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fglaysher
This looks to do what you want with regarding to copying books to the reader.
It is a file manager tool for the reader. It is NOT an ebook library management software, but it CAN create collections based on sub directories.
You can use either the program or windows explorer to copy your folders of ebooks to the appropriate directory on the reader (database/media/books). If you have separate folders inside of this directory, these can easily be turned into collections by the program.
It is a very handy piece of software when one doesn't want to use Calibre or the Sony ebook library software to transfer books.