Struts Assistant picks the wrong config files.

The project I'm working on is built through an ant script so I don't rely on IDEA to do my build. Part of that build is creating the WEB-INF dir for packaging into a war. For some reason, after I run a build the Struts Assistant latches onto the struts-config.xml and tiles-config.xml that are in the build output directory. This causes Struts Assistant to flag all my tiles definitions as duplicates AND misdirects all the IDE navigations away from the configuration files in my source directory.

This is happening even though I've explicitly excluded that folder in the parent module. Is there any way to tell Struts Assistant exactly which files I want it to use for the struts-config.xml and tiles-config.xml?