Improve index conversions
Description
Add functions for converting local and global indices and use them instead of dealing with mesh%vp. This improves on isolating the knowledge about the mesh parallelization to the mesh class. It also simplifies some code with loops that now don't have to know if they are parallel in domain or not
News snippet
Improve index conversions in the code
Checklist
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I have checked that my code follows the Octopus coding standards -
I have added tests for all the new features added in this request.