Only read IN.DATs using the InDat class

[je-cook]

There are currently at least 3 places IN.DATs are read.
Everything should be done through the InDat class.

InDat reading should be modified to include these other read cases

• validation_check (obsolete variables)
• input.py (has its own parse_input function

There may be others.

[clmould]

#4523 Have a draft PR. Moving validate_input() and parse_input_file() functions into InDat class, and also do some tidying to sort PLR1702 errors - all documented in the PR description. More involved than a typical papercut so marked as triaged.