I built a webapp that uses JNDI to lookup JavaMail.

I was getting ClassCastExceptions trying to retreive a mail Session from JNDI, which turned out to be because NetBeans bundled mail.war
in the WAR lib/ (which causes classloader issues when getting a Session that was configured up in Tomcat itself).

Context initCtx = new InitialContext();
        Context envCtx = (Context) initCtx.lookup("java:comp/env");
        Object o = envCtx.lookup("mail/Session"); 
        // the debugger verifies that 'o' holds a javamail Session, but
        // but the next line raises a ClassCastException
        sendMailSession = (Session) o;

My workaround currently is to edit nbproject/build.xml and remove the <copyfiles> element from the 'library-inclusion-in-archive' target.

I couldn't find a knob in the GUI to enable this behaviour, so each time I change project properties I have to re-edit the file.

I may well be doing something wrong, but it'd be good to be able to have this enabled in the UI as an option.