I have some projects with similar structure. After running eclipseClasspath task, I find some projects have multiple output directories like bin/main, bin/test in their .classpath files, some have single output directory bin. What is the logic used by eclipseClasspath in generating .classpath file?
Are we talking about a single multi-project build or a multiple Gradle builds? This logic changed in a recent Gradle version, so if you have different builds, then the reason is probably the Gradle version you are using.