I know there's a project for interacting with and fragging processes in Doom, so why not navigate the filesystem the same way? Walk into subdirectories and find a bunch of Doom3-style PDAs that you can pick up and watch, listen to or read. Want to delete a file? Reach for the plasma rifle. Move? Drop the PDA in another room or just teleport it across the network.
For version 2.0 - combine them. Watch your processes as they read and write files. If one of them tries to open a file it shouldn't - frag the bastard! Open up a door to create a new room or make it a link to an existing room.