Make operation inputs and outputs compatible with simulation operation

[eirrgang]

subtask of #190

depends #203

Allow simulation operation inputs and outputs to interoperate with gmx.InputFile and gmx.OutputFile from #203

Example: Concatenate trajectories produced by an ensemble of simulations

gmx.commandline_operation('gmx', 'trjcat', input={'-f': gmx.gather(md.output.trajectory)})

[eirrgang]

I think I had more notes on this, but I think they got lost in a browser crash. :-\ I think they were notes about broadcast, scatter, gather, reduce, and map concepts, but that is relevant to other issues, too...

[eirrgang]

Note: We know that gmx.commandline_operation inputs are ultimately passed as file names, so we can define default file types for gmxapi operations that can be used in such a context. E.g. md.output.trajectory is implicitly converted to a trr file when used in such a context.