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When I had the NST I rooted it with Nook Manager, which is very, very nice. However I did not find any way to use Calibre for automatic collections. What I did was create collections in my file manager on my computer, using Calibre to save the books to the folders (so the series info would be included) and then drag and drop the files onto the Nook. It is more work then, say, using a Kobo, but it did work wonderfully well once loaded onto the device.
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