diff --git a/src/main/java/org/apache/maven/plugin/eclipse/EclipsePlugin.java b/src/main/java/org/apache/maven/plugin/eclipse/EclipsePlugin.java
index 2bb5e82..2f1fa3a 100644
--- a/src/main/java/org/apache/maven/plugin/eclipse/EclipsePlugin.java
+++ b/src/main/java/org/apache/maven/plugin/eclipse/EclipsePlugin.java
@@ -31,14 +31,17 @@
 import java.util.Set;
 import java.util.TreeSet;
 
+import org.apache.maven.artifact.Artifact;
 import org.apache.maven.artifact.handler.ArtifactHandler;
 import org.apache.maven.model.Resource;
 import org.apache.maven.plugin.MojoExecutionException;
 import org.apache.maven.plugin.eclipse.writers.EclipseClasspathWriter;
+import org.apache.maven.plugin.eclipse.writers.EclipseManifestWriter;
 import org.apache.maven.plugin.eclipse.writers.EclipseOSGiManifestWriter;
 import org.apache.maven.plugin.eclipse.writers.EclipseProjectWriter;
 import org.apache.maven.plugin.eclipse.writers.EclipseSettingsWriter;
 import org.apache.maven.plugin.eclipse.writers.EclipseWriterConfig;
+import org.apache.maven.plugin.eclipse.writers.wtp.EclipseWtpApplicationXMLWriter;
 import org.apache.maven.plugin.eclipse.writers.wtp.EclipseWtpComponent15Writer;
 import org.apache.maven.plugin.eclipse.writers.wtp.EclipseWtpComponentWriter;
 import org.apache.maven.plugin.eclipse.writers.wtp.EclipseWtpFacetsWriter;
@@ -354,6 +357,20 @@
      */
     private boolean isJavaProject;
 
+    /**
+     * Must the manifest files be written for java projects so that that the jee classpath for wtp is correct.
+     * 
+     * @parameter expression="${eclipse.wtpmanifest}" default-value="false"
+     */
+    private boolean wtpmanifest;
+    
+    /**
+     * Must the application files be written for ear projects in a separate directory.
+     * 
+     * @parameter expression="${eclipse.wtpapplicationxml}" default-value="false"
+     */
+    private boolean wtpapplicationxml;
+    
     protected boolean isJavaProject()
     {
         return isJavaProject;
@@ -776,6 +793,10 @@
     {
         EclipseWriterConfig config = createEclipseWriterConfig( deps );
 
+        if (wtpmanifest && isJavaProject())
+        {
+            EclipseManifestWriter.addManifestResource(getLog(), config);
+        }
         // NOTE: This could change the config!
         writeExtraConfiguration( config );
 
@@ -803,7 +824,12 @@
         {
             new EclipseClasspathWriter().init( getLog(), config ).write();
         }
-
+        
+        if (wtpapplicationxml)
+        {
+            new EclipseWtpApplicationXMLWriter().init(getLog(), config).write();
+        }
+        
         if ( pde )
         {
             this.getLog().info( "The Maven Eclipse plugin runs in 'pde'-mode." );
@@ -862,6 +888,8 @@
         String projectName = IdeUtils.getProjectName( config.getProjectNameTemplate(), project );
 
         config.setEclipseProjectName( projectName );
+        
+        config.setWtpapplicationxml(wtpapplicationxml);
 
         Set convertedBuildCommands = new LinkedHashSet();
 
