Inspection Error: Top level element is not completed

I tried using Irida build#3341.
However I get this error message in all my jsp files:

Top level element is not completed

The reason is that the include file contains the top level element of my jsp.
*************************************************
header.jsp contents
*************************************************
********************************************* my_jsp_file.jsp contents <%@ page language="java" contentType="text/html; charset=UTF-8"%> <%@ include file="/include/header.jsp" %> <bean:message key="label.title"></bean:message> ******************************************** Irida higlights in red from ]]> tag down to the end of my jsp file.

Also, I keep on getting this error message:
Operation is not supported

Thus,I can't continue on using Irida for my project.
So, I decided to go back to Idea 4.5.4 again (since it is stable)