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chore: migrate use of deprecated kustomize features #473

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Job	Run time
Small tests	4m 38s
Build binaries	3m 42s
End-to-End Tests (v1.28.7)	5m 32s
End-to-End Tests (v1.29.2)	5m 29s
End-to-End Tests (v1.30.0)	5m 28s
	24m 49s