Fix GIT_DEPTH variable precedence in git operations

What does this MR do?

This MR fixes the issue where the GIT_DEPTH variable does not follow CI/CD variable precedence rules when set in .gitlab-ci.yml vs project/pipeline variables.

Related issues

Closes #28894 (closed)

Author's checklist

• Follow the Contribution Guidelines
• If this MR is the resolution of a security issue, I have read the security process for developers and understand I must not share details of this security issue outside of this MR
• This change is backward compatible. If not, please include steps to communicate to our users
• Tests added for new functionality. If not, please raise an issue to follow up
• Documentation added/updated, if needed

How to test

1. Create a project with a .gitlab-ci.yml that sets GIT_DEPTH: 5
2. Set a project CI/CD variable GIT_DEPTH with value 2
3. Run a pipeline and check the job log
4. The log should show "Fetching changes with git depth set to 2..." (project variable takes precedence)

What are the relevant issue numbers?

Closes #28894 (closed)

Does this MR meet the acceptance criteria?

• Code review guidelines
• Merge request performance guidelines
• Style guides
• Database guides
• Separation of EE specific content

Merge request checklist

• Tests
  • Added for this feature/bug
  • All builds are passing
• Changelog entry
• Documentation (if required)
• Code review