STS deleting classes from Tomcat deployment directory

I recently upgraded to 3.6.1 and created a new Tomcat 8 server. Everything works if I do a full/clean build (Project > Clean) and then startup the server. However, as soon as a I edit a single file, the application hot redeploys and does not find any of my spring configuration:
2014-09-15 10:02:22 [localhost-startStop-1] INFO o.s.w.c.s.AnnotationConfigWebApplicationContext - Refreshing WebApplicationContext for namespace 'SpringMvcServlet-servlet': startup date [Mon Sep 15 10:02:22 EDT 2014]; parent: Root WebApplicationContext
2014-09-15 10:02:22 [localhost-startStop-1] INFO o.s.w.c.s.AnnotationConfigWebApplicationContext - No annotated classes found for specified class/package [com.my.springconfig.MvcConfig]
2014-09-15 10:02:22 [localhost-startStop-1] INFO o.s.w.s.DispatcherServlet - FrameworkServlet 'SpringMvcServlet': initialization completed in 293 ms

If I browse the deployment directory (right-click on the web app in the servers view) I can see that all the classes have been deleted. That is, all the folders exist as they would for a successful deployment, but there are not .class files. The only way to fix it is to shutdown the server and do a Project > Clean again.

This problem did not occur in my previous STS 3.4.x installation. I guess I'll have to revert to using until this bug is fixed.