Programming versus Commissioning
A program is a list of instructions that become part of a fire alarm system. The instructions, being just the equivalent of words on paper, tell the fire alarm controls in the control panel what to do when a device senses fire.
Commissioning the program is thoroughly testing the program. The program was very thoroughly tested (commissioned) by the fire alarm system supplier to make sure the detection devices would correctly turn on the output devices. The program, by itself though, is just words. Without being in a fire alarm system, the program can be well written, but useless.
The fire alarm system is a Fire Detection and Alarm System. It may have a program inside the fire alarm control panel, but really, the fire alarm system is all over the building. Even though the program itself has been thoroughly tested (commissioned), the panel, the devices, the wiring still has to be thoroughly tested (commissioned) to make sure the system will Detect Fire and Sound the Alarm.
Supplier versus Building Fire Alarm System
Another point of view is the fire alarm system supplier provided equipment. As part of the supplying equipment, they provided a program to go into the equipment. They even tested the program thoroughly (commissioned the program).
Once you receive the boxes of equipment, the devices, and the wire, the provided system has to be installed. It's only after the Fire Detection and Alarm System is installed, and working, that the completed system can be thoroughly tested (commissioned).