I have a similar issue - Eclipse 3.4.1, Jboss AS 4.2.3GA, JBoss Tool 3.0.0.CR1, 
Seam 2.0.2SP1

Application is deployed via Eclipse.  It is an EAR project with WAR and EJB.  
When I manually deploy it to JBoss sever inside eclipse, the application starts 
and works fine.

When I change a web page (such as one .xhtml page) and click Save to save the 
file.  In a minute, server starts to publish.  It also tries to publish  the 
java classes.  However, the application will not start because it does not hot 
deploy the application correctly.

As a note, I used to use Eclipse Europa (ie, 3.3.2), and Jboss Tool 3.0.0 
Alpha, and it does not deploy the Java classes.

Here is the console log -

14:44:19,635 INFO  [EJBContainer] STOPPED EJB: 
com.harasoftware.eem.session.AuthenticatorBean ejbName: AuthenticatorBean
14:44:19,639 INFO  [EJBContainer] STOPPED EJB: 
com.harasoftware.eem.session.impl.BookingSumCalculatorBean ejbName: 
BookingSumCalculatorBean
14:44:19,642 INFO  [EJBContainer] STOPPED EJB: 
com.harasoftware.eem.session.impl.CompanyCopyBean ejbName: CompanyCopyBean
14:44:19,645 INFO  [EJBContainer] STOPPED EJB: 
com.harasoftware.eem.session.impl.NumberRangeGeneratorBean ejbName: 
NumberRangeGeneratorBean
14:44:19,655 INFO  [EJBContainer] STOPPED EJB: 
com.harasoftware.eem.session.impl.UserSessionManagerBean ejbName: 
UserSessionManagerBean
14:44:19,663 INFO  [EJBContainer] STOPPED EJB: 
com.harasoftware.eem.session.LoadStructureAction ejbName: LoadStructureAction
14:44:19,672 INFO  [EJBContainer] STOPPED EJB: 
com.harasoftware.eem.session.UIRenderingManagerBean ejbName: 
UIRenderingManagerBean
14:44:19,673 INFO  [EJBContainer] STOPPED EJB: 
com.harasoftware.eem.session.UnitConversion ejbName: UnitConversion
14:44:19,673 INFO  [PersistenceUnitDeployment] Stopping persistence unit 
persistence.units:ear=eem-ear.ear,jar=eem-ejb.jar,unitName=eem
14:44:19,674 INFO  [SessionFactoryImpl] closing
14:44:19,674 INFO  [SessionFactoryObjectFactory] Unbinding factory from JNDI 
name: persistence.units:ear=eem-ear.ear,jar=eem-ejb.jar,unitName=eem
14:44:19,674 INFO  [NamingHelper] JNDI InitialContext 
properties:{java.naming.factory.initial=org.jnp.interfaces.NamingContextFactory,
 java.naming.factory.url.pkgs=org.jboss.naming:org.jnp.interfaces}
14:44:19,676 INFO  [SessionFactoryObjectFactory] Unbound factory from JNDI 
name: persistence.units:ear=eem-ear.ear,jar=eem-ejb.jar,unitName=eem
14:44:19,676 INFO  [ConnectionFactoryBindingService] Unbound ConnectionManager 
'jboss.jca:service=DataSourceBinding,name=eemDatasource' from JNDI name 
'java:eemDatasource'
14:44:19,776 INFO  [ConnectionFactoryBindingService] Bound ConnectionManager 
'jboss.jca:service=DataSourceBinding,name=eemDatasource' to JNDI name 
'java:eemDatasource'
14:44:19,776 INFO  [PersistenceUnitDeployment] Starting persistence unit 
persistence.units:ear=eem-ear.ear,jar=eem-ejb.jar,unitName=eem
14:44:23,897 INFO  [Ejb3Configuration] found EJB3 Entity bean: 
com.harasoftware.eem.entity.Accrual
....
14:44:25,599 INFO  [Configuration] Reading mappings from resource : 
META-INF/orm.xml
14:44:25,619 INFO  [Ejb3Configuration] [PersistenceUnit: eem] META-INF/orm.xml 
found
...
14:44:34,351 INFO  [EJBContainer] STARTED EJB: 
com.harasoftware.eem.session.UIRenderingManagerBean ejbName: 
UIRenderingManagerBean
14:44:34,359 INFO  [EJBContainer] STARTED EJB: 
com.harasoftware.eem.session.UnitConversion ejbName: UnitConversion

and then it hangs ..


If I undeploy the application and redeploy iy again, it start to work again.


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