Implement Dual Input Interface (CLI Args & YAML)

[harryswift01]

• Implement CLI arguments and YAML file for configuration, with YAML as the default.
• CLI arguments should override YAML settings.

[skfegan]

Some extra work:

[ ] some of the arguments in the current parser list related to the poseidon code so should be removed: --cutShell, --pureAtomNum, --excludedResnames, --water, --solvent, --solContact
[ ] add to the input a force_partitioning parameter (default value 0.5)
[ ] add an input parameter for waterEntropy (default false) which we will use as a flag for whether or not we want to use Jas's waterEntropy package to get the orientational entropy.