gmxapi.commandline_operation should gracefully handle input/output file arguments
gmx commands have the effect of modifying a file in place, which is inconsistent with the gmxapi assumptions of immutable data events. As implemented, a command with an input/output filename argument can destroy the output of a previous operation.
The user interface does not need to be changed if we allow an input and output file argument to be duplicated, but we need to add some infrastructure. The simplest fix would be to copy (or hard link) input files that are also output files before using them.