What is the rationale for the .deployed marker? It's really counter-intuitive. Just make a copy to avoid locking/classloading issues and leave the original in place.
Also, for exploded deployments have a different META-INF/jboss-deploy marker to trigger the deployment? Counter-intuitive as well. The whole idea with the ./deploy dir (or whatever is called) is you look there and you know what gets deployed, you don't need to traverse directories to find out. Or unzip something and it gets deployed, no need for extra files.
IMO the AS4 model of hot-deployment (no VFS) was the most practival and successful. People knew that to avoid the "early deployment" problem for large or nested deployments they just have to do an atomic filesystem mv. Through stuff in and it just gets deployed, no markers or any other type of magic. I don't see why we need to re-discover the wheel.