Define API for passing SimulationInput to Mdrunner.

This change establishes a holder that is safe to pass across the library boundary so that we can manage the details of SimulationInput separately from the Mdrunner API. A separate change provides initial functionality with which Mdrunner can be decoupled from some of the filename arguments used to establish the initial simulator state.

The MdrunnerBuilder requires addInput() before build() to acquire a SimulationInputHolder from the client. The client can create the resource with makeSimulationInput and a LegacyMdrunOptions reference.

See also !454 (merged)

Refs #3374 (closed)