feat: always include files from diff in overlay changed files

[sam-robson]

Ensure that overlay changes always include all PR diff files used for diff-informed analysis.

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?

Workflow types:

• Managed - Impacts users with dynamic workflows (Default Setup, Code Quality, ...).

Products:

• Code Scanning - The changes impact analyses when analysis-kinds: code-scanning.
• Code Quality - The changes impact analyses when analysis-kinds: code-quality.

Environments:

• Dotcom - Impacts CodeQL workflows on github.com and/or GitHub Enterprise Cloud with Data Residency.
• GHES - Impacts CodeQL workflows on GitHub Enterprise Server.

How did/will you validate this change?

• Unit tests - I am depending on unit test coverage (i.e. tests in .test.ts files).
• End-to-end tests - I am depending on PR checks (i.e. tests in pr-checks).

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

• Feature flags - All new or changed code paths can be fully disabled with corresponding feature flags.

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

• Telemetry - I rely on existing telemetry or have made changes to the telemetry.
  • Dashboards - I will watch relevant dashboards for issues after the release. Consider whether this requires this change to be released at a particular time rather than as part of a regular release.
  • Alerts - New or existing monitors will trip if something goes wrong with this change.

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

• No special considerations - This change can be merged at any time.
• Special considerations - This change should only be merged once certain preconditions are met. Please provide details of those or link to this PR from an internal issue.

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.