When JIRA starts in Tomcat (as in the standalone distro), the first thing it does is print these warnings:

log4j:WARN No appenders could be found for logger (org.apache.commons.digester.Digester).
log4j:WARN Please initialize the log4j system properly.

This does not affect subsequent operation, but is annoying and should be fixed.

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The problem arose when JIRA migrated from Tyrex to JOTM. Previously the webapp was responsible for obtaining a JTA implementation, but now it obtains one from the app server. The result of this change is that we now require commons-logging.jar in (and only in) the Tomcat classloader, but the actual logging implementation (log4j) is in the JIRA webapp. Somehow, commons-logging is detecting the presence of log4j, but not finding the log4j.properties file.