Don't know why, but for this reason this just don't look right. I searched for a 'standard' META-INF location, but couldn't find an answer, apparently this is an obvious thing except for boneheads like me :-)
Another thing is, (although this may not be the right forum) why Ant <jar> creates META-INF on the root of the war if META-INF is supposed to be on the classpath?
The second is correct because META-INF should be in the place as the .class files. To visualize why this makes sense, think of a jar file. It has a META-INF folder in the root and the top level package also in the root. The same goes for the WEB-INF/classes directory. Both are at the same level.
Some IDEs show the META-INF higher up because they put it with the source code. It still jars up into the standard format though.