There is a simple (and ironic) method of acquiring all commands and files even if you have only just entered the Hacking system. In order to do this, first select "Hacking" from the main menu and load any saved game. It does not have to be a completed game save. You will be presented with the Hacking system interface. You can login as GUEST or FREEMIND if desired. Press the L1 + R1. This may require more than one attempt as it must be done exactly simultaneously. If done correctly, the command list will automatically update itself, and all files will be available. A message will read "All files unlocked", and also ironically states "Remember to remove this feature from the final version".
Alternately, enter the Hacking engine, then hold L1 + L2 + R1 + R2 at the command list to unlock everything in the list.