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I'd like to be able to auto-number equations and label them so i can refer to them in the text. Math Jax provides a built-in way to do this by setting the autoNumber option to AMS. I realize that by adding this option to the universal template, existing code will be affected in such a way that some equations will get unduly auto-numbered. Is there any way to allow individual users to specify this option for their posts, either once and for all, or on a per-post level? If not, what is the recommended way to number equations and refer to them?

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You can use something like this $$ \sum_{k=1}^\infty\frac1{k^2}=\frac{\pi^2}{6}\tag{1}\label{mylabel} $$ and refer to it like $\eqref{mylabel}$

This can also be used in a normal link

Caveat: I believe that these labels need to be unique within a question.

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