The Construction Yard Prototype was the prototype-stage of the Epsilon's Construction Yard during the Third World War. It cannot build anything and the few differences that it has with its finished counterpart are some missing parts and not having an Epsilon symbol.
In the cut Epsilon Co-Op mission Cornered, it reappears as an MCV and must be protected from the Russian-deployed Terror Drones until the tunnel is opened.
The Construction Yard Prototype was only seen deployed in action at Todgha Gorge, Morocco, during Landlocked. It was being studied by the Allies located there and must be destroyed/captured before they realize who it really belongs to.
Behind the scenes
Back in 3.0, the Construction Yard Prototype has a unique build-up animation for itself (presumably used for testing purposes). The animation is no longer used as of 3.3.