Refactor io_value_type

### Are there any linked Issues or Pull Requests?

MetOffice/lfric_core#380

### Brief description

`io_value_type` is being refactored in **lfric_core**. This PR makes use of that new structure.

### Further details of the issue.

A previous issue (#45) to refactor io_value_type so that its attributes were private has been closed. The attributes of key_value_type are purposefully public to make the code simpler.

Start by reading the linked lfric_core issue #380 and the discussion of the earlier refactor in issue #45. Trace the current uses of io_value_type and key_value_type in lfric_apps, then identify the changes required to use the new structure. Done means the application is updated for the refactored type and its existing checks pass.

Written by the indexing model from the issue text.