If you're just getting warnings about ignoring manifest entries then you can ignore them. The exceptions you're getting from your hello.war are not related.
Check that you've got the environment variable JAVA_HOME setup properly.
... Just my 2cents.
You are correct that the exceptions in my hello.war are unrelated--they were due to an incorrectly-sequenced web.xml file. It still seems strange to me that it is considered okay to distribute a system that issues warnings such as this, right "out of the box." But who am I to say how an obviously successful product should behave?