See: https://community.jboss.org/message/800166#800166

What to do:
1. Do not block UI (put error in the log instead producing fatal error)
2. Make error message more clear
3. Try to refresh the project

Test case:

EXECUTE:
1. Create JSF Kick Start Project 'test'
2. Open "/test/WebContent/pages/hello.jsp" in external editor, change it then save
3. Open "/test/JavaSource/demo/User.java" in Eclipse Java Editor
4. Select method getName() then right click on it then select Refactor->Rename
5. Type new name then press Enter
ASSERT:
1. Dialog "Rename Method" appears with Problem: "Be sure, may be..."
2. "Cannot read resource(s). Resource '/test' is not in sync." message in Error Log

EXECUTE:
1. Press Button "Continue"

ASSERT: method renamed