I responded at length to the sibling but just want to say - usually where I've come in there is an operations manual that works very much like a schema. Investigating where it's being overridden in daily practice often helps to form more linear processes / more consistent logic than was in the manuals. Once those are worked out, the software becomes the glue that forces employees to follow the processes, and the manual is about the software. But you're right: Stepping into a messy organic system and writing software around it is hard. It's much harder if they aren't willing to be flexible.
