Both the 'Clear Code' and 'Delete Code' buttons remove the codes inside the box, but neither removes the Command. Selecting 'Add/Remove Command' and unchecking commands no longer seems to remove the unchecked commands from the command set.
Clearing the IR codes (and fixing the syntax error noted below), gets the template working, even if multiple, blank commands are present.
The sharp ones out there looking at the template may have noticed my bone-headed mistake in Ruby Syntax. I've corrected the '$' placement on my machine and will check in once I figure out what's going on with the command display.