Application plugin does not handle dependent classes

Tried up to rc-3 and the issue is the same. When creating an application plugin-based distribution, the application will fail to run if dependencies are non-jars. The generated scripts expect to find arbitrary packages/classes in APP_HOME/lib/classes, but the actual location of the classes is directly at the APP_HOME/lib level (not beneath a classes subdirectory, which doesn’t actually exist).

The applications will run fine using gradle run.