Keep user-provided query filters first #9681

Job	Run time
analyze-actions	56s
check-codeql-versions	50s
analyze-javascript (ubuntu-22.04)	3m 54s
analyze-javascript (ubuntu-22.04, linked)	3m 53s
analyze-javascript (windows-2022)	6m 20s
analyze-javascript (windows-2022, linked)	6m 46s
analyze-javascript (windows-2025)	10m 12s
analyze-javascript (macos-14)	5m 9s
analyze-javascript (windows-2025, linked)	10m 38s
analyze-javascript (ubuntu-24.04, linked)	3m 44s
analyze-javascript (ubuntu-24.04)	3m 56s
analyze-javascript (macos-15, linked)	5m 18s
analyze-javascript (macos-15)	4m 58s
analyze-javascript (macos-14, linked)	4m 45s
analyze-javascript (macos-13, linked)	5m 15s
analyze-javascript (macos-13)	5m 56s
	1h 22m 30s

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