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Late to the party here, but after reading your requirement for folders and organization capabilities, I have to throw in a plug for Calibre Companion. It's almost like having Calibre on your device, and it handles grouping, series, etc., flawlessly. It's also great if you like to try different readers. No need to learn each reader's file storage requirements. You simply pick the book you want to read, then select the reader to use, and away you go. Actively supported, and well worth the couple of bucks to get it.
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