4174 only read indats using the indat class

[clmould]

Description

The functionality from:

• validate_input()
• parse_input_file()
• validate_variable()

should be contained in the InDat class, instead of reading in IN.DATs and parsing the variables in multiple locations.

• The InDat methods should be tidied up and combined where appropriate
• Also fixing the PLR1702 errors as most of them are in these files
• Move data_structure_dicts.py, variable_metadata.py and obsolete_vars.py to data_structure/ folder
• Update ref_IN.DAT as this is very out of date and used in test_write_new_in_dat.py - on main this test passes, but the outdated lines are just skipped, however we should be using up to date files in tests otherwise that isn't a very good test

Checklist

I confirm that I have completed the following checks:

• My changes follow the PROCESS style guide
• I have justified any large differences in the regression tests caused by this pull request in the comments.
• I have added new tests where appropriate for the changes I have made.
• If I have had to change any existing unit or integration tests, I have justified this change in the pull request comments.
• If I have made documentation changes, I have checked they render correctly.
• I have added documentation for my change, if appropriate.