Drop the use of filesonly - it caused failures with some applications that scan Tomcat JARs such as Jira.

git-svn-id: https://svn.apache.org/repos/asf/tomcat/trunk@1573363 13f79535-47bb-0310-9956-ffa450edef68
Alternative solution to avoiding adding empty packages to JARs.

git-svn-id: https://svn.apache.org/repos/asf/tomcat/trunk@1573364 13f79535-47bb-0310-9956-ffa450edef68
Avoid NPE in resource cache when making an invalid request for a resource outside of the web application.

git-svn-id: https://svn.apache.org/repos/asf/tomcat/trunk@1573368 13f79535-47bb-0310-9956-ffa450edef68