I modified my log4j.properties file, it now contains the line

log4j.appender.filelog.File=${catalina.home}/logs/atlassian-jira.log

and the log file is properly generated in Tomcat's /logs directory.

But JIRA can't find it. The System Information page and the Support Request page both contain the error message "Could not find atlassian-jira.log in current working directory".

Of course JIRA should not look in the current working directory, it should look whereever the property log4j.appender.filelog.File points to.