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I also can't remove headers and footers. They get highlighted in the regex wizard just fine, but they are never removed. It may be that I'm trying to use paragraph tags, which folks are saying don't work properly, but there is no point trying to remove some books' footers without </p> because if it's just the page number in the footer or book title in the header, the </p> is the only thing differentiating it from any other number/title in the book.
For now I am using Sigil to edit the epub output from Calibre and the regex find/replace works quite well in Sigil. However, Sigil is extremely slow at processing and making changes, so it'd be much better if it could be fixed in Calibre. =)
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