I'm curious as to what sort of support is planned for site-specific formatting abilities in the SE 2.0 sites. On Math Overflow, for example, they have math formatting with LaTeX-style markup. If the Linguistics proposal on Area51 succeeds, it would benefit greatly from some way to represent IPA, perhaps via X-SAMPA. Even something like the Cooking site could potentially benefit from markup for recipes. How will this be handled?
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We're working on server side extensions, which will be able to operate on both the raw Markdown and the generated HTML. Our test cases will be rewriting some new common syntax for referring to questions and tags, and perhaps some additional escaping for some LaTeX edge cases*.
*This user is a bit confused about how the Markdown -> HTML -> MathJax chain works, but the problem is real.