x_Roo_JavaBean.aj not being generated when entities and repositories created in alternative package

I have created a Spring Roo project using JSF and Primefaces, and have successfully created a basic working web application using the following roo shell commands (Based on the bikeshop example):

entity jpa --class ~.domain.Entity1 --activeRecord false --equals --testAutomatically
entity jpa --class ~.domain.Entity2 --activeRecord false --equals --testAutomatically
entity jpa --class ~.domain.Entity3 --activeRecord false --equals --testAutomatically
repository jpa --interface ~.domain.Entity1
repository jpa --interface ~.domain.Entity2
repository jpa --interface ~.domain.Entity3
web jsf all --package ~.web

A few basic fields were added manually to the entities.

I then wanted to move away from the problem domain and add additional system infrastructure for my application. To highlight this distinction, I wanted to store these entities, repositories and web infrastructure in a package called system. To do this, I entered the following commands at the roo shell.

entity jpa --class ~.system.domain.SystemMessage --activeRecord false --equals --testAutomatically
entity jpa --class ~.system.domain.SystemNotification --activeRecord false --equals --testAutomatically
entity jpa --class ~.system.domain.SystemReminder --activeRecord false --equals --testAutomatically
repository jpa --interface ~.system.domain.SystemMessageRepository
repository jpa --interface ~.system.domain.SystemNotificationRepository
repository jpa --interface ~.system.domain.SystemReminderRepository
web jsf all --package ~.system.web

When accessed from a browser, the menu appears with no page output. The errors that appear at the console indicate:

Aug 29, 2014 9:08:57 PM com.sun.faces.util.Util checkIdUniqueness
SEVERE: JSF1007: Duplicate component ID menuForm:appUserSubmenu found in view.

On closer inspection, the menu contains two instances of every submenu, one after the other.

2nd attempt
---------------
I then threw away the above changes by closing the STS deleting the root folder and getting a new copy of the application files from SVN. This gave me a working system produced from entering the first set of roo shell commands above.

I then typed in the second set of commands into the roo shell with the exception of the web jsf command. Instead I typed:

web jsf all --package ~.web

This is the same command as used in the first set of roo shell commands. This time, the application started and all menu items can be selected correctly except for the SystemMessage options and the SystemNotification options. The SystemReminder options work correctly. The SystemMessage and SystemNotification options generate the following stack trace:

HTTP Status 500 - javax.el.PropertyNotFoundException: Target Unreachable, identifier 'systemMessageBean' resolved to null

type Exception report

message javax.el.PropertyNotFoundException: Target Unreachable, identifier 'systemMessageBean' resolved to null

description The server encountered an internal error that prevented it from fulfilling this request.

exception

javax.servlet.ServletException: javax.el.PropertyNotFoundException: Target Unreachable, identifier 'systemMessageBean' resolved to null
javax.faces.webapp.FacesServlet.service(FacesServlet.java:606)
org.primefaces.webapp.filter.FileUploadFilter.doFilter(FileUploadFilter.java:79)
org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:180)
org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)

root cause

javax.faces.el.EvaluationException: javax.el.PropertyNotFoundException: Target Unreachable, identifier 'systemMessageBean' resolved to null
javax.faces.component.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:95)
com.sun.faces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:102)
javax.faces.component.UICommand.broadcast(UICommand.java:315)
javax.faces.component.UIViewRoot.broadcastEvents(UIViewRoot.java:794)
javax.faces.component.UIViewRoot.processApplication(UIViewRoot.java:1259)
com.sun.faces.lifecycle.InvokeApplicationPhase.execute(InvokeApplicationPhase.java:81)
com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:118)
javax.faces.webapp.FacesServlet.service(FacesServlet.java:593)
org.primefaces.webapp.filter.FileUploadFilter.doFilter(FileUploadFilter.java:79)
org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:180)
org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)

root cause

javax.el.PropertyNotFoundException: Target Unreachable, identifier 'systemMessageBean' resolved to null
org.apache.el.parser.AstValue.getTarget(AstValue.java:98)
org.apache.el.parser.AstValue.invoke(AstValue.java:259)
org.apache.el.MethodExpressionImpl.invoke(MethodExpressionImpl.java:274)
javax.faces.component.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:88)
com.sun.faces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:102)
javax.faces.component.UICommand.broadcast(UICommand.java:315)
javax.faces.component.UIViewRoot.broadcastEvents(UIViewRoot.java:794)
javax.faces.component.UIViewRoot.processApplication(UIViewRoot.java:1259)
com.sun.faces.lifecycle.InvokeApplicationPhase.execute(InvokeApplicationPhase.java:81)
com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:118)
javax.faces.webapp.FacesServlet.service(FacesServlet.java:593)
org.primefaces.webapp.filter.FileUploadFilter.doFilter(FileUploadFilter.java:79)
org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:180)
org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)

On closer inspection, the SystemReminderBean_Roo_ManagedBean.aj file has been generated but the equivalent files for SystemMessage and SystemNotification have not. The sources for the 3 entities are as follows:

@RooJavaBean
@RooToString
@RooJpaEntity
@RooEquals
public class SystemMessage {
}

@RooJavaBean
@RooToString
@RooJpaEntity
@RooEquals
public class SystemNotification {
}

@RooJavaBean
@RooToString
@RooJpaEntity
@RooEquals
public class SystemReminder {
}

I didn't bother creating any fields in them this time. I have performed this test twice now and both times it is the last entity in the System package that works (SystemReminder) and not the first 2.

3rd attempt
--------------
I started from a working system again and then entered the following roo shell commands, which are in the opposite order to the previous test:

entity jpa --class ~.system.domain.SystemReminder --activeRecord false --equals --testAutomatically
entity jpa --class ~.system.domain.SystemNotification --activeRecord false --equals --testAutomatically
entity jpa --class ~.system.domain.SystemMessage --activeRecord false --equals --testAutomatically

repository jpa --interface ~.system.domain.SystemReminderRepository
repository jpa --interface ~.system.domain.SystemNotificationRepository
repository jpa --interface ~.system.domain.SystemMessageRepository

web jsf all --package ~.web

This time the SystemMessage menus worked (The last entity created) and the other two didn't. As expected, a SystemMessageBean_Roo_ManagedBean.aj was created but no equivalents were created for the first two entities in the system package.