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This is a great example of what I keep reminding people of: In calibre, a book isn't a file. A book is an abstract object that consists of zero or more files of content plus calibre's stored metadata. The book isn't the pdf file, or the html file, or the mobi file, or any other file; they're just formats the book contents exist in. So as chaley says, you just have to add whatever formats -- whatever specific files -- you want to the abstraction called a book.
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