fix for mirror extract

[james-bruten-mo]

PR Summary

Sci/Tech Reviewer:
Code Reviewer: @jennyhickson

Fix mirror extract when done as part of rose-stem
Also set the logging module to send errors to stdout
The extract_source task passing using mirrors and this branch can be seen at https://cylchub/services/cylc-review/taskjobs/james.bruten?&suite=test_mirror_fix%2Frun3&cycles=1&task_status=expired&task_status=succeeded

Code Quality Checklist

• I have performed a self-review of my own code
• My code follows the project's style guidelines
• Comments have been included that aid understanding and enhance the readability of the code
• My changes generate no new warnings
• All automated checks in the CI pipeline have completed successfully

Testing

• This change has been tested appropriately (please describe)

Security Considerations

• I have reviewed my changes for potential security issues
• Sensitive data is properly handled (if applicable)
• Authentication and authorisation are properly implemented (if applicable)

AI Assistance and Attribution

• Some of the content of this change has been produced with the assistance of Generative AI tool name (e.g., Met Office Github Copilot Enterprise, Github Copilot Personal, ChatGPT GPT-4, etc) and I have followed the Simulation Systems AI policy (including attribution labels)

Sci/Tech Review

• I understand this area of code and the changes being added
• The proposed changes correspond to the pull request description
• Documentation is sufficient (do documentation papers need updating)
• Sufficient testing has been completed

(Please alert the code reviewer via a tag when you have approved the SR)

Code Review

• All dependencies have been resolved
• Related Issues have been properly linked and addressed
• Code quality standards have been met
• Tests are adequate and have passed
• Security considerations have been addressed
• Performance impact is acceptable

[jennyhickson]

LGTM