Update docs with changes to Transmute

[MetBenjaminWent]

PR Summary

Linked issue: #25

A few issues and PRs to apps and core have adjusted slightly how transmute functions.
To improve the docs and bring them in line with its current usage with the make build system, we need to update a few sections.

See #49, #246 and MetOffice/lfric_core#271

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

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

Test Suite Results - lfric_apps - update_transmute_docs/run1

Suite Information

Item	Value
Suite Name	update_transmute_docs/run1
Suite User	benjamin.went
Workflow Start	2026-02-12T16:20:28
Groups Run	developer

Dependency	Reference	Main Like
casim	MetOffice/casim@2025.12.1	True
jules	MetOffice/jules@69aaf4d	True
lfric_apps	MetBenjaminWent/lfric_apps@update_transmute_docs	False
lfric_core	MetOffice/lfric_core@a9ea959	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

❌ failed tasks - 3

Task	State
generate_weights_lfric2lfric_oasis_clim_gal9_C12-ral_seuk_C16_lam-lbc_azspice_weightgen_script	failed
generate_weights_lfric2lfric_oasis_clim_gal9_C12-ral_seuk_C16_lam_azspice_weightgen_script	failed
run_gungho_model_robert-moist-smag-BiP100x8-10x10_azspice_gnu_fast-debug-64bit	failed

✅ succeeded tasks - 1096

⌛ waiting tasks - 4

Task	State
run_lfric2lfric_oasis_clim_gal9_C12-ral_seuk_C16_lam-lbc_azspice_gnu_fast-debug-64bit	waiting
run_lfric2lfric_oasis_clim_gal9_C12-ral_seuk_C16_lam-lbc_ex1a_cce_fast-debug-64bit	waiting
run_lfric2lfric_oasis_clim_gal9_C12-ral_seuk_C16_lam_azspice_gnu_fast-debug-64bit	waiting
run_lfric2lfric_oasis_clim_gal9_C12-ral_seuk_C16_lam_ex1a_cce_fast-debug-64bit	waiting

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