@@ -1162,4 +1190,11 @@
         }
         return IdeUtils.PROJECT_NAME_DEFAULT_TEMPLATE;
     }
+
+    /**
+     * {@inheritDoc}
+     */
+    public String getProjectNameForArifact(Artifact artifact) {
+        return IdeUtils.getProjectName(calculateProjectNameTemplate(), artifact);
+    }
 }
diff --git a/src/main/java/org/apache/maven/plugin/eclipse/writers/EclipseManifestWriter.java b/src/main/java/org/apache/maven/plugin/eclipse/writers/EclipseManifestWriter.java
new file mode 100644
index 0000000..0e73841
--- /dev/null
+++ b/src/main/java/org/apache/maven/plugin/eclipse/writers/EclipseManifestWriter.java
@@ -0,0 +1,393 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements. See the NOTICE file distributed with this
+ * work for additional information regarding copyright ownership. The ASF
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law
+ * or agreed to in writing, software distributed under the License is
+ * distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the specific language
+ * governing permissions and limitations under the License.
+ */
+package org.apache.maven.plugin.eclipse.writers;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Set;
+import java.util.jar.Attributes;
+import java.util.jar.Manifest;
+
+import org.apache.maven.archiver.ManifestConfiguration;
+import org.apache.maven.archiver.MavenArchiver;
+import org.apache.maven.artifact.repository.ArtifactRepository;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.eclipse.Constants;
+import org.apache.maven.plugin.eclipse.EclipseSourceDir;
+import org.apache.maven.plugin.eclipse.Messages;
+import org.apache.maven.plugin.eclipse.writers.wtp.AbstractWtpResourceWriter;
+import org.apache.maven.plugin.ide.IdeDependency;
+import org.apache.maven.plugin.ide.IdeUtils;
+import org.apache.maven.plugin.logging.Log;
+import org.apache.maven.project.MavenProject;
+
+/**
+ * Create or adapt the manifest files for the RAD6 runtime dependencys.
+ * attention these will not be used for the real ear these are just to get the
+ * runtime enviorment using the maven dependencies. WARNING: The manifest
+ * resources added here will not have the benefit of the dependencies of the
+ * project, since that's not provided in the setup() apis, one of the locations
+ * from which this writer is used in the RadPlugin.
+ * 
+ * @author <a href="mailto:nir@cfc.at">Richard van Nieuwenhoven </a>
+ */
+public class EclipseManifestWriter extends AbstractEclipseWriter {
+
+    private static final String MANIFEST_MF_FILENAME = "MANIFEST.MF";
+
+    private static final String META_INF_DIRECTORY = "META-INF";
+
+    private static final String GENERATED_RESOURCE_DIRNAME = "target" + File.separatorChar + "generated-resources" + File.separatorChar + "eclipse";
+
+    private static final String WEBAPP_RESOURCE_DIR = "src" + File.separatorChar + "main" + File.separatorChar + "webapp";
+
+    /**
+     * Search the project for the existing META-INF directory where the manifest
+     * should be located.
+     * 
+     * @return the apsolute path to the META-INF directory
+     */
+    public String getMetaInfBaseDirectory(MavenProject project) {
+        String metaInfBaseDirectory = null;
+
+        if (this.config.getProject().getPackaging().equals(Constants.PROJECT_PACKAGING_WAR)) {
+            metaInfBaseDirectory = this.config.getProject().getBasedir().getAbsolutePath() + File.separatorChar + EclipseManifestWriter.WEBAPP_RESOURCE_DIR;
+
+            this.log.debug("Attempting to use: " + metaInfBaseDirectory + " for location of META-INF in war project.");
+
+            File metaInfDirectoryFile = new File(metaInfBaseDirectory + File.separatorChar + EclipseManifestWriter.META_INF_DIRECTORY);
+
+            if (metaInfDirectoryFile.exists() && !metaInfDirectoryFile.isDirectory()) {
+                metaInfBaseDirectory = null;
+            }
+        }
+
+        for (int index = this.config.getSourceDirs().length - 1; metaInfBaseDirectory == null && index >= 0; index--) {
+
+            File manifestFile =
+                new File(this.config.getEclipseProjectDirectory(), this.config.getSourceDirs()[index].getPath() + File.separatorChar + EclipseManifestWriter.META_INF_DIRECTORY + File.separatorChar
+                    + EclipseManifestWriter.MANIFEST_MF_FILENAME);
+
+            this.log.debug("Checking for existence of META-INF/MANIFEST.MF file: " + manifestFile);
+
+            if (manifestFile.exists()) {
+                metaInfBaseDirectory = manifestFile.getParentFile().getParent();
+            }
+        }
+
+        return metaInfBaseDirectory;
+    }
+
+    /**
+     * Write the manifest files use an existing one it it exists (it will be
+     * overwritten!! in a war use webapp/META-INF else use the generated rad6
+     * sourcefolder
+     * 
+     * @see AbstractWtpResourceWriter#write(EclipseSourceDir[],
+     *      ArtifactRepository, File)
+     * @param sourceDirs
+     *            all eclipse source directorys
+     * @param localRepository
+     *            the local reposetory
+     * @param buildOutputDirectory
+     *            build output directory (target)
+     * @throws MojoExecutionException
+     *             when writing the config files was not possible
+     */
+    public void write() throws MojoExecutionException {
+        String metaInfBaseDirectory = getMetaInfBaseDirectory(this.config.getProject());
+
+        if (metaInfBaseDirectory == null) {
+            // TODO: if this really is an error, shouldn't we stop the build??
+            throw new MojoExecutionException(Messages.getString("EclipseCleanMojo.nofilefound", new Object[]{
+                EclipseManifestWriter.META_INF_DIRECTORY
+            }));
+        }
+//        if (this.config.getEclipseProjectName().equals(IdeUtils.getProjectName(IdeUtils.PROJECT_NAME_WITH_VERSION_TEMPLATE, this.config.getProject()))) {
+//            MavenArchiver mavenArchiver = new MavenArchiver();
+//            ManifestConfiguration configuration = new ManifestConfiguration() {
+//
+//                public boolean isAddClasspath() {
+//                    return true;
+//                }
+//            };
+//
+//            File manifestFile = new File(metaInfBaseDirectory + File.separatorChar + EclipseManifestWriter.META_INF_DIRECTORY + File.separatorChar + EclipseManifestWriter.MANIFEST_MF_FILENAME);
+//            manifestFile.getParentFile().mkdirs();
+//
+//            try {
+//                PrintWriter printwriter = new PrintWriter(manifestFile);
+//                mavenArchiver.getManifest(this.config.getProject(), configuration).write(printwriter);
+//                printwriter.close();
+//            } catch (Exception e) {
+//                this.log.error(Messages.getString("EclipsePlugin.cantwritetofile", new Object[]{
+//                    metaInfBaseDirectory + File.separatorChar + EclipseManifestWriter.MANIFEST_MF_FILENAME
+//                }));
+//            }
+//        } else {
+            Manifest manifest = createNewManifest();
+
+            File manifestFile = new File(metaInfBaseDirectory + File.separatorChar + EclipseManifestWriter.META_INF_DIRECTORY + File.separatorChar + EclipseManifestWriter.MANIFEST_MF_FILENAME);
+
+            System.out.println("MANIFEST LOCATION: " + manifestFile);
+
+            if (shouldNewManifestFileBeWritten(manifest, manifestFile)) {
+                System.out.println("Writing manifest...");
+
+                manifestFile.getParentFile().mkdirs();
+
+                try {
+                    FileOutputStream stream = new FileOutputStream(manifestFile);
+
+                    manifest.write(stream);
+
+                    stream.close();
+
+                } catch (Exception e) {
+                    this.log.error(Messages.getString("EclipsePlugin.cantwritetofile", new Object[]{
+                        metaInfBaseDirectory + File.separatorChar + EclipseManifestWriter.MANIFEST_MF_FILENAME
+                    }));
+                }
+
+//            }
+        }
+    }
+
+    /**
+     * make room for a Manifest file. use a generated resource for JARS and for
+     * WARS use the manifest in the webapp/META-INF directory.
+     * 
+     * @throws MojoExecutionException
+     */
+    public static void addManifestResource(Log log, EclipseWriterConfig config) throws MojoExecutionException {
+
+        EclipseManifestWriter manifestWriter = new EclipseManifestWriter();
+        manifestWriter.init(log, config);
+
+        String packaging = config.getProject().getPackaging();
+
+        String manifestDirectory = manifestWriter.getMetaInfBaseDirectory(config.getProject());
+
+
+        if (!Constants.PROJECT_PACKAGING_EAR.equals(packaging) && !Constants.PROJECT_PACKAGING_WAR.equals(packaging) && manifestDirectory == null) {
+
