Herr
Commissioning (Cx) has worked it's way into the code. the new International green construction code has a chapter 9 for Cx. Some states have already adopted it.
Cx is required by ASHRAE 90.1 - 6.7.2.4 for controls and for areas over 50,000 SF - so if ASHRAE90.1
systems to be commissioned include HVAC water and air side, Plumbing systems, life safety systems, electrical systems and special systems such as automatic blinds, irrigation systems, grey water systems, etc.. Check the LEED handbook, it will tell you the requirements for a LEED project.
LEED Version 4 (in 2014 I hear) is moving towards requiring Exterior Enclosure Commissioning in addition to above.
You do need a Cx Plan and Cx specs (can be found in your set of Masterspecs). You need to hire a Cx Authority (CxA) who will provide the testing procedures and forms, but systems to be commissioned and the original Cx Plan (updated by the CxA) are the responsibility of the designer.
heuhhhh - Commissioning is a trade nowadays Manu, it starts at the planning stages, definitely during design.