Update CLI config test to account for overlay db changes on PRs

[mbg]

Updates the codescanning-config-cli.yml workflow to account for the case where overlay analysis is enabled and the workflow runs for a pull request.

Risk assessment

For internal use only. Please select the risk level of this change:

• Low risk: Changes are fully under feature flags, or have been fully tested and validated in pre-production environments and are highly observable, or are documentation or test only.

Which use cases does this change impact?

Environments:

• Testing/None - This change does not impact any CodeQL workflows in production.

How did/will you validate this change?

CI.

If something goes wrong after this change is released, what are the mitigation and rollback strategies?

• Rollback - Change can only be disabled by rolling back the release or releasing a new version with a fix.

How will you know if something goes wrong after this change is released?

N/A

Are there any special considerations for merging or releasing this change?

• No special considerations - This change can be merged at any time.

Merge / deployment checklist

• Confirm this change is backwards compatible with existing workflows.
• Consider adding a changelog entry for this change.
• Confirm the readme and docs have been updated if necessary.

[Copilot]

Pull request overview

This PR updates the codescanning-config-cli.yml workflow to handle overlay analysis behavior on pull requests. The test now has separate variants for PR and non-PR events, since overlay analysis changes the CLI configuration on PRs by adding query filters.

• Splits the "Empty file" test into two conditional variants based on event type
• Adds expected query-filters configuration for PR events that includes the "exclude-from-incremental" tag filter