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Keep in mind that the mimetype file must be uncompressed in the zip archive as well as first. In my experience, there's very few "standard" archiving programs that give you enough control to guarantee everything gets put in the archive correctly (without jumping through a variety of hoops). It's best to use something specifically designed for ePubs. I've never used the one Doitsu mentioned, but it looks like it would do the trick. There's also an applescript floating around here somewhere that will do the job for OS X users.
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