AJS.conglomerate.cookie can be written with invalid data that prevents other Atlassian applications from logging in.

• Run JIRA under "/jira" context (http://localhost:8080/jira)
• Go to UPM (plugin manager) and switch to install tab.
• Logout and login to JIRA

Actual: The AJS.conglomerate.cookie is saved under "/" (root context) with a value similar to:

__utma=111872281.2081964729.1332130805.1332130805.1332130805.1; __utmz=111872281.1332130805.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); AJS.conglomerate.cookie="||||||upm.tab=install; JSESSIONID=4D26AF92A8827231F3BAF4B7387DD6F2

Notice the missing closing quote in the value.

Now, attempt to login to Confluence running on http://localhost:8090. This cookie will be sent to confluence as well (since it is saved in root) and the application will fail to authenticate the user

Screen recording: http://screencast.com/t/6GwtrTAw

Notes:

• I am uncertain if the cookie will be set to this wrong value just by visiting this install tab (you might have to play a little with UPM to arrive at this state)
• We have confirmed that if the closing quote is added to the cookie, user is able to login successfully to Confluence.