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I read that kind of book on ipad or my Windows 8 tablet. No problem there to annotate (I use PDF Expert on ipad and Drawboard PDF on Windows 8). When I convert the book to PDF using calibre, metadata and cover are all included. For existing files, the new option "Embed metadata" can be used (or sending it to device or a folder does the same). The only manual step that might be needed is if you want to add a cover to a book that is already in PDF format.
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