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Yep, no way to do that unfortunately.
The Goodreader app has it's own file system, so you could recreate it on there, but from the little I've played around with, that would be very clunky to do with a lot of PDFs in a lot of different folders compared to just having a file system so you could just drag it over and keep the file structure in tact.
I doubt that's something Apple will add either--at best they'll put a central file location to through all your PDFs and other docs with no way (at least on a non-jailbroken iPad) to see the file structure). But at least then multiple Apps could access it.
Otherwise, all you (and I since that's a deal breaker for me) is wait and see what other tablets come out.
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