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In the case of MobiPocket, what is holding folder support back is that Windows MobiPocket Reader does not "do" folders. All the files it lists are from a single directory (usually My Documents\My eBooks\Mobipocket). If you open (import) an ebook from a different directory, the very first thing that Windows MR does is copy it into the Mobipocket folder.
So, if you want Windows MR to manage your ebook device it can't use folders. This is an issue already on the iLiad, where the Books/Mobipocket folder has to be treated differently to all other folders in order to allow Windows MR to sync ebooks in this folder. Since the iLiad uses its "contentlister" for file navigation, you can use folders with ebooks on the iLiad - but only by avoiding Windows MR ebook synchronization.
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