4174 only read indats using the indat class

[clmould]

Description

• Moves validate_input to the InDat class and rename to check_obsolete_variables
• parse_input_file no longer re-reads the file line by line
• Removes tests/integration/data/ref_IN.DAT as this was too outdated and couldn't be updated, and instead uses large_tokamake_IN.DAT for test_write_new_in_dat -> the test passes on main since all the obsolete lines are skipped, however we should be using up to date files in tests otherwise this isn't a very good test
• Fix PLR1702 errors in these files

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.