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I use calibre and have never felt the need to attempt to modify how it arranges books in folders. Organization on a Sony reader is handled with Collections, which are just lists of your books. When sending books to the device, by default they are assigned to Collections based on what you've entered in the Tags and Series columns in calibre. You can modify how calibre builds and names the Collections, giving you a lot of flexibility. You can experiment with how Collections are built without modifying how the books are actually arranged in storage.
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