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Add pyrefly suppressions #2759

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Run time

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Job	Run time
build-windows	2m 48s
test-osx	5m 37s
test-windows	4m 36s
build-test-linux	10m 40s
build-push-docker	1m 52s
build-osx	35s
upload-installers	-1s
	26m 7s