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Just out of of curiosity: Which tools did you use to write the book? I know it's especially hard to create different file format (HTML, epub, PDF).

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HTML to write a book. PrinceXML to generate a PDF out of it. Then calibre for Mac to generate epub/mobi from HTML. I had to edit manually the output from calibre though.

Take a look at Scrivener[1], it might be a good fit for you.

[1] https://www.literatureandlatte.com/scrivener.php

Sigil is really good for tweaking your EPUBs http://sigil-ebook.com/

I use Pandoc to generate my EPUB and then Sigil to do a bit of tidying. Usually just the front matter etc.

Some other resources here, the slides from ConFoo are the most up to date http://rachelandrew.co.uk/presentations/css-books

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