Remove unused inputs

[lrobion]

All inputs not listed under "Bugs" in #121 are rejected by APCEMM and throw an error. Keys previously marked as deprecated are now promoted to throwing errors instead of warnings.

This is the "rip the bandaid" approach, we could have warnings instead but this forces this all changes in one go which I'd prefer. I can change this if needed.

Two notes:

• The "bugs" in Remove unused inputs #121 will be dealt with in other PRs
• The implementation throws as soon as we find an unsupported key, we could instead group all issues with an input file together and throw a single nicer message. I think this would require a larger refactor of the YAML reader and could be done later as it's only an error reporting change, not an API or science change.

When would we want to merge this @sdeastham given it will interfere with the current changes you are making?