Make parameter handling more robust

[matt-gretton-dann]

Command line option handling and reading of input files do not give helpful errors when inputs are incorrect. This issue is to work through some of these and improve command-line and input file parsing. Ideally adding unit/regression tests as we go:

• [ ] Ensure for command line options taking an input file name we check the file exists
• [ ] Make parameter file handling robust:
  • [ ] When using values passed via /CLP#: erroring if /CLP# wasn't specified on command line
  • [ ] Issuing warnings about what options weren't used.
  • [ ] Issuing warning if we can't parse the value for a parameter
  • [ ] Highlighting where one value overrides another
  • [ ] Enable output of a parameter file which merges all values read.

[Feynstein]

I've also noticed that some parameters could be seen as subsets of other parameters. Merging then could shrink the size of the param struct. The image was used for another issue but you can see some of those parameters that could be aggregated, or placed in some sort of hierarchy structure.