Keep user-provided query filters first #9683

Job	Run time
analyze-actions	58s
check-codeql-versions	51s
analyze-javascript (ubuntu-22.04)	4m 3s
analyze-javascript (ubuntu-22.04, linked)	3m 54s
analyze-javascript (ubuntu-24.04, linked)	3m 52s
analyze-javascript (windows-2022)	6m 27s
analyze-javascript (ubuntu-24.04)	3m 52s
analyze-javascript (windows-2025)	7m 21s
analyze-javascript (macos-14)	4m 52s
analyze-javascript (windows-2022, linked)	6m 35s
analyze-javascript (macos-13, linked)	5m 45s
analyze-javascript (macos-15, linked)	7m 49s
analyze-javascript (macos-15)	5m 18s
analyze-javascript (macos-13)	7m 16s
analyze-javascript (macos-14, linked)	4m 26s
analyze-javascript (windows-2025, linked)	6m 12s
	1h 19m 31s

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