How to Configure JIRA for Google Indexing
In JIRA 6.x these changes have to be made to both files in order to apply to all JIRA pages.
Note that you can also add a noindex tag, like:
<meta name="robots" content="noindex">
Once these changes have been made to the .jsp file(s), you will need to save that file and the restart JIRA in order for these changes to take effect.