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When they took off, the autonomous navigation wasn't even close to complete. They pushed that software once the two Rovers were already on Mars.

(I was working on the Rover team at the time)



I was gonna say the only reason I can think of to not load the software before it takes off is because it isn't finished yet. I'd imagine memory is pretty small/inexpensive even if it has to be specially fitted to get blasted across the solar system and work next to a nuclear power plant.




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