Refactors to parun, NumericalSolution, Profiling

* Remove some dead code
* Refactor profiling calls into dispatcher
* Add ability to just set up the Numerical Solution without calling Solver
Merge remote-tracking branch 'origin' into ahmadia/refactor_parun_ns_profiling

Conflicts:
	src/Profiling.py
Merge pull request #105 from erdc-cm/ahmadia/refactor_parun_ns_profiling

Refactors to parun, NumericalSolution, Profiling