+            String generatedResourceDir = config.getProject().getBasedir().getAbsolutePath() + File.separatorChar + EclipseManifestWriter.GENERATED_RESOURCE_DIRNAME;
+
+            manifestDirectory = generatedResourceDir + File.separatorChar + "META-INF";
+
+            try {
+                new File(manifestDirectory).mkdirs();
+                File manifestFile = new File(manifestDirectory + File.separatorChar + "MANIFEST.MF");
+                if (manifestFile.exists()) {
+                    manifestFile.delete();
+                }
+                manifestFile.createNewFile();
+            } catch (IOException e) {
+                log.error(Messages.getString("EclipsePlugin.cantwritetofile", new Object[]{
+                    manifestDirectory + File.separatorChar + "META-INF" + File.separatorChar + "MANIFEST.MF"
+                }));
+            }
+
+            log.debug("Adding " + EclipseManifestWriter.GENERATED_RESOURCE_DIRNAME + " to eclipse sources ");
+
+            EclipseSourceDir[] sourceDirs = config.getSourceDirs();
+            EclipseSourceDir[] newSourceDirs = new EclipseSourceDir[sourceDirs.length + 1];
+            System.arraycopy(sourceDirs, 0, newSourceDirs, 0, sourceDirs.length);
+            newSourceDirs[sourceDirs.length] = new EclipseSourceDir(EclipseManifestWriter.GENERATED_RESOURCE_DIRNAME, null, true, false, null, null, false);
+            config.setSourceDirs(newSourceDirs);
+        }
+
+        if (Constants.PROJECT_PACKAGING_WAR.equals(packaging)) {
+            new File(config.getProject().getBasedir().getAbsolutePath() + File.separatorChar + "src" + File.separatorChar + "main" + File.separatorChar + "webapp"
+                + File.separatorChar + "META-INF").mkdirs();
+        }
+
+        // special case must be done first because it can add stuff to the
+        // classpath that will be
+        // written by the superclass
+        manifestWriter.write();
+    }
+
+    /**
+     * Add one dependency to the black separated classpath stringbuffer. When
+     * the project is available in the reactor (current build) then the project
+     * is used else the jar representing the artifact. System dependencies will
+     * only be included if they are in this project.
+     * 
+     * @param classpath
+     *            existing classpath to append
+     * @param dependency
+     *            dependency to append as jar or as project
+     */
+    private void addDependencyToClassPath(StringBuffer classpath, IdeDependency dependency) {
+        if (!dependency.isTestDependency() && !dependency.isProvided() && !dependency.isSystemScopedOutsideProject(this.config.getProject())) {
+
+            // blank is the separator in manifest classpath's
+            if (classpath.length() != 0) {
+                classpath.append(' ');
+            }
+            // if the dependency is a workspace project add the project and not
+            // the jar
+            if (!dependency.isReferencedProject()) {
+                classpath.append(dependency.getFile().getName());
+            } else {
+                classpath.append(dependency.getEclipseProjectName() + ".jar");
+            }
+        }
+    }
+
+    /**
+     * Check if the two manifests are equal. Manifest.equal can not be used
+     * because of the special case the Classpath entr, witch must be comaired
+     * sorted so that a different oder in the classpath does not result in "not
+     * equal". This not not realy correct but in this case it is more important
+     * to reduce the number of version-controll files.
+     * 
+     * @param manifest
+     *            the new manifest
+     * @param existingManifest
+     *            to compaire the new one with
+     * @return are the manifests equal
+     */
+    private boolean areManifestsEqual(Manifest manifest, Manifest existingManifest) {
+        if (existingManifest == null) {
+            return false;
+        }
+
+        Set keys = new HashSet();
+        Attributes existingMap = existingManifest.getMainAttributes();
+        Attributes newMap = manifest.getMainAttributes();
+        keys.addAll(existingMap.keySet());
+        keys.addAll(newMap.keySet());
+        Iterator iterator = keys.iterator();
+        while (iterator.hasNext()) {
+            Attributes.Name key = (Attributes.Name) iterator.next();
+            String newValue = (String) newMap.get(key);
+            String existingValue = (String) existingMap.get(key);
+            // special case classpath... they are qual when there entries
+            // are equal
+            if (Attributes.Name.CLASS_PATH.equals(key)) {
+                newValue = orderClasspath(newValue);
+                existingValue = orderClasspath(existingValue);
+            }
+            if ((newValue == null || !newValue.equals(existingValue)) && (existingValue == null || !existingValue.equals(newValue))) {
+                return false;
+            }
+        }
+        return true;
+    }
+
+    /**
+     * Convert all dependencies in a blank seperated list of jars and projects
+     * representing the classpath.
+     * 
+     * @return the blank separeted classpath string
+     */
+    private String constructManifestClasspath() {
+        StringBuffer stringBuffer = new StringBuffer();
+        IdeDependency[] deps = this.config.getDeps();
+
+        for (int index = 0; index < deps.length; index++) {
+            addDependencyToClassPath(stringBuffer, deps[index]);
+        }
+
+        return stringBuffer.toString();
+    }
+
+    /**
+     * Create a manifest contaigning the required classpath.
+     * 
+     * @return the newly created manifest
+     */
+    private Manifest createNewManifest() {
+        Manifest manifest = new Manifest();
+        manifest.getMainAttributes().put(Attributes.Name.MANIFEST_VERSION, "1.0");
+        manifest.getMainAttributes().put(Attributes.Name.CLASS_PATH, constructManifestClasspath());
+        return manifest;
+    }
+
+    /**
+     * Aphabeticaly sort the classpath. Do this by splitting it up, sort the
+     * entries and gleue them together again.
+     * 
+     * @param newValue
+     *            classpath to sort
+     * @return the sorted classpath
+     */
+    private String orderClasspath(String newValue) {
+        if (newValue == null) {
+            return null;
+        }
+        String[] entries = newValue.split(" ");
+        Arrays.sort(entries);
+        StringBuffer buffer = new StringBuffer(newValue.length());
+        for (int index = 0; index < entries.length; index++) {
+            buffer.append(entries[index]);
+            buffer.append(' ');
+        }
+        return buffer.toString();
+    }
+
+    /**
+     * Read and parse the existing manifest file.
+     * 
+     * @param manifestFile
+     *            file
+     * @return the read manifest
+     * @throws IOException
+     *             if the file could not be read
+     */
+    private Manifest readExistingManifest(File manifestFile) throws IOException {
+        if (!manifestFile.exists()) {
+            return null;
+        }
+
+        Manifest existingManifest = new Manifest();
+        FileInputStream inputStream = new FileInputStream(manifestFile);
+        existingManifest.read(inputStream);
+        inputStream.close();
+        return existingManifest;
+    }
+
+    /**
+     * Verify is the manifest sould be overwritten this sould take in account
+     * that the manifest should only be written if the contents of the classpath
+     * was changed not the order. The classpath sorting oder should be ignored.
+     * 
+     * @param manifest
+     *            the newly created classpath
+     * @param manifestFile
+     *            the file where the manifest
+     * @return if the new manifest file must be written
+     * @throws MojoExecutionException
+     */
+    private boolean shouldNewManifestFileBeWritten(Manifest manifest, File manifestFile) throws MojoExecutionException {
+        try {
+            Manifest existingManifest = readExistingManifest(manifestFile);
+            if (areManifestsEqual(manifest, existingManifest)) {
+                this.log.info(Messages.getString("EclipseCleanMojo.unchanged", manifestFile.getAbsolutePath()));
+                return false;
+            }
+        } catch (Exception e) {
+            throw new MojoExecutionException(Messages.getString("EclipseCleanMojo.nofilefound", manifestFile.getAbsolutePath()), e);
+        }
+        return true;
+    }
+}
diff --git a/src/main/java/org/apache/maven/plugin/eclipse/writers/EclipseWriterConfig.java b/src/main/java/org/apache/maven/plugin/eclipse/writers/EclipseWriterConfig.java
index 1db9438..8784811 100644
--- a/src/main/java/org/apache/maven/plugin/eclipse/writers/EclipseWriterConfig.java
+++ b/src/main/java/org/apache/maven/plugin/eclipse/writers/EclipseWriterConfig.java
@@ -123,6 +123,10 @@
     
