My knowledge about Java is several years out of date, but I know that Java couldn't detect symbolic links at one stage. For a backup application, this sort of thing is useful. Similarly, think of all the other whacky platform specific file things, that probably aren't in the Java view of the world (resource forks in OSX, alternative streams in NFS, device files, named pipes, sockets, etc). I can imagine that writing a backup application that can't see past the abstraction chosen by Java would cause a lot of trouble.