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I've had a few recent ones that even required multiple trips thru Calibre (and I wish you could turn off the "orig_xxx" creation, as it keeps wanting to run the conversion from that, if it exists), in order to do cleanup. One was numbered on every single line (so, removing line numbers, extra hard returns, formatting paragraphs, dumping header/footers, fixing chapters, adding hard new page, etc. More than could be done with the limit of 3 REGEX per conversion in Calibre. In the end, though, I have a nice, clean file (I did have to cheat a bit and do some cut/paste in the files inside the epub, this was one stubbornly badly formatted galley).
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