Java application distribution as classes instead of jar file

I’m working on a project that is using an embedded version of Tomcat. I’m currently using the application plugin to create my application and distribution. This bundles my application code into a jar file, which is normally what one wants. However I’m having problems with Tomcat finding annotations inside this jar file. I found that if I didn’t bundle my classes into a jar file and pointed Tomcat at the classes directory instead of the jar, everything works.
So I’m wondering, is it possible to configure the application plugin to not create a jar file and just package up the class files from the application and the jar files from all dependencies?

I realize I could use the distribution plugin and manually specify what files to include. Then I would just need to create my own run target. Although this seems like reinventing the wheel, so I thought I’d ask first.