     private String contextName;
     
+    /**
+     * @see EclipsePlugin#wtpapplicationxml()
+     */
+    private boolean wtpapplicationxml;
     
     /**
      * Getter for <code>deps</code>.
@@ -416,4 +420,13 @@
         this.contextName = deployName;
     }
     
+    public boolean getWtpapplicationxml()
+    {
+         return this.wtpapplicationxml;
+    }
+    
+    public void setWtpapplicationxml( boolean wtpapplicationxml )
+    {
+        this.wtpapplicationxml = wtpapplicationxml;
+    }    
 }
diff --git a/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/AbstractWtpResourceWriter.java b/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/AbstractWtpResourceWriter.java
index cced0fa..1034a3e 100644
--- a/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/AbstractWtpResourceWriter.java
+++ b/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/AbstractWtpResourceWriter.java
@@ -19,6 +19,7 @@
 package org.apache.maven.plugin.eclipse.writers.wtp;
 
 import org.apache.maven.artifact.repository.ArtifactRepository;
+import org.apache.maven.model.Plugin;
 import org.apache.maven.plugin.MojoExecutionException;
 import org.apache.maven.plugin.eclipse.Messages;
 import org.apache.maven.plugin.eclipse.writers.AbstractEclipseWriter;
@@ -27,8 +28,11 @@
 import org.apache.maven.plugin.ide.JeeUtils;
 import org.apache.maven.project.MavenProject;
 import org.codehaus.plexus.util.xml.XMLWriter;
+import org.codehaus.plexus.util.xml.Xpp3Dom;
 
 import java.io.File;
+import java.util.Iterator;
+import java.util.List;
 
 /**
  * Base class to hold common constants used by extending classes.
@@ -149,7 +153,7 @@
      * @param basedir
      * @throws MojoExecutionException
      */
-    protected void addDependency( XMLWriter writer, IdeDependency dep, ArtifactRepository localRepository, File basedir )
+    protected void addDependency( XMLWriter writer, IdeDependency dep, ArtifactRepository localRepository, File basedir, String deployPath )
         throws MojoExecutionException
     {
         String handle;
@@ -161,7 +165,7 @@
             // <dependency-type>uses</dependency-type>
             // </dependent-module>
 
-            handle = "module:/resource/" + dep.getArtifactId() + "/" + dep.getArtifactId(); //$NON-NLS-1$ //$NON-NLS-2$
+            handle = "module:/resource/" + dep.getEclipseProjectName() + "/" + dep.getEclipseProjectName(); //$NON-NLS-1$ //$NON-NLS-2$
         }
         else
         {
@@ -199,7 +203,9 @@
 
         writer.startElement( ELT_DEPENDENT_MODULE );
 
-        writer.addAttribute( ATTR_DEPLOY_PATH, "/WEB-INF/lib" ); //$NON-NLS-1$
+        writer.addAttribute( "archiveName",dep.getEclipseProjectName()+"."+dep.getType()); 
+
+        writer.addAttribute( ATTR_DEPLOY_PATH, deployPath ); //$NON-NLS-1$
         writer.addAttribute( ATTR_HANDLE, handle );
 
         writer.startElement( ELT_DEPENDENCY_TYPE );
@@ -212,7 +218,15 @@
     protected void writeWarOrEarResources( XMLWriter writer, MavenProject project, ArtifactRepository localRepository )
         throws MojoExecutionException
     {
-
+        // use /WEB-INF/lib for war projects and / or the configured defaultLibBundleDir for ear projects  
+    	String deployDir = IdeUtils.getPluginSetting( config.getProject(), ARTIFACT_MAVEN_EAR_PLUGIN,
+                "defaultLibBundleDir",
+                "/" );
+        
+        if (project.getPackaging().equals("war")) 
+        {
+            deployDir = "/WEB-INF/lib";
+        }
         // dependencies
         for ( int j = 0; j < config.getDeps().length; j++ )
         {
@@ -220,11 +234,11 @@
             String type = dep.getType();
 
