We propose a methodology to study and visualize the evolution of the modular structure of a network of functional dependencies in a software system. Our method identifies periods of significant refactoring activities, also known as the evolutionary hot spots in software systems. Our approach is based on clustering design structure matrices of functional dependencies and Kleinberg’s method of identifying evolutionary hot-spots in dynamic networks. As a case study, we characterize the evolution of the modular structure of Octave over its entire life cycle.