1. A method for managing, in a computer system, design of a software system containing a plurality of domains, the method comprising: in a first computer process, extracting atoms and dependencies from the software system for a first one of the domains and a second one of the domains; in a second computer process, generating a hierarchy of partitions for each of the first and second domains based on the extracted atoms and dependencies; in a third computer process, with respect to atoms associated with both the first and the second domains, merging partitions of the first and second domains into a merged partition containing such atoms; storing a representation of the software system based on results of the first, second, and third computer processes; and providing a graphical output, from the computer system, based on the stored representation of the software system, in which appears a display of the merged partition in a hierarchy within a dependency structure matrix, such matrix graphically indicating the dependency relationships in the merged partition.