### Eclipse Workspace Patch 1.0
#P org.jboss.tools.hibernate.jpt.core
Index: src/org/jboss/tools/hibernate/jpt/core/internal/context/AddGeneratedClassesJob.java
===================================================================
--- src/org/jboss/tools/hibernate/jpt/core/internal/context/AddGeneratedClassesJob.java	(revision 0)
+++ src/org/jboss/tools/hibernate/jpt/core/internal/context/AddGeneratedClassesJob.java	(revision 0)
@@ -0,0 +1,170 @@
+/*******************************************************************************
+ * Copyright (c) 2012 Red Hat, Inc.
+ * Distributed under license by Red Hat, Inc. All rights reserved.
+ * This program is made available under the terms of the
+ * Eclipse Public License v1.0 which accompanies this distribution,
+ * and is available at http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributor:
+ *     Red Hat, Inc. - initial API and implementation
+ ******************************************************************************/
+package org.jboss.tools.hibernate.jpt.core.internal.context;
+
+import java.util.List;
+
+import org.eclipse.core.resources.IResource;
+import org.eclipse.core.resources.IResourceRuleFactory;
+import org.eclipse.core.resources.ResourcesPlugin;
+import org.eclipse.core.resources.WorkspaceJob;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.core.runtime.IStatus;
+import org.eclipse.core.runtime.Status;
+import org.eclipse.core.runtime.SubMonitor;
+import org.eclipse.jdt.core.IType;
+import org.eclipse.jdt.core.JavaModelException;
+import org.eclipse.jpt.common.utility.internal.CollectionTools;
+import org.eclipse.jpt.common.utility.internal.iterables.FilteringIterable;
+import org.eclipse.jpt.common.utility.internal.iterables.TransformationIterable;
+import org.eclipse.jpt.jpa.core.JpaProject;
+import org.eclipse.jpt.jpa.core.context.persistence.MappingFileRef;
+import org.eclipse.jpt.jpa.core.context.persistence.Persistence;
+import org.eclipse.jpt.jpa.core.context.persistence.PersistenceUnit;
+import org.eclipse.jpt.jpa.core.context.persistence.PersistenceXml;
+import org.eclipse.jpt.jpa.core.internal.JptCoreMessages;
+import org.eclipse.jpt.jpa.core.resource.persistence.PersistenceFactory;
+import org.eclipse.jpt.jpa.core.resource.persistence.XmlJavaClassRef;
+import org.eclipse.jpt.jpa.core.resource.persistence.XmlPersistence;
+import org.eclipse.jpt.jpa.core.resource.persistence.XmlPersistenceUnit;
+import org.eclipse.jpt.jpa.core.resource.xml.JpaXmlResource;
+
+/**
+ * @author Dmitry Geraskov (geraskov@gmail.com)
+ *
+ */
+public class AddGeneratedClassesJob extends WorkspaceJob {
+	
+	private JpaProject jpaProject;
+	
+	private List<IResource> javaFilesToAdd;
+		
+	public AddGeneratedClassesJob(JpaProject jpaProject, List<IResource> javaFilesToAdd) {
+		super(JptCoreMessages.SYNCHRONIZE_CLASSES_JOB);
+		IResourceRuleFactory ruleFactory = ResourcesPlugin.getWorkspace().getRuleFactory();
+		setRule(ruleFactory.modifyRule(jpaProject.getProject()));
+		this.jpaProject = jpaProject;
+		this.javaFilesToAdd = javaFilesToAdd;
+	}
+	
+	@Override
+	public IStatus runInWorkspace(IProgressMonitor monitor) {
+		if (monitor.isCanceled()) {
+			return Status.CANCEL_STATUS;
+		}
+		final SubMonitor sm = SubMonitor.convert(monitor, JptCoreMessages.SYNCHRONIZING_CLASSES_TASK, 20);
+		final JpaXmlResource resource = jpaProject.getPersistenceXmlResource();
+		if (resource == null) {
+			//the resource would only be null if the persistence.xml file had an invalid content type
+			return Status.OK_STATUS;
+		}
+		if (sm.isCanceled()) {
+			return Status.CANCEL_STATUS;
+		}
+		sm.worked(1);
+		
+		resource.modify(new Runnable() {
+			public void run() {
+				XmlPersistence persistence = (XmlPersistence) resource.getRootObject();					
+				XmlPersistenceUnit persistenceUnit;
+				
+				if (persistence.getPersistenceUnits().size() > 0) {
+					persistenceUnit = persistence.getPersistenceUnits().get(0);
+				}
+				else {
+					persistenceUnit = PersistenceFactory.eINSTANCE.createXmlPersistenceUnit();
+					persistenceUnit.setName(jpaProject.getName());
+					persistence.getPersistenceUnits().add(persistenceUnit);
+				}
+				sm.worked(1);
+				
+				
+				//for (XmlJavaClassRef xmlJavaClassRef : classes) {
+					
+				//}
+				sm.worked(1);
+		
+				addNewClassRefs(sm.newChild(17), jpaProject, persistenceUnit);
+			}
+		});
+		return Status.OK_STATUS;
+	}
+	
+	protected void addNewClassRefs(IProgressMonitor monitor, JpaProject jpaProject, XmlPersistenceUnit persistenceUnit) {
+		Iterable<String> mappedClassNames = getMappedNewClassNames(jpaProject, '$');
+		final SubMonitor sm = SubMonitor.convert(monitor, CollectionTools.size(mappedClassNames));
+		
+		for (String fullyQualifiedTypeName : mappedClassNames) {
+			if ( ! mappingFileContains(jpaProject, fullyQualifiedTypeName)) {
+				XmlJavaClassRef classRef = PersistenceFactory.eINSTANCE.createXmlJavaClassRef();
+				classRef.setJavaClass(fullyQualifiedTypeName);
+				persistenceUnit.getClasses().add(classRef);
+			}
+			sm.worked(1);
+		}
+	}
+
+	protected Iterable<String> getMappedNewClassNames(final JpaProject jpaProject, final char enclosingTypeSeparator) {
+		return new TransformationIterable<IType, String>(
+				new FilteringIterable<IType>(
+						new TransformationIterable<String, IType>(
+								jpaProject.getMappedJavaSourceClassNames()) {
+							@Override
+							protected IType transform(String fullyQualifiedName) {
+								return AddGeneratedClassesJob.this.findType(jpaProject, fullyQualifiedName);
+							}
+						}){
+					@Override
+					protected boolean accept(IType o) {
+						for (IResource res : javaFilesToAdd) {
+							if (res.equals(o.getResource())){
+								return true;
+							}
+						}
+						return false;
+					}
+				}) {
+			@Override
+			protected String transform(IType jdtType) {
+				return jdtType.getFullyQualifiedName(enclosingTypeSeparator);
+			}
+		};
+	}
+	
+	protected IType findType(JpaProject jpaProject, String typeName) {
+		try {
+			return jpaProject.getJavaProject().findType(typeName);
+		} catch (JavaModelException ex) {
+			return null;  // ignore exception?
+		}
+	}
+
+	boolean mappingFileContains(JpaProject jpaProject, String fullyQualifiedTypeName) {
+		PersistenceXml persistenceXml = jpaProject.getRootContextNode().getPersistenceXml();
+		if (persistenceXml == null) {
+			return false;
+		}
+		Persistence persistence = persistenceXml.getPersistence();
+		if (persistence == null) {
+			return false;
+		}
+		if (persistence.persistenceUnitsSize() == 0) {
+			return false;
+		}
+		PersistenceUnit persistenceUnit = persistence.persistenceUnits().next();
+		for (MappingFileRef mappingFileRef : CollectionTools.iterable(persistenceUnit.mappingFileRefs())) {
+			if (mappingFileRef.getPersistentType(fullyQualifiedTypeName) != null) {
+				return true;
+			}
+		}
+		return false;
+	}
+}
\ No newline at end of file
Index: META-INF/MANIFEST.MF
===================================================================
--- META-INF/MANIFEST.MF	(revision 41199)
+++ META-INF/MANIFEST.MF	(working copy)
@@ -22,7 +22,9 @@
  org.eclipse.jst.j2ee;bundle-version="1.1.500",
  org.eclipse.persistence.jpa.jpql;bundle-version="1.0.0",
  org.eclipse.jst.j2ee.core;bundle-version="1.2.100",
- org.hibernate.eclipse.libs;bundle-version="3.4.0"
+ org.hibernate.eclipse.libs;bundle-version="3.4.0",
+ org.eclipse.wst.common.emf;bundle-version="1.2.100",
+ org.eclipse.emf.ecore.xmi;bundle-version="2.7.0"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.6
 Bundle-Vendor: %Bundle-Vendor.0
 Export-Package: org.jboss.tools.hibernate.jpt.core.internal,
#P org.jboss.tools.hibernate.jpt.ui
Index: src/org/jboss/tools/hibernate/jpt/ui/wizard/GenerateEntitiesWizard.java
===================================================================
--- src/org/jboss/tools/hibernate/jpt/ui/wizard/GenerateEntitiesWizard.java	(revision 41199)
+++ src/org/jboss/tools/hibernate/jpt/ui/wizard/GenerateEntitiesWizard.java	(working copy)
@@ -10,15 +10,29 @@
   ******************************************************************************/
 package org.jboss.tools.hibernate.jpt.ui.wizard;
 
