I'm using Diana build #8664.
When I make rebuild project sometimes in war file IDEA doesn't create folder for some GWT module(I'm using GWT 1.5.2) and placed all files of that module just in root folder of war.
My suggestions that it could depends on length of module name or some symbols in module name or smthng else.
It is bug of IDEA. To solve the problem I've modified module name(made name more complicated-added one word). Hope it helps anybody. And please fix this bug.