Fractionated spacecraft are clusters of small, independent modules that interact wirelessly to realize the functionality of a traditional monolithic spacecraft. System F6 (F6 stands for Future, Fast, Flexible, Fractionated, Free-Flying spacecraft) is a DARPA program for fractionated spacecraft. Software applications in F6 are implemented in the context of the F6 Information Architecture Platform (IAP), which provides component-based abstractions for composing distributed applications. The lifecycle of these distributed applications must be managed autonomously by a deployment and configuration (D&C) infrastructure, which can redeploy and reconfigure the running applications in response to faults and other anomalies that may occur during system operation. Addressing these D&C requirements is hard due to the significant fluctuation in resource availabilities, constraints on resources, and safety and security concerns. This paper presents the key architectural ideas that are required in realizing such a D&C infrastructure.