Remove all usage of namelist collection object modeldb%configuration (Full Purge)

[mo-rickywong]

PR Summary

Sci/Tech Reviewer: N/A
Code Reviewer:

Technical infrastructure change, no change to major structure, SciTech not required.

Removes remain usage of configuration access that was missed before:

• modeldb%configuration no longer initialised
• Usage of configuration_mod should be swapped with config_loader_mod

Linked PRs

• linked Remove all usage of namelist collection object modeldb%configuration from LFRic Apps (Full Purge) lfric_apps#225

Blocking PR

• is blocked-by Remove module scope access of namelist variables by coordinate/native jacobian. #249
• is blocked-by Purge Intermediate Api access to configuration object from in favor of new config_type object #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 Core rose-stem suite
• If required (e.g. API changes) I have also run the LFRic Apps test suite using this branch
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• 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)

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Performance Impact

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AI Assistance and Attribution

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Documentation

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

PSyclone Approval

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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
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• 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