Reverse engineering legacy software systems often involves the employment of clustering algorithms that automatically decompose a software system into subsys- tems. The decompositions created by existing software clustering algorithms are often nested, i.e. subsystems may contain other finer-grained subsystems as well as system resources, such as source files. It is rather sur- prising then, that almost all existing methods for de- composition comparison assume flat decompositions, i.e. subsystems only contain system resources. In this paper, we introduce UpMoJo, a novel com- parison method for software decompositions that can be applied to both nested and flat decompositions. The ben- efits of utilizing this method are presented in both ana- lytical and experimental fashion. We also compare Up- MoJo to the END framework, the only other existing method for nested decomposition comparison.