From Confluence version 5.2.5 to latest when you hit the diagnostic mode in the UI, all the debug logging will go to the tomcat terminal instead of the atlassian-confluence.log.

Steps to reproduce:

1. Go to Confluence Admin > Logging and Profiling.
2. Hit the "Diagnostics" button under Log4j Logging.
3. Navigate in Confluence and make any changes you like (create/delete a space/page).
4. If you open the <Confluence Home>\llogs\atlassian-confluence.log, you will only see this line:

   2014-01-30 19:03:38,256 DEBUG [http-8090-1] [atlassian.confluence.logging.ConfluenceHomeLogAppender] shutdown closing appender
   

5. Now if you check the Tomcat Terminal you will see all the debug information being generated in there:
   

This was done in a windows environment, however we have a customers with linux that also have the same behaviour, the logging doesn't go to catalina.out either or any of the other Confluence logs.

This works fine in Confluence version 5.2.3, but it shows this behaviour from version 5.2.5 to latest.

Work Around:

1. Shutdown Confluence.
2. Navigate to <Confluence Install>\confluence\WEB-INF\classes.
3. Backup the log4j.properties file.
4. Edit the file.
5. Search for the first uncommented "log4j.logger".
6. Under it add the classes you want like below example:

   log4j.logger.com.atlassian.confluence.extra.jira=DEBUG
   log4j.logger.com.atlassian.applinks.applinks-plugin=DEBUG
   

7. Save the file and start Confluence.
8. The DEBUG will show up in atlassian-confluence log in the way it supposed to.
9. Once you get the information you want, restore the log4j.properties file to it's previous version