+import java.util.LinkedList;
+import java.util.List;
+
+import org.eclipse.core.resources.IFile;
+import org.eclipse.core.resources.IResource;
+import org.eclipse.core.resources.IResourceChangeEvent;
+import org.eclipse.core.resources.IResourceChangeListener;
+import org.eclipse.core.resources.IResourceDelta;
+import org.eclipse.core.resources.IResourceDeltaVisitor;
+import org.eclipse.core.resources.ResourcesPlugin;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.debug.core.ILaunchConfigurationWorkingCopy;
 import org.eclipse.debug.core.ILaunchManager;
+import org.eclipse.jdt.core.IJavaProject;
+import org.eclipse.jdt.core.IPackageFragmentRoot;
+import org.eclipse.jdt.core.JavaModelException;
 import org.eclipse.jface.viewers.IStructuredSelection;
 import org.eclipse.jface.wizard.Wizard;
 import org.eclipse.jpt.jpa.ui.internal.JptUiMessages;
 import org.hibernate.console.KnownConfigurations;
 import org.hibernate.eclipse.launch.HibernateLaunchConstants;
 import org.jboss.tools.hibernate.jpt.core.internal.HibernateJpaProject;
+import org.jboss.tools.hibernate.jpt.core.internal.context.AddGeneratedClassesJob;
 import org.jboss.tools.hibernate.jpt.ui.HibernateJptUIPlugin;
 import org.jboss.tools.hibernate.jpt.ui.internal.platform.HibernateJpaPlatformUi;
 
