2) I also would like to get 3 sub dirs in the "resource" folder:  
"META-IINF" for files that goes in the ear (ie application.xml), WEB- 
INF for the web module and JPA for file that go into the jpa-ejb jar


This is a big change, but again, we need to address the entire way we  
structure examples in Seam 3, and align with JBoss Tools so that our  
examples work ootb there. This means adopting the JBT structure for  
projects I think.

Again, we need to start a wiki page for this :-)

One thing that should help is that we know integrate with m2eclipse allowing you to at least use maven.

I still don't know (haven't had time to look into it) how we are going to handle (in any IDE) that there are
multiple deployment/configuration descriptors in one project - most non-jbosstools-tools assumes
a specific structure (i.e. persistence.xml is in META-INF and not called something else) - but maybe
maven's profile feature can be used for it....something to explore at least.