So it tells me that greenhouse should be rotating to create artificial gravity.
It would be CEA (Controlled Environment Agriculture). It would use visible light plus some frequencies of ultraviolet. No infrared light.
A human produces between 1 and 2 kg of urine a day, which means that in one year you have almost a ton of urine. Without hygienizator you also would be creating a biohazard, so it seems that if you lack the hardware, you better dump it.
But if you have hardware, you can sell it. Urea has nitrogen, potassium and a third substance I do not remember, that are useful not only for agriculture but also for other industrial uses. Indeed potassium would be used to create KO2 that can be used to absorb CO2 in case lithium based components are depleted. So basically your urine would let you breath...
I already have the almost clean cycle that would minimize waste. I haven't found the perfectly clean process and some hardware is semifictional but possible, for the principle exists but not really such specific hardware.
My idea (I haven't implemented yet in the game, for I am working on finances part) is that you buy the hardware required for a clean process, so you not only reduce costs, but also you could make some extra money trading the clean product obtained from your waste. The most problematic waste is human waste.
In order to make things easier for player, so they can see benefits of a clean process, DGIV will have plenty of room for all the substances that you might need to purchase of a 4 year trip. So just imagine it, carrying 27.5 tons of weightless water (won't add to DGIV mass) for 5 people during 4 years, instead of recycling water by buying proper hardware. Water is very expensive in outer space...
Imagine yourself dumping 2 kg of water a day as urine into space, instead of using urea and sell its components at the base.
That's the concept I have. All the recycling process and CEA will be automated, depending on hardware available in the vessel. This simplifies the code for the game, and gives the idea of an advanced automation. It looks like I need to add non operatinng income to the accounting, since selling these goods is not ordinary revenue from your business.