In the area of Search-Based Software Engineering, software engineering issues are formulated and tackled as optimization problems. Among the problems within this area, the Software Module Clustering Problem (SMCP) consists of finding an organization of a software project that minimizes coupling and maximizes cohesion. Since modular code is easier to understand, the objective of this problem is to increase the quality of software projects, thus increasing their maintainability and reducing the associated costs. In this work we study a recently proposed objective function named Function of Complexity Balance (FCB). Since this problem has been demonstrated to be NP-hard, we propose a new heuristic algorithm based on the General Variable Neighborhood Search (GVNS) schema to tackle the problem. For the GVNS, we propose six different neighborhood structures and categorize them into three different groups. Then, we analyze their contribution to the results obtained by the algorithm. In order to improve the efficiency of the proposed approach, we leverage domain-specific information to perform incremental evaluations of the objective function and to explore only areas of interest in the search space. The proposed algorithm has been tested over a set of real world software repositories, achieving better results than the previous state-of-the-art method, a Hybrid Genetic Algorithm, in terms of both quality and computing times. Furthermore, the relevance of the improvement produced by our proposal has been corroborated by non-parametric statistical tests.