Fix incremental syncs for prjs with submodules #475

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Run time

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Job	Run time
test (ubuntu-20.04, 3.6)	26s
test (ubuntu-20.04, 3.7)	50s
test (ubuntu-20.04, 3.8)	31s
test (ubuntu-20.04, 3.9)	40s
test (ubuntu-20.04, 3.10)	41s
test (ubuntu-20.04, 3.11)	39s
test (ubuntu-20.04, 3.12)	42s
test (macos-latest, 3.6)	5s
test (macos-latest, 3.7)	6s
test (macos-latest, 3.8)	3m 37s
test (macos-latest, 3.9)	4m 58s
test (macos-latest, 3.10)	54s
test (macos-latest, 3.11)	1m 1s
test (macos-latest, 3.12)	4m 47s
test (windows-latest, 3.6)	3m 28s
test (windows-latest, 3.7)	6h 0m 8s
test (windows-latest, 3.8)	6h 0m 8s
test (windows-latest, 3.9)	15m 4s
test (windows-latest, 3.10)	15m 17s
test (windows-latest, 3.11)	15m 6s
test (windows-latest, 3.12)	15m 11s
	13h 24m 19s