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When you're serious about growing a cash crop indoors(i.e. marijuana), you basically have an airlock. No unfiltered air exchange. No outside clothes or footwear. You also have control of the environment and can regulate humidity to help control fungus. When something does get inside, you potentially scrap the crop, sterilize, and start over. I don't know anything about these robotic grow ops, but I bet they do something similar.

This isn't like growing in a greenhouse where you use screens to keep out bugs.