Hi Jordan,
have you tried Gradle 2.14.1 and Buildship 1.0.17? Buildship now correctly filters the classpath entries for war/ear projects to only include those that should be deployed to the server, so your classpath in Eclipse and in Gradle should match.
As for Java applications, there is still more work to do to get the test dependencies out of the runtime classpath. We don’t have a clear timeline for this at the moment. If a community member would like to step up, I’d be happy to guide them through the design and review process. Alternatively, it is also possible to develop this as an open source partnership.
Cheers,
Stefan