align} x &= 42 \end{align}


\begin{align} x &= 42 \end{align}

I think the reason is that to solve other bugs, once you enter a math environment the MarkDown stop getting processed. So the >! that appears before and after x&= 42 are considered by the software as part of the math environment, and not part of MarkDown.

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