Allow all arbitrary runtime arguments to gmxapi.mdrun

gmxapi.mdrun is severely limited by a combination of

• slow progress on API features for simulation and work load input
• shifting behavior with respect to mdrun command line options

Since these are not likely to be resolved soon, we might as well let gmxapi.mdrun accept arbitrary command line arguments, subject only to the usual mdrun user input handling.

The -s option (TPR file) is still reserved, since it is essential that the API instrumentation manage the main input source.

The initial merge request must patch the libgmxapi C++ code to allow for the possibility of all other user-provided options, while guaranteeing that a trajectory output and a checkpoint output will be available at a knowable location.

(A follow-up merge request adds a runtime_args key word argument to gmxapi.mdrun(), accepting a dictionary of input.)