my experience tells me that missing persistence.xml,will generate the same exception too.
i caught the same error msg today when i tried to run a jar package packed by ant.
when i used jar tvf to check the content of the jar file, i realized that "ant" forgot to pack the persistnece.xml for me.
after I manually repacked the jar file ,the error msg disappered.
so i believe maybe you should try simplely putting META-INF under src directory and placing your persistence.xml there.