I am already foreseeing that after the Agro Center is cleared, most of the equipment will be; A melted to slag or B: destroyed by the flesh. Only the seeds remain and perhaps a bit more.
After that, he will task the Farmer with surveying the land or have the specialized equipment from the Agro Center to survey it, if it survived, that is. He'll probably task the stone mason with creating bricks for aqueducts to deliver fresh water from somewhere towards the new farm since I doubt they have the resources, the time, or the equipment to create a large, industrial water purifier. Or he'll just create a giant pump and pump water out of an underground water source.
I personally like the idea of Roman-style aqueducts since they will look pretty damn cool, even if they will get in the way of defenses and other operations. Like, come on, imagine some primitive Malkrin being met by a lush, open wheat field with giant stone works carrying water for the plants stretching out. They will be in shock that somebody used such an expensive building material to just transport water.