The Eclipse plugin currently always generates classpath entries with the "exported" attribute set to "true". In multi-project builds this means that depending Eclipse projects see all dependencies of dependent Eclipse projects, even dependencies which Gradle would typically not export.

This is an issue for testCompile and testRuntime dependencies, and it's also an issue when creating a "provided" configuration as described in the EclipseClasspath documentation. "provided" dependencies should never be exported, and can cause conflicts in depending projects.

This is an issue with a rather large and complicated build I'm currently involved with using the gradle-m2metadata plugin.