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One thing I'm seeing that's hard to get used to is the folder organization. Calibre is dumping everything in one top level folder, organized by author name. My personal system for folders is hierarchical: genre->author->series - I'm sure others have their own methods. I'd like to see more flexibility on Calibre's part here.
On the technical side, I've had zero problems importing mobi-formatted books from my collection. I'm still scratching my head regarding .oebzip books.
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