             // NB war is needed for ear projects, we suppose nobody adds a war dependency to a war/jar project
-            // exclude test and provided deps
-            if ( ( !dep.isTestDependency() && !dep.isProvided() )
+            // exclude test and provided and system dependencies outside the project 
+            if ( ( !dep.isTestDependency() && !dep.isProvided() && !dep.isSystemScopedOutsideProject(project))
                             && ( "jar".equals( type ) || "ejb".equals( type ) || "ejb-client".equals( type ) || "war".equals( type ) ) ) //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
             {
-                addDependency( writer, dep, localRepository, config.getProject().getBasedir() );
+                addDependency( writer, dep, localRepository, config.getProject().getBasedir(), deployDir );
             }
         }
     }
diff --git a/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/EclipseWtpApplicationXMLWriter.java b/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/EclipseWtpApplicationXMLWriter.java
new file mode 100644
index 0000000..b883cb4
--- /dev/null
+++ b/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/EclipseWtpApplicationXMLWriter.java
@@ -0,0 +1,514 @@
+package org.apache.maven.plugin.eclipse.writers.wtp;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+
+import org.apache.maven.artifact.repository.ArtifactRepository;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.eclipse.EclipseSourceDir;
+import org.apache.maven.plugin.ide.IdeDependency;
+import org.codehaus.plexus.util.FileUtils;
+import org.codehaus.plexus.util.IOUtil;
+import org.codehaus.plexus.util.xml.PrettyPrintXMLWriter;
+import org.codehaus.plexus.util.xml.XMLWriter;
+import org.codehaus.plexus.util.xml.Xpp3Dom;
+import org.codehaus.plexus.util.xml.Xpp3DomBuilder;
+import org.codehaus.plexus.util.xml.Xpp3DomWriter;
+
+/**
+ * This writer creates the application.xml and the .modulemaps files for RAD6
+ * the the META-INF directory in the project root. this is where RAD6 requires
+ * the files to be. These will be independent of the real application.xml witch
+ * will be generated the stad. maven way.
+ * 
+ * @author <a href="mailto:nir@cfc.at">Richard van Nieuwenhoven</a>
+ */
+public class EclipseWtpApplicationXMLWriter extends AbstractWtpResourceWriter {
+	private static final String APPLICATION_XML_APPLICATION = "application";
+
+	private static final String APPLICATION_XML_CONTEXT_ROOT = "context-root";
+
+	private static final String APPLICATION_XML_DESCRIPTION = "description";
+
+	private static final String APPLICATION_XML_DISPLAY_NAME = "display-name";
+
+	private static final String APPLICATION_XML_FILENAME = "application.xml";
+
+	private static final String APPLICATION_XML_MODULE = "module";
+
+	private static final String APPLICATION_XML_WEB = "web";
+
+	private static final String APPLICATION_XML_WEB_URI = "web-uri";
+
+	private static final String HREF = "href";
+
+	private static final String ID = "id";
+
+	private static final String MODULEMAP_EARPROJECT_MAP = "modulemap:EARProjectMap";
+
+	private static final String MODULEMAPS_APPLICATION_EJB_MODULE = "application:EjbModule";
+
+	private static final String MODULEMAPS_APPLICATION_WEB_MODULE = "application:WebModule";
+
+	private static final String MODULEMAPS_FILENAME = ".modulemaps";
+
+	private static final String MODULEMAPS_MAPPINGS = "mappings";
+
+	private static final String MODULEMAPS_PROJECT_NAME = "projectName";
+
+	private static final String MODULEMAPS_UTILITY_JARMAPPINGS = "utilityJARMappings";
+
+	private static final String URI = "uri";
+
+	private static final String VERSION = "version";
+
+	private static final String XMI_ID = "xmi:id";
+
+	private static final String XMI_TYPE = "xmi:type";
+
+	private static final String XMI_VERSION = "xmi:version";
+
+	private static final String XMLNS = "xmlns";
+
+	private static final String XMLNS_APPLICATION = "xmlns:application";
+
+	private static final String XMLNS_MODULEMAP = "xmlns:modulemap";
+
+	private static final String XMLNS_SCHEMA_LOCATION = "xmlns:schemaLocation";
+
+	private static final String XMLNS_XMI = "xmlns:xmi";
+
+	private static final String XMLNS_XSI = "xmlns:xsi";
+
+	private Xpp3Dom[] applicationXmlDomChildren;
+
+	private Xpp3Dom[] modulemapsXmlDomChildren;
+
+	private Xpp3Dom[] webModulesFromPoms;
+
+	/**
+	 * write the application.xml and the .modulemaps file to the META-INF
+	 * directory.
+	 * 
+	 * @see AbstractWtpResourceWriter#write(EclipseSourceDir[],
+	 *      ArtifactRepository, File)
+	 * @throws MojoExecutionException
+	 *             when writing the config files was not possible
+	 */
+	public void write() throws MojoExecutionException {
+		String packaging = this.config.getProject().getPackaging();
+		if ("ear".equalsIgnoreCase(packaging)) {
+			File applicationXmlFile = new File(this.config.getEclipseProjectDirectory(), "target" + File.separator + "eclipseEar" + File.separator + "META-INF" + File.separator
+					+ EclipseWtpApplicationXMLWriter.APPLICATION_XML_FILENAME);
+			// create the directory structiure for eclipse deployment
+			applicationXmlFile.getParentFile().mkdirs();
+			// copy all deployment files to the eclipse deployment
+			copyApplicationFiles();
+			// delete any existing application.xml so that it will be
+			// overwritten.
+			applicationXmlFile.delete();
+
+			Xpp3Dom applicationXmlDom = readXMLFile(applicationXmlFile);
+			if (applicationXmlDom == null) {
+				applicationXmlDom = createNewApplicationXml();
+			}
