Introduce SimulationInput abstraction

Remove direct references to -s and -cpi filename arguments in gmx::Mdrunner. Unite these input sources into a SimulationInput object.

Initial implementation wraps read_tpx_state() and load_checkpoint() into facilities based on the SimulationInput object to break the explicit dependence of these inputs on filename arguments.

Additional work should allow the files to be read arbitrarily early in the SimulationInput creation, and the extracted data should be managed granularly so that SimulationInput consumers are not constrained by the call signatures warranted by direct coupling to filesystem I/O. This likely means migrating to an implementation more dependent on the serialization infrastructure, which should also allow us to encapsulate run-time details regarding distributed data.

See also !465 (merged)

Refs #3374 (closed)