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Add pyrefly suppressions #2732

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Run time

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Job	Run time
build-test-linux	10m 23s
build-push-docker	1m 58s
build-osx	46s
test-windows	4m 39s
build-windows	2m 51s
test-osx	6m 36s
upload-installers	-1s
	27m 12s