+			this.applicationXmlDomChildren = applicationXmlDom.getChildren(EclipseWtpApplicationXMLWriter.APPLICATION_XML_MODULE);
+
+			File modulemapsXmlFile = new File(this.config.getEclipseProjectDirectory(), "target" + File.separator + "eclipseEar" + File.separator + "META-INF" + File.separator
+					+ EclipseWtpApplicationXMLWriter.MODULEMAPS_FILENAME);
+			Xpp3Dom modulemapsXmlDom = readXMLFile(modulemapsXmlFile);
+			if (modulemapsXmlDom == null) {
+				modulemapsXmlDom = createNewModulemaps();
+			}
+			this.modulemapsXmlDomChildren = modulemapsXmlDom.getChildren();
+
+			this.webModulesFromPoms = ((Xpp3Dom) ((org.apache.maven.model.Plugin) this.config.getProject().getBuild().getPluginsAsMap().get("org.apache.maven.plugins:maven-ear-plugin"))
+					.getConfiguration()).getChild("modules").getChildren("webModule");
+
+			IdeDependency[] deps = this.config.getDeps();
+			for (int index = 0; index < deps.length; index++) {
+				updateApplicationXml(applicationXmlDom, modulemapsXmlDom, deps[index]);
+			}
+
+			removeUnusedEntries(applicationXmlDom, modulemapsXmlDom);
+
+			writePrettyXmlFile(applicationXmlFile, applicationXmlDom);
+			writePrettyXmlFile(modulemapsXmlFile, modulemapsXmlDom);
+		}
+	}
+
+	/**
+	 * Copy all files from application directory to the target eclipseEar
+	 * directory.
+	 * 
+	 * @throws MojoExecutionException
+	 *             wenn an error occures during file copieing
+	 */
+	private void copyApplicationFiles() throws MojoExecutionException {
+		try {
+			File applicationDirectory = new File(this.config.getEclipseProjectDirectory(), "src" + File.separator + "main" + File.separator + "application");
+			File eclipseApplicationDirectory = new File(this.config.getEclipseProjectDirectory(), "target" + File.separator + "eclipseEar");
+			copyDirectoryStructure(applicationDirectory, eclipseApplicationDirectory);
+		} catch (IOException e) {
+			throw new MojoExecutionException("could not copy files the the eclipseEar directory", e);
+		}
+	}
+
+	/**
+	 * Copies a entire directory structure without scm files.
+	 * 
+	 * Note:
+	 * <ul>
+	 * <li>It will include empty directories.
+	 * <li>The <code>sourceDirectory</code> must exists.
+	 * </ul>
+	 * 
+	 * @param sourceDirectory
+	 * @param destinationDirectory
+	 * @throws IOException
+	 */
+	public static void copyDirectoryStructure(File sourceDirectory, File destinationDirectory) throws IOException {
+		if (!sourceDirectory.exists()) {
+			return;
+		}
+
+		File[] files = sourceDirectory.listFiles();
+
+		String sourcePath = sourceDirectory.getAbsolutePath();
+
+		for (int i = 0; i < files.length; i++) {
+			File file = files[i];
+
+			String dest = file.getAbsolutePath();
+
+			dest = dest.substring(sourcePath.length() + 1);
+
+			File destination = new File(destinationDirectory, dest);
+
+			if (file.isFile()) {
+				destination = destination.getParentFile();
+
+				FileUtils.copyFileToDirectory(file, destination);
+			} else if (file.isDirectory() && !file.getName().equals(".svn") && !file.getName().equals("CVS")) {
+				if (!destination.exists() && !destination.mkdirs()) {
+					throw new IOException("Could not create destination directory '" + destination.getAbsolutePath() + "'.");
+				}
+
+				copyDirectoryStructure(file, destination);
+			}
+		}
+	}
+
+	/**
+	 * there is no existing application.xml file so create a new one.
+	 * 
+	 * @return the domtree representing the contents of application.xml
+	 */
+	private Xpp3Dom createNewApplicationXml() {
+		Xpp3Dom result = new Xpp3Dom(EclipseWtpApplicationXMLWriter.APPLICATION_XML_APPLICATION);
+		result.setAttribute(EclipseWtpApplicationXMLWriter.ID, "Application_ID");
+		result.setAttribute(EclipseWtpApplicationXMLWriter.VERSION, "1.4");
+		result.setAttribute(EclipseWtpApplicationXMLWriter.XMLNS, "http://java.sun.com/xml/ns/j2ee");
+		result.setAttribute(EclipseWtpApplicationXMLWriter.XMLNS_XSI, "http://www.w3.org/2001/XMLSchema-instance");
+		result.setAttribute(EclipseWtpApplicationXMLWriter.XMLNS_SCHEMA_LOCATION, "http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/application_1_4.xsd");
+		result.addChild(new Xpp3Dom(EclipseWtpApplicationXMLWriter.APPLICATION_XML_DESCRIPTION));
+		Xpp3Dom name = new Xpp3Dom(EclipseWtpApplicationXMLWriter.APPLICATION_XML_DISPLAY_NAME);
+		name.setValue(this.config.getEclipseProjectName());
+		result.addChild(name);
+		return result;
+	}
+
+	/**
+	 * there is no existing .modulemaps file so create a new one.
+	 * 
+	 * @return the domtree representing the contents of the .modulemaps file
+	 */
+	private Xpp3Dom createNewModulemaps() {
+		Xpp3Dom result = new Xpp3Dom(EclipseWtpApplicationXMLWriter.MODULEMAP_EARPROJECT_MAP);
+		result.setAttribute(EclipseWtpApplicationXMLWriter.XMI_VERSION, "2.0");
+		result.setAttribute(EclipseWtpApplicationXMLWriter.XMLNS_XMI, "http://www.omg.org/XMI");
+		result.setAttribute(EclipseWtpApplicationXMLWriter.XMLNS_APPLICATION, "application.xmi");
+		result.setAttribute(EclipseWtpApplicationXMLWriter.XMLNS_MODULEMAP, "modulemap.xmi");
+		result.setAttribute(EclipseWtpApplicationXMLWriter.XMI_ID, "EARProjectMap_" + System.identityHashCode(this));
+		return result;
+	}
+
+	/**
+	 * find an existing module entry in the application.xml file by looking up
+	 * the id in the modulemaps file and then using that to locate the entry in
+	 * the application.xml file.
+	 * 
+	 * @param applicationXmlDom
+	 *            application.xml dom tree
+	 * @param mapping
+	 *            .modulemaps dom tree
+	 * @return dom tree representing the module
+	 */
+	private Xpp3Dom findModuleInApplicationXml(Xpp3Dom applicationXmlDom, Xpp3Dom mapping) {
