The snapshots are no longer duplicated when running eclipse, however the versions are still duplicated.

Can you elaborate on what you mean by that, and how it can be reproduced?

Nevermind, seemed to be running the wrong gradle version.

Before, we would see that if we changed a version of a non-snapshot dependency, the dependency would remain inside the deployment assembly of eclipse unless the cleanEclipse command would run out. For example:

apply plugin: 'war'
apply plugin: 'eclipse-wtp'

repositories {
        mavenCentral()
}

dependencies {
      compile 'junit:junit:4.8.1'
        // run eclipse command, comment out above line, uncomment bottom line, then rerun eclipse
//        compile 'junit:junit:4.8.2'
}

This test case would generate two junit dependencies inside the deployment assembly, but not inside the .classpath. This has been fixed in 1.4.