Make program-changing updates atomic (#191) #407

Job	Run time
repository-contract	25s
test-windows (3)	1m 38s
test-windows (5)	2m 4s
test (ubuntu-latest)	23s
test (macos-latest)	52s
test-windows (4)	1m 19s
component-control-program-compiler	13s
component-surface-parity	18s
component-kernel-mechanism	9s
component-plant-integration	22s
component-standard-flow	10s
test-windows (2)	1m 6s
component-extension-conformance	13s
test-windows (1)	47s
test-windows (0)	1m 8s
	11m 7s

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