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In JBoss 5 the datasource definitions for databases and an XML file configuring JBoss JNDI were generated during the Installer step and copied to the JBoss deploy directory. This is no longer the way to do things for JBoss EAP 6.1. Production services has to make sure that the configuration file for the JBoss instance contains the XML to define datasources and JNDI.
To Work on Current Release
Check out from SVN the current version of the cas-server source. (If the Yale source is in a separate directory check it out too, but it has probably been added as subdirectories of the cas-server directory.) Check out the Installer project directory.
If it is at all possible, make changes only to the WAR Overlay project subdirectory.
Sometimes you need behavior that is just slightly different from an existing JASIG version of some bean. The design of CAS is to have standard interfaces, classes that implement these interfaces, and configuration done with Spring XML files that select the appropriate implementation class using a <bean> element. If the class you want to change is configured this way to Spring (search for its class name in XML files), then you can often make a copy of the JASIG source in the WAR Overlay src/main/java tree, changing the org.jasig package name to edu.yale and so on. Then change the behavior of the source you just copied. Now go to the XML configuration that references the original class by name and change the fully qualified classname to match the new class you just created. Typically the interfaces don't change between releases, so you may not have to update your modified source when you migrate to a new release.
What cannot be changed in the WAR Overlay project? If a class or interface is referenced by import in Java source, then the Java mechanism to search for a class by name (the "ClassLoader") typically searches first for a class of the desired name that came from the same source as the class that is looking for it. JBoss regards the WEB-INF/lib and the WEB-INF/classes as two separate sources. Although WEB-INF/classes is said to be "searched first", when some code in cas-server-core is looking for a class name it will find the version of that name that is also in cas-server-core and will not find something with the same name in WEB-INF/classes. So in general you cannot simply copy any org.jasig source to the WAR Overlay source directory, compile it, and then assume that the version you just compiled will override the original code because it is in the "classes" directory and "classes is searched before lib". Think really hard if you need to change something here, but then if you really need to change it you need to make a modification to the original JASIG source and then copy and reconcile that change to each subsequent release.