The System Files were the histories and guides written by the Terradonians and passed down the generations by the Alzarians.
Guides
The majority of the System Files listed the details of the starliner. They lacked the key information on how to pilot the ship as the pages referring to take off were damaged when the starliner crashed into Alzarius. The Fourth Doctor showed them how to operate this mechanism. The Deciders declared that the System Files were so extensive they would allow them to take apart and rebuild the entire ship. The civilians were unaware of their inabiltiy to ever go anywhere and that they worked in vain. (TV: Full Circle)
Histories
Some of the System Files were the histories of the Alzarians left to each head Decider as he was appointed. They contained information on the progression of the Marshmen into Alzarians as well as the history of Mistfall. These were never discussed and the head Decider was left to bear the secrets alone. Both Decider Draith and Nefred, however, hinted at what they contained. They were eventually revealed when the Marshmen attacked the starliner. (TV: Full Circle)