3DAvenue have posted a guide to the 'hacking' mode in Enter The Matrix for the PC. Included is a thorough outline of all the steps to completing this mode.
"Take note, the commands in this hacking system are not identical to your typical DOS commands. The structure itself revolves around the 'DIR' command, which lists directories and even executes programs when needed. You basically don't move at all within the system, so the DOS 'CD' command is non existent. What happens is you list directories with the 'DIR' command, get the path to the desired programs, then execute it. It is a little time consuming at times but relatively easy to get used to."