Add test support for modifiable inputs to command line tools
Some tools (such as gmx solvate and gmx genion) modify topologies in place. The command line testing tools aren't set up to test in-place modification, which requires a copy of the original file to work on.
Add testing utility for in-place modification of input files
Adds setModifiableInput and setInputAndOutputFile as options to
the command line testing utility. This is useful for tools such as
gmx solvate and gmx genion which when given "-p topol.top", modify
the topology in place.