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the only alternatives I know of right now is to manage the Collections through another device and then import them over to the new Touch.
You are correct in that the Touch is doing something different. Nobody has been able to find a Collections file being created/changed in the visible file system. I'm guessing we might get somewhere if and when somebody manages to jailbreak it. Until then, none of the old method (Calibre Plug-In and the various 3rd party programs) are going to work.
I wish I had better news.
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