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pass in logger to agent-run.ts #3598

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Run time

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Job	Run time
build-and-check	2m 39s
test-integration-npm-app	29s
test-integration-common	29s
test-.agents	28s
test-integration-.agents	30s
test-backend	47s
test-common	32s
test-npm-app	33s
test-integration-backend	31s
	6m 58s