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I think if you talk to Hadrien about this he would have a lot to say. Hadrien runs the Feedbooks site and is a frequent poster here at MobileRead. I'm not sure whether he stores the source as XML, HTML, XHTML, or some variant of one of these.
I'm still trying to learn the various book-making programs and I'm definitely interested in learning how to produce the best input source file to make sure that what comes out of each conversion tool is the highest quality book. Maybe some of the more experienced book makers can offer some wisdom here.
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