JIRA 7 switched to precompiles jsp, that means usual .jsp template is not read by Tomcat any more.
Previously in JIRA 6, users are able to modify the default .jsp template file where customisation is possible by following this documentation JIRA Template & JSP's. However, at this moment, there is no documentation on how this can be achieved for JIRA 7.
To have documentation as per JIRA Template & JSP's for JIRA 7 and steps on how to make the changes done on the JSP files to be accepted by JIRA 7
<atlassian-jira>/atlassian-jira/includes/decorators/aui-layout/header.jsp page is not injected into every page in JIRA. So documentation should include new instructions, if possible.