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The simple answer is: It depends!
If you use the servlet protocol (org.jboss.arquillian.protocol:arquillian-protocol-servlet:1.1.2.Final) with a managed or remote container adapter the tests are run in the context of a web application.
Arquillian will either add itself to the only web module of an ear or add a new one if there is none or you can designate the one to be used.
I am not sure about the context when using an embedded container as I am working with JBoss AS 7 & WebSphere for the most part and these containers don't have embedded container adapters.
When using the JMX protocol I don't know the context either but it is not an the context of some EJB but probably the JMX adapter of the AppServer. So it is rather no context at all. I also had lots of trouble with that when working with multiple deployments in one container that use the same classes.
So I would recommend using the Servlet protocol (2.5 or 3.0). Then you have a well defined context being either your web module or the one created by Arquillian that you can adjust appropriately by adding required refs etc.