+		String id = getIdFromMapping(mapping);
+		Xpp3Dom[] children = applicationXmlDom.getChildren();
+		for (int index = 0; index < children.length; index++) {
+			String childId = children[index].getAttribute(EclipseWtpApplicationXMLWriter.ID);
+			if (childId != null && childId.equals(id)) {
+				return children[index];
+			}
+		}
+		return null;
+	}
+
+	/**
+	 * find an artifact in the modulemaps dom tree, if it is missing create a
+	 * new entry in the modulemaps dom tree.
+	 * 
+	 * @param dependency
+	 *            dependency to find
+	 * @param modulemapXmlDom
+	 *            dom-tree of modulemaps
+	 * @return dom-tree representing the artifact
+	 */
+	private Xpp3Dom findOrCreateArtifact(IdeDependency dependency, Xpp3Dom modulemapXmlDom) {
+		// first try to find it
+		Xpp3Dom[] children = modulemapXmlDom.getChildren();
+		for (int index = 0; index < children.length; index++) {
+			if (children[index].getAttribute(EclipseWtpApplicationXMLWriter.MODULEMAPS_PROJECT_NAME).equals(dependency.getEclipseProjectName())) {
+				if ((dependency.getType().equals("ejb") || dependency.getType().equals("ejb3"))  && children[index].getName().equals(EclipseWtpApplicationXMLWriter.MODULEMAPS_MAPPINGS)
+						&& children[index].getChild(EclipseWtpApplicationXMLWriter.APPLICATION_XML_MODULE).getAttribute(EclipseWtpApplicationXMLWriter.XMI_TYPE).equals(EclipseWtpApplicationXMLWriter.MODULEMAPS_APPLICATION_EJB_MODULE)) {
+					return children[index];
+				} else if (dependency.getType().equals("war") && children[index].getName().equals(EclipseWtpApplicationXMLWriter.MODULEMAPS_MAPPINGS)
+						&& children[index].getChild(EclipseWtpApplicationXMLWriter.APPLICATION_XML_MODULE).getAttribute(EclipseWtpApplicationXMLWriter.XMI_TYPE).equals(EclipseWtpApplicationXMLWriter.MODULEMAPS_APPLICATION_WEB_MODULE)) {
+					return children[index];
+				} else if (dependency.getType().equals("jar") && children[index].getName().equals(EclipseWtpApplicationXMLWriter.MODULEMAPS_UTILITY_JARMAPPINGS)) {
+					return children[index];
+				} else {
+					modulemapXmlDom.removeChild(index);
+					break;
+				}
+			}
+		}
+		// ok, its missing (or it changed type). create a new one based on its
+		// type
+		long id = System.identityHashCode(dependency);
+		if (dependency.getType().equals("ejb") || dependency.getType().equals("ejb3")) {
+			Xpp3Dom mapping = new Xpp3Dom(EclipseWtpApplicationXMLWriter.MODULEMAPS_MAPPINGS);
+			mapping.setAttribute(EclipseWtpApplicationXMLWriter.XMI_ID, "ModuleMapping_" + id);
+			mapping.setAttribute(EclipseWtpApplicationXMLWriter.MODULEMAPS_PROJECT_NAME, dependency.getEclipseProjectName());
+			Xpp3Dom module = new Xpp3Dom(EclipseWtpApplicationXMLWriter.APPLICATION_XML_MODULE);
+			module.setAttribute(EclipseWtpApplicationXMLWriter.XMI_TYPE, EclipseWtpApplicationXMLWriter.MODULEMAPS_APPLICATION_EJB_MODULE);
+			module.setAttribute(EclipseWtpApplicationXMLWriter.HREF, "META-INF/application.xml#EjbModule_" + id);
+			mapping.addChild(module);
+			modulemapXmlDom.addChild(mapping);
+			return mapping;
+		} else if (dependency.getType().equals("war")) {
+			Xpp3Dom mapping = new Xpp3Dom(EclipseWtpApplicationXMLWriter.MODULEMAPS_MAPPINGS);
+			mapping.setAttribute(EclipseWtpApplicationXMLWriter.XMI_ID, "ModuleMapping_" + id);
+			mapping.setAttribute(EclipseWtpApplicationXMLWriter.MODULEMAPS_PROJECT_NAME, dependency.getEclipseProjectName());
+			Xpp3Dom module = new Xpp3Dom(EclipseWtpApplicationXMLWriter.APPLICATION_XML_MODULE);
+			module.setAttribute(EclipseWtpApplicationXMLWriter.XMI_TYPE, EclipseWtpApplicationXMLWriter.MODULEMAPS_APPLICATION_WEB_MODULE);
+			module.setAttribute(EclipseWtpApplicationXMLWriter.HREF, "META-INF/application.xml#WebModule_" + id);
+			mapping.addChild(module);
+			modulemapXmlDom.addChild(mapping);
+			return mapping;
+		} else {
+			Xpp3Dom utilityJARMapping = new Xpp3Dom(EclipseWtpApplicationXMLWriter.MODULEMAPS_UTILITY_JARMAPPINGS);
+			utilityJARMapping.setAttribute(EclipseWtpApplicationXMLWriter.XMI_ID, "UtilityJARMapping_" + id);
+			utilityJARMapping.setAttribute(EclipseWtpApplicationXMLWriter.MODULEMAPS_PROJECT_NAME, dependency.getEclipseProjectName());
+			utilityJARMapping.setAttribute(EclipseWtpApplicationXMLWriter.URI, dependency.getEclipseProjectName() + ".jar");
+			modulemapXmlDom.addChild(utilityJARMapping);
+			return utilityJARMapping;
+		}
+	}
+
+	/**
+	 * get the id from the href of a modulemap.
+	 * 
+	 * @param mapping
+	 *            the dom-tree of modulemaps
+	 * @return module identifier
+	 */
+	private String getIdFromMapping(Xpp3Dom mapping) {
+		if (mapping.getChildCount() < 1) {
+			return "";
+		}
+		String href = mapping.getChild(0).getAttribute(EclipseWtpApplicationXMLWriter.HREF);
+		String id = href.substring(href.indexOf('#') + 1);
+		return id;
+	}
+
+	/**
+	 * mark the domtree entry as handled (all not handled ones will be deleted).
+	 * 
+	 * @param xpp3Dom
+	 *            dom element to mark handled
+	 */
+	private void handled(Xpp3Dom xpp3Dom) {
+		for (int index = 0; index < this.applicationXmlDomChildren.length; index++) {
+			if (this.applicationXmlDomChildren[index] == xpp3Dom) {
+				this.applicationXmlDomChildren[index] = null;
+			}
+		}
+		for (int index = 0; index < this.modulemapsXmlDomChildren.length; index++) {
+			if (this.modulemapsXmlDomChildren[index] == xpp3Dom) {
+				this.modulemapsXmlDomChildren[index] = null;
+			}
+		}
+	}
+
+	/**
+	 * read an xml file (application.xml or .modulemaps).
+	 * 
+	 * @param xmlFile
+	 *            an xmlfile
+	 * @return dom-tree representing the file contents
+	 */
