I have yet to download and use the beta version of Calibre, but it's on my list of things that I really want to do. So, I'm not sure how Calibre manages the inventory of books in this release.
What *I* want is a program that will create an index of the books -- exactly where they are in the file system. I do not want a program that moves them into a new location on the hard drive(s). I do not want them filed in folders by author since I have chosen to organize them by source. But an index would allow me to view by author *across the existing directories*. And that's a very good thing.