The basis of a strong commissioning program has always been a strong design intent document (DID). Commissioning has also been a process focused on building "systems" as opposed to individual pieces of equipment. As such, most of the DIDs I've seen over the past few years have been organized in terms of systems - i.e., one section for the HVAC system, one section for the fire alarm system, one section for the lighting system, and so on.
This is a great improvement over the first generation of DIDs, which were organized around pieces of equipment - fans, pumps, heat exchangers, generators, transfer switches, light fixtures, etc. The owners and designers who thought in those terms were really regurgitating equipment schedule information and thinking it was a DID. A true DID is something that defines the owner's desired performance from groups of individual pieces of equipment working together as systems. Examples include temperature, humidity, IAQ, noise levels, light levels, smoke removal rates, etc.