Well just to be clear, you do still have the CIWS, you just have to target it manually.
I don't have time to finish my LAN testing right now, but so far it looks like even with multiple attack vectors the CIWS can defeat a 16 missile salvo on automatic. It was a close call though. I'll try to look into this a little more tonight after I figure out the precise limitations of the missile seeker to get the best possible separation.
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