 <p>You'll find that many open-source projects follow the <a href="http://maven.apache.org/guides/introduction/introduction-to-the-standard-directory-layout.html" rel="nofollow noreferrer">directory structure used by Maven</a>. In this setup your application source code is kept in src/main/java, application resources, including properties files, in src/main/resources, and other config files in src/main/config. Files related to unit tests use a similar directory structure; src/test/java and src/test/resources.</p> <p>Personally I tend to use this layout because of its widespread use. I also keep an "etc" directory beneath the project root to house files that aren't directly related to the application. For example, I keep configuration files for PMD and Checkstyle in etc.</p>