We're trying to orchestrate a horde of agents. The workers (polecats?) are the main problem solvers. Now you need a top level agent (mayor) to breakdown the problem and delegate work, and then a merger to resolve conflicts in the resulting code (refinery). Sometimes agents get stuck and need encouragement.
The molecules stuff confused me, but I think they're just "policy docs," checklists to do common tasks.
But this is baby stuff. Only one level of hierarchy? Show me a design for your VP agent and I'll be impressed for real.