I cloned a production server to test the upgrade to newer versions of JIRA, Confluence, FishEye and Crowd before rolling it out on the production environment.
After cloning and changing all references to the new hostname everything seemed to be working, except the application links were dead. Trying to relocate them to the new hostname only resulted in the error message
The application at URL '...' is not responding. Please confirm that you want to use this URL.