I'll try to do my best with the explanation, but I don't know if it will be clear
enough...
Every component on a J2EE has its own "environment" with which the component can
reference another component (an EJB, datasource...) by a "logical" name. This logical
component name is used by programmers to reference another component in programming
time because they must not know the real JNDI name of the component they are
accessing, which may be known on deployment time. That name is not (or may not be) the
real name of the other component, so when deploying that component there has to be a
mapping between these two references (the logical one, that is, the one used on the
component; and the real one, that is, the one in the JNDI).
To give you an example, an EJB accessing another EJB uses in its code this lookup:
ic.lookup("java:comp/env/ejb/Users");
and in the ejb-jar.xml defines that reference with "ejb/Users" and its local and local
home interfaces. Another EJB can access another EJB using the same logical name, but
using other interfaces because it has another reference definition (every EJB has its
own logical definitions, which are not shared between each other).
Then, using the jboss.xml file (on the JBoss AS), the deployer maps this logical
references to real JNDI names.
Well, now the difference using XDoclet. If you use logical component names, you define
a reference and then map it to the real JNDI name; in the other hand, if you use
physical JNDI names, you directly access the real JNDI names, without using a logical
mapping. Using one or another is your choice.
I hope I was able to clearly explain you the difference.
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