rosjava dependencies

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In the version of rosjava before using Gradle, Java files for all messages in packages depended on in manifest.xml would be created in ~/.ros/rosjava. I am trying to convert an old package to use the new Gradle build system but I get the following errors for all of my imports:

error: package org.ros.message.geometry_msgs does not exist

Also ~/.ros/rosjava is not created. Is there something extra I need to do with Gradle to make Java files created for these non-rosjava packages?