Multi-module Cyber-Physical Systems (CPS), such as satellite clusters, swarms of Unmanned Aerial Vehicles (UAV), and fleets of Unmanned Underwater Vehicles (UUV) provide a CPS cluster-as-a-service for CPS applications. The distributed and remote nature of these systems often necessitates the use of Deployment and Configuration (D&C) services to manage the lifecycle of these applications. Fluctuating resources, volatile cluster membership and changing environmental conditions necessitate resilience. Thus, the D&C infrastructure does not only have to undertake basic management actions, such as activation of new applications and deactivation of existing applications, but also has to autonomously reconfigure existing applications to mitigate failures including D&C infrastructure failures. This paper describes the design and architectural considerations to realize such a D&C infrastructure for component-based distributed systems. Experimental results demonstrating the autonomous resilience capabilities are presented.