Multi-module Cyber-Physical Systems (CPSs), such as satellite clusters, swarms of Unmanned Aerial Vehicles (UAV), and fleets of Unmanned Underwater Vehicles (UUV) are examples of managed distributed real-time systems where mission-critical applications, such as sensor fusion or coordinated flight control, are hosted. These systems are dynamic and reconfigurable, and provide a "CPS cluster-as-a-servicetextquoterighttextquoteright for mission-specific scientific applications that can benefit from the elasticity of the cluster membership and heterogeneity of the cluster members. Distributed and remote nature of these systems often necessitates the use of Deployment and Configuration (D&C) services to manage lifecycle of software applications. Fluctuating resources, volatile cluster membership and changing environmental conditions require resilience. However, due to the dynamic nature of the system, human intervention is often infeasible. This necessitates a self-adaptive D&C infrastructure that supports autonomous resilience. Such an infrastructure must have the ability to adapt existing applications on the fly in order to provide application resilience and must itself be able to adapt to account for changes in the system as well as tolerate failures. This paper describes the design and architectural considerations to realize a self-adaptive, D&C infrastructure for CPSs. Previous efforts in this area have resulted in D&C infrastructures that support application adaptation via dynamic re-deployment and re-configuration mechanisms. Our work, presented in this paper, improves upon these past efforts by implementing a self-adaptive D&C infrastructure which itself is resilient. The paper concludes with experimental results that demonstrate the autonomous resilience capabilities of our new D&C infrastructure.