Allow parameter modification from an input file for restarts

[pgrete]

PR Summary

What is says on the label quality of life improvement.
Our use case is that we use Parthenon for post-processing and thus need to pass (significant amounts) of new parameters, e.g., for histograms which gets hard to manage (and some even hit a limit in terms of what the bash allows).

PR Checklist

• Code passes cpplint
• New features are documented.
• Adds a test for any bugs fixed. Adds tests for new features.
• Code is formatted
• Changes are summarized in CHANGELOG.md
• Change is breaking (API, behavior, ...)
  • Change is additionally added to CHANGELOG.md in the breaking section
  • PR is marked as breaking
  • Short summary API changes at the top of the PR (plus optionally with an automated update/fix script)
• CI has been triggered on Darwin for performance regression tests.
• Docs build
• (@lanl.gov employees) Update copyright on changed files

[Yurlungur]

This looks fine, but we should probably check this machinery all works nicely somehow... maybe with the restart regression test?

[lroberts36]

LGTM

[pdmullen]

Should we warn the user if CLI and an input file try to override the same parameter in ParameterInput?

[pgrete]

Should we warn the user if CLI and an input file try to override the same parameter in ParameterInput?

As discussed during the last sync, this would require quite a bit of additional machinery so we'll not warn (for now).

[pgrete]

This looks fine, but we should probably check this machinery all works nicely somehow... maybe with the restart regression test?

done