NetBeans 7.4 not creating jar files properly - netbeans

Question

I am developing a project for a Java Enterprise Applications class. I have an application with an ejb module that has "facade" classes from a class library that connects to a simple Twitter-like database. All the logic is working fine, however, when I add the remote beans for the facade and try to run it, the application crashes with the stack trace included at the end.
Looking throught the GlassFish output screen, I found the following warnings:
WARNING: ACDEPL112: The following extensions or libraries are referenced from the manifest of C:\Users[project_path]\Questions\dist\gfdeploy\Questions\QuestionClient.jar but were not found where indicated: QuestionLib.jar ; ignoring and continuing
INFO: ACDEPL103: Java Web Start services started for the app client Questions/QuestionClient.jar (contextRoot: /Questions/QuestionClient)
INFO: Questions was successfully deployed in 3,097 milliseconds.
WARNING: The collection of metamodel [EntityType] types is empty. Model classes may not have been found during entity search for Java SE and some Java EE container managed persistence units. Please verify that your entity classes are referenced in persistence.xml using either elements or a global false element. The lookup on [class com.problemSet3.db.Questions] will return null.
WARNING: EJB5184:A system exception occurred during an invocation on EJB QuestionsFacade, method: public java.util.List com.problemSet3.db.AbstractFacade.findAll()
When I checked the path, I found that the .jar file mentioned exists where it should, but it is instead named QuestionLib_jar and it is a folder with all the contents of the jar file. This files are being generated by NetBeans, I don't know how the jar files are being compiled to folders instead of actual jars.
How can I fix this?
Stack trace
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.glassfish.appclient.client.acc.AppClientContainer.launch(AppClientContainer.java:446)
at org.glassfish.appclient.client.AppClientFacade.launch(AppClientFacade.java:183)
at org.glassfish.appclient.client.AppClientGroupFacade.main(AppClientGroupFacade.java:65)
Caused by: javax.ejb.EJBException
at com.sun.ejb.containers.EJBContainerTransactionManager.processSystemException(EJBContainerTransactionManager.java:748)
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:698)
at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:503)
at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4475)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2009)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:1979)
at com.sun.ejb.containers.EJBObjectInvocationHandler.invoke(EJBObjectInvocationHandler.java:212)
at com.sun.ejb.containers.EJBObjectInvocationHandlerDelegate.invoke(EJBObjectInvocationHandlerDelegate.java:79)
at com.sun.proxy.$Proxy295.findAll(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at com.sun.corba.ee.impl.presentation.rmi.ReflectiveTie.dispatchToMethod(ReflectiveTie.java:143)
at com.sun.corba.ee.impl.presentation.rmi.ReflectiveTie._invoke(ReflectiveTie.java:173)
at com.sun.corba.ee.impl.protocol.ServerRequestDispatcherImpl.dispatchToServant(ServerRequestDispatcherImpl.java:528)
at com.sun.corba.ee.impl.protocol.ServerRequestDispatcherImpl.dispatch(ServerRequestDispatcherImpl.java:199)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.handleRequestRequest(MessageMediatorImpl.java:1549)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.handleRequest(MessageMediatorImpl.java:1425)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.handleInput(MessageMediatorImpl.java:930)
at com.sun.corba.ee.impl.protocol.giopmsgheaders.RequestMessage_1_2.callback(RequestMessage_1_2.java:213)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.handleRequest(MessageMediatorImpl.java:694)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.dispatch(MessageMediatorImpl.java:496)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.doWork(MessageMediatorImpl.java:2222)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.performWork(ThreadPoolImpl.java:497)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.run(ThreadPoolImpl.java:540)
Caused by: java.lang.IllegalArgumentException: No [EntityType] was found for the key class [com.problemSet3.db.Questions] in the Metamodel - please verify that the [Entity] class was referenced in persistence.xml using a specific com.problemSet3.db.Questions property or a global false element.
at org.eclipse.persistence.internal.jpa.metamodel.MetamodelImpl.entityEmbeddableManagedTypeNotFound(MetamodelImpl.java:173)
at org.eclipse.persistence.internal.jpa.metamodel.MetamodelImpl.entity(MetamodelImpl.java:193)
at org.eclipse.persistence.internal.jpa.querydef.CommonAbstractCriteriaImpl.internalFrom(CommonAbstractCriteriaImpl.java:114)
at org.eclipse.persistence.internal.jpa.querydef.AbstractQueryImpl.from(AbstractQueryImpl.java:246)
at com.problemSet3.db.AbstractFacade.findAll(AbstractFacade.java:43)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4695)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:630)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:582)
at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:55)
at sun.reflect.GeneratedMethodAccessor115.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:582)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4667)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4655)
at com.sun.ejb.containers.EJBObjectInvocationHandler.invoke(EJBObjectInvocationHandler.java:205)
... 19 more
Java Result: 1

Answer 1

Well, after a painful night and morning I finally solved it. The persistence.xml file that was being used by the ejb module had this line:
<exclude-unlisted-classes>false</exclude-unlisted-classes>
I went into the properties and made it include each class manually, so now it looks like this:
<class>com.problemSet3.db.Answers</class>
<class>com.problemSet3.db.Questions</class>
<class>com.problemSet3.db.Users</class>
<exclude-unlisted-classes>true</exclude-unlisted-classes>
plus the other generated code. I still get the warning on GlassFish, but no exceptions are thrown.