It seems that on the way to JBoss 8.0, the structure of the "modules" directory was modified: it is now "modules\system\layers\base" instead of just "modules".
This prevents creation of a server runtime in Eclipse, because it checks for existence of a specific file in this path. I don't know whether this also has impact on running the server or on JavaEE project classpaths.

The JIRA for this change is https://issues.jboss.org/browse/AS7-6344

I observed this with a snapshot from http://hudson.jboss.org/hudson/view/JBoss%20AS/job/JBoss-AS-7.0.x/ (which contains a 8.0 Alpha actually)