When you put the war file into webapps, and just don't use any Context information in server.xml (ie: do *not* put a context there for your webapp),
Tomcat has been able to unpack the WAR.
If you have a context, however, Tomcat isn't so smart..even with the proper attribute in place. That's been my experience.
So what if you want to set things up in your Context, like loggers ? You need to unpack the WAR file yourself, is the short answer.