Many mainstream programming languages lack extensive support for architectural constructs, such as software components, which limits software developers in employing many benefits of architecture-based development. To address this issue, Java, one of the most popular and widely-used programming languages, has introduced the Java Platform Module System (JPMS) in its 9th and subsequent versions. JPMS provides the notion of architectural constructs, i.e., software components, as an encapsulation of modules that helps developers construct and maintain large applications efficiently—as well as improving the encapsulation, security, and maintainability of Java applications in general and the JDK itself. However, ensuring that module declarations reflect the actual usage of modules in an application remains a challenge that results in developers mistakenly introducing inconsistent module dependencies at both compile- and run-time. In this paper, we studied JPMS properties and architectural notions in-depth and defined a defect model consisting of eight inconsistent modular dependencies that may arise in Java applications. Based on this defect model, we also present DARCY, a framework that leverages the defect model and static analysis techniques to automatically detect and repair the specified inconsistent dependencies within Java applications at both compile- and run-time. The results of our experiments, conducted over 52 open-source Java 9+ applications, indicate that architectural inconsistencies are widespread and demonstrate DARCY’s effectiveness for automated resolution of these inconsistencies.