http://confluence.atlassian.com/display/DOC/Editing+the+Footer - explains how . Basically you need to change vi property files inside of a jar file.
Instead, I just keep it simple, edit footer-content.vm and comment the first instance of,
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#*$action.getText('licensefooter.community',[$action.getText('url.atlassian'), $action.getText('hitcounter.community'), $license.organisation])*#<br> |