Personally, I follow the Maven build pattern - I first gather the contents of the WAR in a single directory location, then I package up the whole directory. That way I have both a packaged WAR file and an "exploded" WAR directory.
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.
An IDE is no substitute for an Intelligent Developer.