@@ -33,7 +47,6 @@
 	
 	private GenerateEntitiesWizardPage initPage;
 	
-	
 	public GenerateEntitiesWizard( HibernateJpaProject jpaProject, IStructuredSelection selection) {
 		super();
 		this.jpaProject = jpaProject;
@@ -71,7 +84,18 @@
 			wc.setAttribute(HibernateLaunchConstants.ATTR_EXPORTERS + '.' + HibernateJpaPlatformUi.exporter_id + ".extension_id",  //$NON-NLS-1$
 						HibernateLaunchConstants.ATTR_PREFIX + "hbm2java"); //$NON-NLS-1$
 			try {
+				NewJavaFilesListener rcl = new NewJavaFilesListener(jpaProject.getJavaProject());;
+				if (!jpaProject.discoversAnnotatedClasses()){
+					ResourcesPlugin.getWorkspace().addResourceChangeListener(rcl);
+				}				
 				wc.launch(ILaunchManager.RUN_MODE, null);
+				if (!jpaProject.discoversAnnotatedClasses()){
+					ResourcesPlugin.getWorkspace().removeResourceChangeListener(rcl);
+					if (rcl.generatedJavaFiles.size() > 0){
+						AddGeneratedClassesJob job = new AddGeneratedClassesJob(jpaProject, rcl.generatedJavaFiles);
+						job.schedule();
+					}
+				}
 			} catch (CoreException e) {
 				HibernateJptUIPlugin.logException(e);
 			} finally{
@@ -84,3 +108,71 @@
 	}
 
 }
+
+class NewJavaFilesListener implements IResourceChangeListener {
+
+	List<IResource> generatedJavaFiles = new LinkedList<IResource>();
+	private List<IPackageFragmentRoot> sourceRoots = new LinkedList<IPackageFragmentRoot>();
+
+	/**
+	 * @param projectName
+	 */
+	public NewJavaFilesListener(IJavaProject project) {
+		try {
+			IPackageFragmentRoot[] allPackageFragmentRoots = project.getAllPackageFragmentRoots();
+			for (int j = 0; j < allPackageFragmentRoots.length; j++) {
+				if (!allPackageFragmentRoots[j].isArchive()){
+					sourceRoots.add(allPackageFragmentRoots[j]);
+				}
+			}
+		} catch (JavaModelException e) {
+			e.printStackTrace();
+		}
+	}
+
+	@Override
+	public void resourceChanged(IResourceChangeEvent event) {
+		IResourceDelta delta = event.getDelta();
+		try {
+			delta.accept(new IResourceDeltaVisitor() {
+				
+				@Override
+				public boolean visit(IResourceDelta delta) throws CoreException {
+					IResource resource = delta.getResource();
+					int type = resource.getType();
+					//we also have to consider projects we dependent on here!!!
+					if (type == IResource.ROOT
+							|| type == IResource.PROJECT
+							|| type == IResource.FOLDER)
+						return true;
+
+					if (resource instanceof IFile && delta.getKind() == IResourceDelta.ADDED) {
+						// see if this is it
+						IFile candidate = (IFile) resource;
+						if (isJavaSourceFile(candidate)) {
+							generatedJavaFiles.add(candidate);
+						}
+					}
+					return false;
+				}
+
+				private boolean isJavaSourceFile(IResource candidate) {
+					if (candidate.getName().endsWith(".java")){ //$NON-NLS-1$
+						while (candidate.getParent() != null){
+							for (IPackageFragmentRoot root : sourceRoots) {
+								if (root.getResource().equals(candidate.getParent())){
+									return true;
+								}
+							}
+							candidate = candidate.getParent();
+						}
+					}
+					return false;
+				}
+			});
+		} catch (CoreException e) {
+			e.printStackTrace();
+		}
+	}
+	
+}