I started with a "vanilla" AppFuse 2.0-M5 (Spring-MVC modular), where "mvn site" works as expected. I then checked out the core classes as described in the Wiki (http://appfuse.org/display/APF/AppFuse+Core+Classes) and left them unchanged.

After that I ran the following commands on the root pom in this order:
mvn clean
mvn install
mvn site
mvn site -Dmaven.test.skip=true

Both of the site tasks failed with the same error message quoted below:

--- SNIP ---

[INFO] ------------------------------------------------------------------------
[ERROR] FATAL ERROR
[INFO] ------------------------------------------------------------------------
[INFO] Unable to load class declared as <mapping class="org.appfuse.model.User"/> in the configuration:
[INFO] ------------------------------------------------------------------------
[INFO] Trace
org.hibernate.MappingException: Unable to load class declared as <mapping class="org.appfuse.model.User"/> in the configuration:
        at org.hibernate.cfg.AnnotationConfiguration.parseMappingElement(AnnotationConfiguration.java:545)
[...]
Caused by: java.lang.ClassNotFoundException: org.appfuse.model.User
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
[...]
--- SNAP ---

Seems like there's something missing in the maven.test.classpath.

-------------------------------------------------------------
Workaround by Matt:
Adding <skip>${maven.test.skip}</skip> to the "componentProperties" section of the hibernate3 plugin, allows the 2nd command to work.