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This addresses the following issues:
#679
#677
#676
#630
Since upgrades now require you to unlock them, it's best to start a new vessel in the VAB, add a procedural avionics unit, right click on Show GUI, and purchase the available upgrades. (You just need to buy the last one in each category. Buying a higher level automatically purchases the ones below it - their cost is calculated into the cost of the higher level)
Crafts already in flight should be grandfathered in, but to build new vessels, you'll need to unlock the new tech.