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The issue, to be more specific, is that on the Kindle Touch the collections data is stored on a hidden internal partition, not on the "drive" that mounts when you connect the Kindle to your PC, hence there's no way for any Calibre plugin to get at that data in order to modify it.
The indications are that the Paperwhite uses the same firmware as the Kindle Touch, so one might reasonably expect that the same issue will exist on the PW. We'll know in a few weeks when people get their hands on the device.
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