I'd like to retain my directory structure that has been introduced by BibDesk:
It is useful as directories with 500+ documents are rarely comfortable to browse.
My idea is the following: Use the same pattern mechanism as for BibTeX-keys. If the corresponding directory does not exist during copy or moving, just create it.
Currently order in the file directory is strongly linked to the BibTeX key in Jabref. Unfortunately that key cannot always be easily changed without breaking other kind of software. So it would be very helpful if JabRef could provide better means to structure the paper repository.