Second on Peter's suggestion.
I did learn a LONG time ago that it's best to make project directories either read-only or write-only, regardless of the build system you're using. I normally build an exploded WAR and feed that directly to
Tomcat for debugging, then jar up the exploded WAR when I want to make a distribution module. In keeping with not having permanent files in an output directory, I copy them from a static file source directory (or directories) into the exploded WAR directory when I do a build, just as I compile to the exploded WAR's WEB-INF/classes directory.