Lift adjustable psyclone command options into adjustable flag

[MetBenjaminWent]

PR Summary

For PSyKAl command makefile.
This issue MetOffice/simulation-systems#574 has requested the ability to adjust the line length for the Transmute command due to compiler issues at their site.
We have agreed to also modify the PSyKAl command in the same way.
-l all seems to be the only option that should be overridable.
Users should be able to use this variable, but privatised for a file by file basis, though this has not yet been explored.

Twin but not linked Apps change PR: MetOffice/lfric_apps#246

Sci/Tech Reviewer: @andrewcoughtrie
Code Reviewer: @harry-shepherd

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 Core rose-stem suite
• If required (e.g. API changes) I have also run the LFRic Apps test suite using this branch
• 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)

trac.log

Test Suite Results - lfric_core - psyclone_command_flags_override/run1

Suite Information

Item	Value
Suite Name	psyclone_command_flags_override/run1
Suite User	benjamin.went
Workflow Start	2026-02-11T11:57:52
Groups Run	developer

Dependency	Reference	Main Like
lfric_core	MetBenjaminWent/lfric_core@psyclone_command_flags_override	False
SimSys_Scripts	MetOffice/SimSys_Scripts@2025.12.1	True

Task Information

✅ succeeded tasks - 382

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

[MetBenjaminWent]

In the short term, users should be able to override PSYCLONE_PSYKAL_EXTRAS in their site specific cylc file, in the build step:
https://github.com/MetOffice/lfric_apps/blob/main/rose-stem/site/nci/common/suite_config_gadi.cylc

[andrewcoughtrie]

The implementation is fine with me, the only thing to fix is the tabs and spaces used on the new lines as they don't align with the other lines.

[MetBenjaminWent]

I've adjusted the tabbing to align exactly with the lines above. I'll have a look at the apps ticket.

[andrewcoughtrie]

That all looks fine now.

[MetBenjaminWent]

Docs updated here: MetOffice/lfric_apps#261