Please close issue APF-784. This issue replaces it.
I really wanted to reopen issue APF-712.

Anyways here are the steps to reproduce this issue with 2.0-m5

Summary:
1. create basic Spring MVC project.
2. change project to use jpa-hibernate
4. change project to include full source
4. mvn jetty:run-war

Detailed steps:
1. mvn archetype:create -DarchetypeGroupId=org.appfuse -DarchetypeArtifactId=appfuse-basic-spring -DremoteRepositories=http://static.appfuse.org/repository -DarchetypeVersion=2.0-m5 -DgroupId=com.mycompany.app -DartifactId=myproject
2. cd myproject
3. follow steps found here http://appfuse.org/display/APF/Using+JPA for enabling JPA.
    A. Change the <dao.framework> property in your pom.xml to be jpa-hibernate instead of hibernate.
    B. Modify the configuration for the Hibernate3 Maven Plugin: change <implementation>annotationconfiguration</implementation> to <implementation>jpaconfiguration</implementation> in your pom.xml.
    C. DON't delete hibernate.cfg.xml upon recommendation that I need to keep it around to have things autogenerated.
4. mvn appfuse:full-source
5. mvn jetty:run-war

During step 5 I see this:

[INFO] [compiler:compile]
[INFO] Nothing to compile - all classes are up to date
[INFO] [resources:testResources]
[INFO] Using default encoding to copy filtered resources.
[INFO] Preparing hibernate3:hbm2ddl
[WARNING] Removing: hbm2ddl from forked lifecycle, to prevent recursive invocation.
[INFO] [native2ascii:native2ascii {execution: native2ascii-utf8}]
[INFO] [native2ascii:native2ascii {execution: native2ascii-8859_1}]
[INFO] [resources:resources]
[INFO] Using default encoding to copy filtered resources.
[INFO] [hibernate3:hbm2ddl {execution: default}]
[INFO] ------------------------------------------------------------------------
[ERROR] FATAL ERROR
[INFO] ------------------------------------------------------------------------
[INFO] No name provided and several persistence units found
[INFO] ------------------------------------------------------------------------
[INFO] Trace
javax.persistence.PersistenceException: No name provided and several persistence units found
        at org.hibernate.ejb.Ejb3Configuration.configure(Ejb3Configuration.java:226)
        at org.codehaus.mojo.hibernate3.configuration.JPAComponentConfiguration.createConfiguration(JPAComponentConfiguration.java:26)
        at org.codehaus.mojo.hibernate3.configuration.AbstractComponentConfiguration.getConfiguration(AbstractComponentConfiguration.java:32)
        at org.codehaus.mojo.hibernate3.exporter.Hbm2DDLExporterMojo.doExecute(Hbm2DDLExporterMojo.java:87)
        at org.codehaus.mojo.hibernate3.HibernateExporterMojo.execute(HibernateExporterMojo.java:139)
        at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:443)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:539)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalWithLifecycle(DefaultLifecycleExecutor.java:480)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.forkProjectLifecycle(DefaultLifecycleExecutor.java:896)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.forkLifecycle(DefaultLifecycleExecutor.java:739)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:510)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeStandaloneGoal(DefaultLifecycleExecutor.java:493)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:463)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:311)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:278)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:143)
        at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:334)
        at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:125)
        at org.apache.maven.cli.MavenCli.main(MavenCli.java:272)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315)
        at org.codehaus.classworlds.Launcher.launch(Launcher.java:255)
        at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430)
        at org.codehaus.classworlds.Launcher.main(Launcher.java:375)
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 9 seconds
[INFO] Finished at: Wed May 30 09:54:14 ADT 2007
[INFO] Final Memory: 13M/24M
[INFO] ------------------------------------------------------------------------


NOTE:

the first time you run mvn jetty:run-war you see this


Downloading: http://static.appfuse.org/repository/org/hibernate/hibernate-entitymanager/${hibernate.version}/hibernate-entitymanager-${hibernate.version}.jar
[INFO] ------------------------------------------------------------------------
[ERROR] BUILD ERROR
[INFO] ------------------------------------------------------------------------
[INFO] Failed to resolve artifact.

Missing:
----------
1) org.hibernate:hibernate-entitymanager:jar:${hibernate.version}

Try downloading the file manually from the project website.

Then, install it using the command:
      mvn install:install-file -DgroupId=org.hibernate -DartifactId=hibernate-entitymanager \
          -Dversion=${hibernate.version} -Dpackaging=jar -Dfile=/path/to/file

Path to dependency:
        1) com.mycompany.app:myproject:war:1.0-SNAPSHOT
        2) org.hibernate:hibernate-entitymanager:jar:${hibernate.version}

----------
1 required artifact is missing.

for artifact:
  com.mycompany.app:myproject:war:1.0-SNAPSHOT


I worked around that by adding in the pom.xml properties section the following
<hibernate.version>3.2.1.ga</hibernate.version>