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We present a hybrid, hierarchical architecture for mission control of autonomous underwater vehicles (AUVs). The architecture is model based and is designed with semiautomatic verification of safety and performance specifications as a primary capability in addition to the usual requirements such as real-time constraints, scheduling, shared-data integrity, etc. The architecture is realized using a commercially available graphical hybrid systems design and code generation tool. While the tool facilitates rapid redesign and deployment, it is crucial to include safety and performance verification into each step of the (re)design process. A formal model of the interacting hybrid automata in the design tool is outlined, and a tool is presented to automatically convert hybrid automata descriptions from the design tool into a format required by two hybrid verification tools. The application of this mission control architecture to a survey AUV is described and the procedures for verification outlined.