In this paper, we present a control system for a fully autonomous material handling facility. The scenario we are considering is motivated by the 2011 IEEE Virtual Manufacturing Automation Challenge (VMAC). It consists of multiple autonomously guided vehicles (AGVs), transporting pallets of various goods between several input and output locations, through an unstructured warehouse environment. Only a map of the warehouse and a pallet delivery list are provided a priori. Pallets must be delivered to the output locations in the shortest time possible, while respecting the ordering of different pallet types specified by the delivery list. The presented control system handles all aspects of warehouse operation, from individual vehicle control to high-level mission planning and coordination. Delivery mission assignments are optimized using dynamic programming and simulated annealing techniques. Mission executions are coordinated using graph search methods and a modified version of the Banker's algorithm, to ensure safe, collision and deadlock-free system operation. System performance is evaluated on a virtual warehouse model, using the high fidelity USARSim simulator.