Thanks for coming to the forum with your issue.
Just to make sure we are going on the same assumptions... when you say you are building the war file in STS, I assume that means you are using the Graills Command Prompt popup dialog to run the war command... right? (Or maybe you are using the Run On Server functionality, which doesn't work quite the same way).
I have recently discovered that grails war command uses the same target directory for compiling source code as our (STS) Groovy Eclipse compiler. If you are seeing files in the war file you didn't expect to see, then it is probably files that were compiled by the Groovy Eclipse compiler.
Stuff from plugins can indeed end up in the WEB_INF\classes folder that way because plugin source folders are added to the project's classpath for the Greclipse compiler.
This shouldn't really be a problem... but maybe we are compiling things that we shouldn't be compiling and need to tweak some of the classpath entries we create for plugin sources.
While I'm not 100% sure this explanation is right, this is probably what is happening.
Also I think we should consider this a bug in STS Grails tooling, and it needs to be fixed somehow.
I may need your help in figuring out the exact nature of the problem and the best way to implement the fix. I'm hoping that, since this bug is a bit of pain to you, you'll be willing to work with me a bit to get this fixed properly.
I'll post a link to the Jira issue I'm going to create shortly.
Kris De Volder -- SpringSource