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The design of autonomous vehicles (AVs) and the design of AV-enabled mobility systems are closely coupled. Indeed, knowledge about the intended service of AVs would impact their design and deployment process, whilst insights about their technological development could significantly affect transportation management decisions. This calls for tools to study such a coupling and co-design AVs and AV-enabled mobility systems in terms of different objectives. In this paper, we instantiate a framework to address such co-design problems. In particular, we leverage the recently developed theory of co-design to frame and solve the problem of designing and deploying an intermodal Autonomous Mobility-on-Demand system, whereby AVs service travel demands jointly with public transit, in terms of fleet sizing, vehicle autonomy, and public transit service frequency. Our framework is modular and compositional, allowing one to describe the design problem as the interconnection of its individual components and to tackle it from a system-level perspective. To showcase our methodology, we present a real-world case study for Washington D.C., USA. Our work suggests that it is possible to create user-friendly optimization tools to systematically assess costs and benefits of interventions, and that such analytical techniques might gain a momentous role in policy-making in the future.