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Just for completeness attached is a basic mathjax plugin and a sample epub file it works on. I only tested it on my machine, so it may be that it needs more fonts in the bundle. Also in a production quality plugin you shoud scan for a
<meta name="calibre-enable-mathjax" value="input/TeX" />
tag and only load mathjax if it is present, with the correct input filter as per the value. Zipped up, the plugin is only 2.7MB, so if you can refine it a bit and test it on a few more machines, I might be willing to add it to calibre.
NOTE that you have to be running calibre from trunk for this plugin to work and you may have trouble with file paths on windows, I only tested it on linux.
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