The war plugin bundles up the files in the runtime configuration to package in the resulting war. It does not however, depend on the projects in this configuration so they may not be build. This causes the current java multiproject sample to fail in a clean directory with "gradle dists".
Curiously it does not currently cause any integration tests failures. I'll add tests for this case.
One other note, this was previously working because tests (which were run because of the previous dependencies of the Java plugin) were adding the dependencies needed to build the dependent project. If you have run tests in the past, the needed api-1.0.jar has already been built and uploaded to the internal repository. This will then cause dists to work - EVEN AFTER A CLEAN since clean does not remove the jars from the internal repo. I think this is bad and will file another Jira to discuss getting clean to remove internal repo jars.