Update Apps to work with purge of intermediate configuration object api on lfric core

[mo-rickywong]

PR Summary

This is a technical infrastructure change, it does not change science or the overall structure of applications. SciTech is N/A though code owners may wish to check their relevant code areas in case they have comments/objections.

Sci/Tech Reviewer: @allynt
Code Reviewer: @oakleybrunt

NOTE: @ukmo-juan-castillo added to review changes in a Code Owner capacity only

MetOffice/lfric_core#262 Removes instances of usage of the intermediate api to access namelist configurations from lfric_core. This however means that some routines in lfric_core have their argument lists changed, this may impact some applications in lfric_apps.

This PR only changes what is required to work with the linked MetOffice/lfric_core#262. Further PRs to remove usage of the Intermediate api from Lfric_apps will follow.

Linked PRs

• Purge Intermediate Api access to configuration object from in favor of new config_type object lfric_core#262

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)

trac.log

Testing was done with developer group and lfric_atm_extra as some iau is not exercised in the main developer group.

Test Suite Results - lfric_apps - AppsIntermediateApiPurge/run4

Suite Information: lfric_atm_extra group

Item	Value
Suite Name	AppsIntermediateApiPurge/run4
Suite User	ricky.wong
Workflow Start	2026-02-03T10:08:00
Groups Run	lfric_atm_extra

Dependency	Reference	Main Like
casim	MetOffice/casim@2025.12.1	True
jules	MetOffice/jules@69aaf4d	True
lfric_apps	mo-rickywong/lfric_apps@AppsIntermediateApiPurge	False
lfric_core	mo-rickywong/lfric_core@IntermediateApiPurge	True
moci	MetOffice/moci@2025.12.1	True
SimSys_Scripts	MetOffice/SimSys_Scripts@2025.12.1	True
socrates	MetOffice/socrates@2025.12.1	True
socrates-spectral	MetOffice/socrates-spectral@2025.12.1	True
ukca	MetOffice/ukca@2025.12.1	True

Task Information

✅ succeeded tasks - 173

Test Suite Results - lfric_apps - AppsIntermediateApiPurge/run5

Suite Information: Developer group

Item	Value
Suite Name	AppsIntermediateApiPurge/run5
Suite User	ricky.wong
Workflow Start	2026-02-03T10:08:51
Groups Run	developer

Dependency	Reference	Main Like
casim	MetOffice/casim@2025.12.1	True
jules	MetOffice/jules@69aaf4d	True
lfric_apps	mo-rickywong/lfric_apps@AppsIntermediateApiPurge	False
lfric_core	mo-rickywong/lfric_core@IntermediateApiPurge	True
moci	MetOffice/moci@2025.12.1	True
SimSys_Scripts	MetOffice/SimSys_Scripts@2025.12.1	True
socrates	MetOffice/socrates@2025.12.1	True
socrates-spectral	MetOffice/socrates-spectral@2025.12.1	True
ukca	MetOffice/ukca@2025.12.1	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

N/A

• 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)

No AI was used on this PR developerment

Documentation

N/A

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

PSyclone Approval

N/A

• 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

N/A : Code owners may wish to review / comment

• 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

[jennyhickson]

While this is a non-scientific change its still too large for only one review, please can you organise a SciTech reviewer as well?

[ss421]

This change will need to have a linked PR in lfric-jedi. We can create a PR for this and test it. Since we have an issue with the change in MetOffice/lfric_core#175 I think its worth waiting for a fix before doing the test although it will likely just work with this change if I understand this correctly.

Ive added this PR to the list or required updates documented in: https://github.com/JCSDA-internal/lfric-jedi/pull/1206

@DanStoneMO - could you take a look at this please? Thanks.

[mo-rickywong]

This change will need to have a linked PR in lfric-jedi. We can create a PR for this and test it. Since we have an issue with the change in MetOffice/lfric_core#175 I think its worth waiting for a fix before doing the test although it will likely just work with this change if I understand this correctly.

Ive added this PR to the list or required updates documented in: https://github.com/JCSDA-internal/lfric-jedi/pull/1206

@DanStoneMO - could you take a look at this please? Thanks.

The lfric-jedi link is not reachable, can you reference the linked PR when available.