EJB3 deployment fails silently when deploying with an old version of persistence.xml (pre-RC4/5)

When you convert an application from the EJB 3.0 RC3 release to RC4/5, the persistence.xml file format has changed. If you don't change you persistence.xml, but change everything else, the application deploys without any errors or exceptions being thrown or written to the log. At runtime, you will get an error like the following:

Unable to inject jndi dependency: env/jira.ejb.JiraTestOuterBean/jiraTestInner into field private jira.ejb.JiraTestInner jira.ejb.JiraTestOuterBean.jiraTestInner

It seems like you are having a problem with dependency injection on the stateless session bean, but the fact that the stateless session depends on the undeployed entity is the real issue.