Fix generated application.xml

The application.xml file generated by the preprocessor contains invalid module declarations.
In JBoss4 we are using "java" type modules to declare POJO jars - which is WRONG. EAR modules of type "java" must be used to define J2EE Client Application Modules.

See http://download.oracle.com/docs/cd/E13222_01/wls/docs90/client/thinclient.html#1079680

So the POJO jars must be added on the class path like any other third part libraries - and not deployed like JEE modules.

I will provide first a compatibility fix to be able to use the preprocessor on both jboss5 and jboss4 in a first time.
This fix is intercepting "module" contributions and is removing on the fly any java module if finds.
When we move on jboss5 the fix must be removed. See:

System.setProperty("org.nuxeo.runtme.preprocessing.jboss5", "true");
in NuxeoStructureDeployer.preprocess()

and i org.nuxeo.runtime.deployment.preprocessor.template.Template
remove code indicated by XXX sections.

After switching to JBoss5 deployment-fragment.xml files must be updated and <java> ,mdoules removed
Now the deployment-fragment file is optional and should only be used to generate configuration at preprocess time and by EJBs and connectors.