Method, apparatus, and computer readable medium for restructuring a software program hierarchy having interface files and implementation files that include the interface files are described. In one example, dependencies between program units in the interface files and the implementation files are determined. The dependencies are represented as a plurality of bit strings. Correlated bitstrings of the plurality of bit strings are clustered into a plurality of partitions. Each of the plurality of partitions is transformed into corresponding program units. New interface files are respectively created having the corresponding program units for each of the plurality of partitions.