Replace filename-based initialization functions.

Replace filename-based initialization functions.

Decouple Mdrunner from the details of `-s` and `-cpi`
filename arguments when establishing initial simulation state.

Declare gmx::SimulationInput and the library utilities needed to
replace direct reference to TPR and CPT files in Mdrunner.
Use SimulationInput and accompanying utilities to remove read_tpx_state
and load_checkpoint from Mdrunner.

Allows TPR and checkpoint file handling to be considered separately
from Mdrunner initialization in future development.

Refs #3374