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Specifically in the case of complex mechanical space vehicles (e.g. rovers, landers), do we just refuel and send the battle tested and carefully fine tuned prototype on the mission, or do we take the risk of trying to make a near perfect replica and send it after basic lab testing?
Did the actual Curiosity rove Earth before Mars?
Normally you build 2 prototypes of a spacecraft; one is called the engineering prototype (or model), and the other one is called the protoflight.
Both must be identical, but the engineering model is normally reassembled several times during development and testing, and will stay on earth as a faithful reference of the flight model.
The protoflight must be handled with extreme care (to avoid any damaging of connectors, or ageing of mechanical components). It is the protoflight that must undergo all final qualification tests (thermal-vacuum, vibration, acoustic, outgassing).
Note that for beasts such as telecommunications satellites, there is no budget for building a complete engineering model. These are integrated based on already tested and reliable components (avionics, propulsion, solar panels, transponders, antennas, etc.).
Curiosity drove in a clean room on Earth, but it never got dirty until it got to Mars.
Different engineering models were used to test those aspects of the rover in the dirty outdoor Mars Yard at JPL.
In general the actual flight vehicles are treated somewhat schizophrenically, handled very gently and with great care in clean rooms, then beaten all to hell in vibration and shock testing and frozen and heated in thermal vacuum chambers.
Generally the "battle-tested" engineering model is not "fine tuned". It is hay-wired, jury-rigged, and duct-taped as needed to get it to work. The flight hardware implements changes learned from the engineering model as well as for other reasons, e.g. changes in interfaces, and also it has all flight components where there may have been compromises in the components used in the engineering model. It is a very rare, perhaps mythical, engineering model that can be flown.
In the context of Interplanetary contamination, any craft that leaves earth for an interplanetary mission from most countries falls under the Planetary protection section of the Outer Space treaty.
The COSPAR defines categories within mission targets and indicates the precautions to take.
Mars is in category III/IV, and therefore requires the craft to be perfectly clean. The decontamination procedure is described on the planetary protection page. It includes clean room assembly and components sterilization before assembly. I am pretty sure this rules out the possibility for the protoflight to make a test run outside the clean room before takeoff.
