Systems and methods are described for capturing and utilizing specific module dependency information. A hierarchical model can be created to arrange the components an existing software system in a particular hierarchy. The model defines a priority of dependencies among the components. A tool is provided for analyzing each class file of the system for references to other class files and determining, for each said class file, whether each reference is acceptable according to the hierarchical model. Once the class files and references have been analyzed, a surrogate class file can be automatically generated for the references that are determined to be unacceptable according to the hierarchical model. This process can utilize white lists and black lists associated with the class files, where the white lists specify modules to which references are acceptable and the black lists specify modules to which references are unacceptable.