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When I end up with an ebook where the formatting is totally cheesed, I usually end up converting it to text, and then writing a quick PERL or PHP script to re-format it for me. I had a book recently (Brother Odd I believe) which had the hard line-breaks, and page numbers and such throughout the text. Seven lines of scripting completely fixed the formatting including re-joining paragraphs which spanned page breaks, indenting paragraphs, fixing chapter marks, etc. Doing that sort of thing isn't too difficult once you get the hang of it. Since I run into that infrequently I typically just modify the script for the book instead of writing a full blown tool to handle a myriad of formatting issues.
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