Independently of the OS used, this limiation of the physical world was built into most file systems as tree structure (barring symbolic links on UNIX which becomes quite messy after a while). If I am not mistaken there were some attempts to use a database of some sort and tagging for meta data which then allows building graphs, or views in whatever way the user wants to cut through data. It did not catch on, perhaps because we still want to be able to "move" branches of file system trees around with the reassuring feeling of control over one's hard disk.