Modify LFRic Apps files that call native/coordinate Jacobian files

[mo-rickywong]

PR Summary

Sci/Tech Reviewer:
Code Reviewer: @mo-lucy-gordon

In preparation to remove configuration variables from module scope, MetOffice/lfric_core#249 moves such practice in coordinate/native Jacobian routines to the kernel level. This PR is to modify calls to the updated Jacobian routines from kernels/unit-tests in LFRic_apps. Changes in this PR will be similar in nature, though touch a large number of files

This change doesn't change any KGOs and is an infrastructure change.

Linked PR

• Remove module scope access of namelist variables by coordinate/native jacobian. lfric_core#249

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

• I have tested this change locally, using the LFRic Apps rose-stem suite
• If any tests fail (rose-stem or CI) the reason is understood and acceptable (e.g. kgo changes)
• I have added tests to cover new functionality as appropriate (e.g. system tests, unit tests, etc.)
• Any new tests have been assigned an appropriate amount of compute resource and have been allocated to an appropriate testing group (i.e. the developer tests are for jobs which use a small amount of compute resource and complete in a matter of minutes)

Test Suite Results - lfric_apps - AppsFloatJacobian/run9

Suite Information

Item	Value
Suite Name	AppsFloatJacobian/run9
Suite User	ricky.wong
Workflow Start	2026-01-27T15:59:47
Groups Run	developer

Dependency	Reference	Main Like
casim	MetOffice/[email protected]	True
jules	MetOffice/[email protected]	True
lfric_apps	mo-rickywong/lfric_apps@AppsFloatJacobian	False
lfric_core	mo-rickywong/lfric_core@FloatJacobian	True
moci	MetOffice/[email protected]	True
SimSys_Scripts	MetOffice/[email protected]	True
socrates	MetOffice/[email protected]	True
socrates-spectral	MetOffice/[email protected]	True
ukca	MetOffice/[email protected]	True

Task Information

✅ succeeded tasks - 1106

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)

Performance Impact

• Performance of the code has been considered and, if applicable, suitable performance measurements have been conducted

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)

Documentation

• Where appropriate I have updated documentation related to this change and confirmed that it builds correctly

PSyclone Approval

• If you have edited any PSyclone-related code (e.g. PSyKAl-lite, Kernel interface, optimisation scripts, LFRic data structure code) then please contact the TCD Team

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
• CLA compliance has been confirmed
• Code quality standards have been met
• Tests are adequate and have passed
• Documentation is complete and accurate
• Security considerations have been addressed
• Performance impact is acceptable