The ship has a strong suggestion of organic technology, and "feeds" off energy. It's possible that it can create much or all of what it needs so long as it has raw materials to work with. How far down do those raw materials go? All the way down to being able to convert energy to matter?

This is giving me an eerie thought. The question of "What happened to the Liberator's first crew?" has come up from time to time. Given what we saw of the System, it would value the ship over any crew. Could the DSV have broken down its own crew for material after it was damaged? After bonding with Jenna, obviously some reprogramming was done of the computer via her brain; this might have included her values of human life above the ship.