The war directory is kind of none of the developers business. It's a directory that's chosen and owned by JBoss/Tomcat.
If you want to generate resources like pdf files and make them available as part of the same web context, I suggest using a download servlet. In the web.xml you can associate a url pattern like /download/* or something with a servlet. The servlet could load and pipe the pdf file through its servlet output stream.
This servlet could pull the pdf file from a database or some kind of temporary directory - which is controlled and owned by the servlet.
Well, how about the EOD Java programs which refers to the WAR application's classes directory?