Fix bug in pathnames when using --fullcheck

[r-sharp]

PR Summary

Sci/Tech Reviewer:
Code Reviewer: @james-bruten-mo

The TLD was being repeated when using --fullcheck option. Not sure how this crept in, but I discovered it when trying to work on some optimisations.

Whilst the propesed 'fix' might look a bit clunky (generating relative paths to the TLD in get_files_to_check only to add the TLD once the list is returned). This is to accomodate planned changes to only add the TLD at the point the file is opened and always use just the relative path when reporting on the success/failure of a particular file.
I'm fixing the bug here - no implementing the future change.

• is blocked-by Unifying the style checkers #196
  The list of commits below looks to include all the commints in Unifying the style checkers #196.
  Only the commit 545580b relates to this bugfix...

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
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Testing

• This change has been tested appropriately (please describe)

On the command line, this change allows the script to run on a specified directory in both 'cms' and fullcheck modes.
It also passes all the pytest tests.

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AI Assistance and Attribution

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AI only used for "line completion" where it matched what I was going to type.

Sci/Tech Review

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Code Review

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• Performance impact is acceptable