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Use `applyAnalysisKindConfig` in `loadUserConfig` #16421

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Job	Run time
Other checks	20s
Unit Tests (ubuntu-latest, 24)	1m 1s
Unit Tests (ubuntu-latest, 20)	1m 4s
Unit Tests (macos-latest, 20)	1m 24s
Unit Tests (windows-latest, 24)	1m 22s
Unit Tests (windows-latest, 20)	1m 28s
Unit Tests (macos-latest, 24)	1m 2s
Post repo size comment	-1s
	7m 40s