For the web layer, you can header based authentication.  You will need some 
form of an authenticator.  Look here for guidance:
http://wiki.jboss.org/wiki/Wiki.jsp?page=GenericHeaderBasedAuthentication

Once the login module is invoked, then the JBoss security layer takes care of 
the subject/caching etc. The authenticator should pluck the relevant 
information from the http request and then pass them to the jaas layer.

Now for the ejb layer, I guess you will have to write a new interceptor and 
replace the security interceptor in the container configuration in 
conf/standardjboss.xml or write your own container config in jboss.xml in ejb 
jar.

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