Add testing utility for in-place modification of input files

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.

refs #2731

Change-Id: Ibdd0462ea7bcfd6f05ee7b7f96618c0fd6457d80