Remove module scope access of namelist variables by coordinate/native jacobian.

[mo-rickywong]

PR Summary

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

As part of work to remove configuration namelist access from module scope, configuration variables will need to be passed
by argument. Configuration variables passed by argument to kernels is more involved, so this PR moves the use _config_mod from the Jacobian routines up to the to the kernel level in preparation of further changes.

Linked PRs
MetOffice/lfric_apps#184

Code Quality Checklist

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Rose test-suite Runs Green

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Code Review

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