Linux command line scripts show JVM UI popup upon failure

At !73 (comment 10795), @ahofkamp notes:

An error in execution like cd bin; ./cif2cif throws an error due to missing arguments (which is correct). It also pops up a graphical window from the VM saying it failed with the execution options and flags details. You have to close that window manually before the prompt returns. As such the bin programs are useless for automagic use in their current form.