I use both files, located in:

  war\WEB-INF\classes\log4j.properties
  war\WEB-INF\classes\logging.properties


In my "appengine-web.xml" file, I have the following extract for you:

  <?xml version="1.0" encoding="UTF-8"?>
  <appengine-web-app xmlns="http://appengine.google.com/ns/1.0";>
    <system-properties>
      <property
       name="java.util.logging.config.file"
       value="WEB-INF/classes/logging.properties"
      />
      <property
       name="log4j.configuration"
       value="file:WEB-INF/classes/log4j.properties"
      />
    </system-properties>
  </appengine-web-app>


I remember that I had a problem where the two file names included
capital letters, so reluctantly I made them both pure lower case!

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