The "eclipseClasspath" task seems to ignore configuration excludes when generating the Eclipse .classpath file. The resulting .classpath file includes all transitive dependencies, even ones that have been excluded by configuration.

Here is an example script that demonstrates the issue:

apply plugin: "java"
apply plugin: "eclipse"

repositories {
mavenCentral()
}

configurations {
compile

}

dependencies {
compile "org.springframework:spring-core:3.0.3.RELEASE"
}

When you run "gradle eclipseCp" with 0.9preview3, commons-logging is not added to the .classpath file, as expected. When you run "gradle eclipseClasspath" with 0.9rc1, commons-logging IS added to the .classpath file.