Draw your unit as a line. Raw straw and manure storage sits at the dirty end, then the Phase I yard, transfer, the Phase II tunnel, ready compost and spawning. Spent compost from the cropping rooms sits outside that line, because it is the dirtiest material on the farm.
Work should move along that line and never back up it. The same rule covers people. A worker clearing spent beds should not enter the ready compost bay in the same boots, and a visitor from the cropping room should not be shown the tunnel.