Hmm..don't worry about it. I have decided to simplify things a bit by not using a client-jar,and by sticking my ejb-project and web-project in the same EAR. It seems that when I build it publishes to the server automatically(can't seem to find the option to switch it off)It's really quite strange how the glassfish tools bundle for eclipse behaves....It tells me that it can't deploy aplication 'xxx' but then if I look in the autodeploy folder or the admin console application 'xxx' isn't listed.
The glassfish tools bundle for eclipse is doesn't seem to generate the sun-ejb-jar.xml either unless I ask it to create a client-jar.
There also seems to be a bug with my version of eclipse..if you add the JPA facet to a project and then remove it...it will complain that the project still has it bla bla bla