Atlassian JIRA 3.12 through 4.1 allows remote authenticated administrators to execute arbitrary code by modifying the (1) attachment (aka attachments), (2) index (aka indexing), or (3) backup path and then uploading a file, as exploited in the wild in April 2010.
https://exchange.xforce.ibmcloud.com/vulnerabilities/57828
http://www.securityfocus.com/bid/39485
http://www.openwall.com/lists/oss-security/2010/04/16/4
http://www.openwall.com/lists/oss-security/2010/04/16/3
http://secunia.com/advisories/39353
http://jira.atlassian.com/browse/JRA-21004
http://jira.atlassian.com/browse/JRA-20995
http://confluence.atlassian.com/display/JIRA/JIRA+Security+Advisory+2010-04-16