Record the simulation input for each iteration and phase.

[eirrgang]

Additional metadata to be managed by RunData and stored in the state.json file: SimulationInput.

Includes the TPR source and the most recent checkpoint file, if any.

Each phase has exactly one TPR source that is immutable once the phase starts.

A checkpoint file is part of the simulation input, but is also part of the simulation output, and may or may not be the same file (-cpi vs. -cpo).

The purpose of this addition is to allow the RunData state to be set before entering the dispatch function for a particular phase run(). I don't believe we need to record the output checkpoint file. We can continue to infer it (the way we do now) when the final checkpoint from one phase is used as the initial checkpoint for a later phase.

For portablity, the paths to files in the BRER directory tree should be recorded as relative paths.