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Projects such as JPackage that repackage Tomcat for Linux typically move the configuration to a directory dictated by the FHS standard (http://www.pathname.com/fhs/), and therefore use the java.util.logging.config.file property to set the location of the logging.properties file in the Tomcat startup script.

On Fedora this the startup script in typically located in /etc/rc.d/init.d/ and on Gentoo linux it is located in /etc/init.d/.