BaseTools/CodeQl: Give preference to Plugin settings

[abdattar]

For the CodeQl AuditOnly flag,
prioritize Plugin settings over global settings.

This patch adjusts the logic for the global AuditOnly setting, placing it before the Plugin setting code.
This ensures that Plugin settings take precedence over global settings.

Cc: Sean Brogan [email protected]
Cc: Joey Vagedes [email protected]
Cc: Michael D Kinney [email protected]
Cc: Liming Gao [email protected]

Description

This patch adjusts the logic for the global AuditOnly setting, placing it before the Plugin setting code.
This ensures that Plugin settings take precedence over global settings.

• Breaking change?
  • Breaking change - Does this PR cause a break in build or boot behavior?
  • Examples: Does it add a new library class or move a module to a different repo.
• Impacts security?
  • Security - Does this PR have a direct security impact?
  • Examples: Crypto algorithm change or buffer overflow fix.
• Includes tests?
  • Tests - Does this PR include any explicit test code?
  • Examples: Unit tests or integration tests.

How This Was Tested

Tested with stuart_ci_build locally on AMD platforms.

Integration Instructions

N/A

[tianocore-assign-reviewers]

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Non-collaborators requested:

• @Javagedes

Attn Admins:

• @jljusten
• @bcran
• @lgao4
• @mdkinney
• @vincent-j-zimmer
• @jkmathews
• @miki-intel-work

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