JIRA requires that your <JIRA-home> directory is not the same or a sub-directory of your <JIRA-Installation> directory. Use the following process to separate the two folders.

1. Stop JIRA
2. Backup your current installation directory
3. Create a new directory meant to used for your <JIRA-home>
4. Move the following files/folders from your <JIRA-Installation> into the new <JIRA-home> directory
   • caches
   • data
   • databases (might not exist)
   • export
   • import
   • log
   • logos
   • monitor
   • plugins
   • tmp
   • dbconfig.xml
   • jira-config.properties (might not exist)
5. Edit your <JIRA-installation/atlassian-jira/WEB-INF/classes/jira-application.properties> file to point to the new location of the home directory
6. Start JIRA

When starting JIRA, you should be back to what your old instance looks like. If you are prompted to create a new instance shut JIRA down and make sure you've defined your <JIRA-home> correctly.