Extensions don't get checked in to the master repository, as they are not deployable software. Instead they are installed into the framework of the ePO server. The nature of ePO means that you can only have one extension per product - for this reason, extensions are designed to be backwards-compatible: so the MA 4.5 Patch 1 extension, for example, is capable of controlling MA 4.0 agents as well.
I thought that may be the case but wasnt completely sure. Thats good to know.
So a mixed environment of 3.6 and 4.0 agents can be supported via just the McAfee Agent 4.0 (or above) NAP/Extension?
Yep, that's correct (assuming that we're talking about supported agent versions - so the MA 4.5 extension is not guaranteed to accurately control CMA 3.5 agents, for example.)