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Also, yes - if you kill a Codex, you will get the Codex Brain, but can't do anything with it until the objective comes up as normal.
CharTemplate.SpawnRequirements.RequiredObjectives.AddItem('T1_M2_HackACaptain');
Updated with avatars too at FL 18 and 20, edit encounterlists if you don't want them—I'd rather not make a separate mod for such a similar adjustment to the game.