1. A system that generates a configuration-hypothesis for a subject complex system that includes a number of components, the system comprising: one or more processors, one or more data-storage devices, including an electronic memory; observed configuration data for the subject complex system stored in one or more of the one or more data-storage devices; and computer instructions stored in one or more of the one or more data-storage devices that control the system to generate a set of initial candidate hypotheses and store the initial candidate hypotheses in a data-storage device as a current set of candidate hypotheses, each hypothesis representing a logic-based explanation of the observed configuration data for a number of target components less than or equal to the number of components, iteratively generate a new set of candidate hypotheses from the current set of hypotheses, select, from the new set of candidate hypotheses, a set of selected hypotheses based on a score assigned by a scoring function to each hypotheses in the new set of candidate hypotheses, and store the selected hypotheses in the data-storage device as the current set of candidate hypotheses, select, based on a score assigned by a scoring function to each hypotheses in the current set of hypotheses, a final hypothesis that describes the observed configuration data, and store the selected final hypothesis in one of the one or more data-storage devices.