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Not all of them, but it's pretty spotty. In some places it's been replaced by $ $ for inline equation rendering, but it doesn't seem consistent. I've been looking at the raw html of the original. There are also a lot of name tags for the index. If we're not doing an index, we probably don't need them, but they're probably harmless if we add some with copy/paste. It might have been easier to start from the html version, but we'll lose a lot of work if we try that now.
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