+	private Xpp3Dom readXMLFile(File xmlFile) {
+		try {
+			FileReader reader1 = new FileReader(xmlFile);
+			Xpp3Dom applicationXmlDom = Xpp3DomBuilder.build(reader1);
+			return applicationXmlDom;
+		} catch (FileNotFoundException e) {
+			return null;
+		} catch (Exception e) {
+			this.log.error("cantreadfile" + xmlFile.getAbsolutePath());
+			// this will trigger creating a new file
+			return null;
+		}
+	}
+
+	/**
+	 * delete all unused entries from the dom-trees.
+	 * 
+	 * @param applicationXmlDom
+	 *            dom-tree of application.xml
+	 * @param modulemapsXmlDom
+	 *            dom-tree of modulemaps
+	 */
+	private void removeUnusedEntries(Xpp3Dom applicationXmlDom, Xpp3Dom modulemapsXmlDom) {
+		for (int index = 0; index < this.modulemapsXmlDomChildren.length; index++) {
+			if (this.modulemapsXmlDomChildren[index] != null) {
+				Xpp3Dom[] newModulemapsXmlDomChildren = modulemapsXmlDom.getChildren();
+				for (int newIndex = 0; newIndex < newModulemapsXmlDomChildren.length; newIndex++) {
+					if (newModulemapsXmlDomChildren[newIndex] == this.modulemapsXmlDomChildren[index]) {
+						modulemapsXmlDom.removeChild(newIndex);
+						break;
+					}
+				}
+			}
+		}
+		for (int index = 0; index < this.applicationXmlDomChildren.length; index++) {
+			if (this.applicationXmlDomChildren[index] != null) {
+				Xpp3Dom[] newApplicationXmlDomChildren = applicationXmlDom.getChildren();
+				for (int newIndex = 0; newIndex < newApplicationXmlDomChildren.length; newIndex++) {
+					if (newApplicationXmlDomChildren[newIndex] == this.applicationXmlDomChildren[index]) {
+						applicationXmlDom.removeChild(newIndex);
+						break;
+					}
+				}
+			}
+		}
+	}
+
+	/**
+	 * update the application.xml and the .modulemaps file for a specified
+	 * dependency.all WAR an EJB dependencies will go in both files all others
+	 * only in the modulemaps files. Webapplications contextroots are corrected
+	 * to the contextRoot specified in the pom.
+	 * 
+	 * @param applicationXmlDom
+	 *            dom-tree of application.xml
+	 * @param modulemapXmlDom
+	 *            dom-tree of modulemaps
+	 * @param dependency
+	 *            the eclipse dependency to handle
+	 */
+	private void updateApplicationXml(Xpp3Dom applicationXmlDom, Xpp3Dom modulemapXmlDom, IdeDependency dependency) {
+        if (dependency.isTestDependency() || dependency.isProvided() || dependency.isSystemScopedOutsideProject(this.config.getProject())) 
+        {
+            return;
+        }
+		Xpp3Dom mapping = findOrCreateArtifact(dependency, modulemapXmlDom);
+		handled(mapping);
+		if (dependency.getType().equals("ejb") || dependency.getType().equals("ejb3") ) {
+			Xpp3Dom module = findModuleInApplicationXml(applicationXmlDom, mapping);
+			if (module == null) {
+				module = new Xpp3Dom(EclipseWtpApplicationXMLWriter.APPLICATION_XML_MODULE);
+				module.setAttribute(EclipseWtpApplicationXMLWriter.ID, getIdFromMapping(mapping));
+				Xpp3Dom ejb = new Xpp3Dom("ejb");
+				ejb.setValue(dependency.getEclipseProjectName() + ".jar");
+				module.addChild(ejb);
+				applicationXmlDom.addChild(module);
+			} else {
+				handled(module);
+				module.getChild("ejb").setValue(dependency.getEclipseProjectName() + ".jar");
+			}
+		} else if (dependency.getType().equals("war")) {
+			String contextRootInPom = getContextRootFor(dependency.getEclipseProjectName());
+			Xpp3Dom module = findModuleInApplicationXml(applicationXmlDom, mapping);
+			if (module == null) {
+				module = new Xpp3Dom(EclipseWtpApplicationXMLWriter.APPLICATION_XML_MODULE);
+				module.setAttribute(EclipseWtpApplicationXMLWriter.ID, getIdFromMapping(mapping));
+				Xpp3Dom web = new Xpp3Dom(EclipseWtpApplicationXMLWriter.APPLICATION_XML_WEB);
+				Xpp3Dom webUri = new Xpp3Dom(EclipseWtpApplicationXMLWriter.APPLICATION_XML_WEB_URI);
+				webUri.setValue(dependency.getEclipseProjectName() + ".war");
+				Xpp3Dom contextRoot = new Xpp3Dom(EclipseWtpApplicationXMLWriter.APPLICATION_XML_CONTEXT_ROOT);
+				contextRoot.setValue(contextRootInPom);
+				web.addChild(webUri);
+				web.addChild(contextRoot);
+				module.addChild(web);
+				applicationXmlDom.addChild(module);
+			} else {
+				handled(module);
+				module.getChild(EclipseWtpApplicationXMLWriter.APPLICATION_XML_WEB).getChild(EclipseWtpApplicationXMLWriter.APPLICATION_XML_WEB_URI).setValue(dependency.getEclipseProjectName() + ".war");
+				module.getChild(EclipseWtpApplicationXMLWriter.APPLICATION_XML_WEB).getChild(EclipseWtpApplicationXMLWriter.APPLICATION_XML_CONTEXT_ROOT).setValue(contextRootInPom);
+			}
+		}
+	}
+
+	/**
+	 * Find the contextRoot specified in the pom and convert it into contectroot
+	 * for the application.xml.
+	 * 
+	 * @param artifactId
+	 *            the artifactid to search
+	 * @return string with the context root
+	 */
+	private String getContextRootFor(String artifactId) {
+		for (int index = 0; index < this.webModulesFromPoms.length; index++) {
+			if (this.webModulesFromPoms[index].getChild("artifactId").getValue().equals(artifactId)) {
+                return new File(this.webModulesFromPoms[index].getChild("contextRoot").getValue()).getName();
+            }
+		}
+		return artifactId;
+	}
+
+	/**
+	 * write back a domtree to a xmlfile and use the pretty print for it so that
+	 * it is human readable.
+	 * 
+	 * @param xmlFile
+	 *            file to write to
+	 * @param xmlDomTree
+	 *            dom-tree to write
+	 * @throws MojoExecutionException
+	 *             if the file could not be written
+	 */
+	private void writePrettyXmlFile(File xmlFile, Xpp3Dom xmlDomTree) throws MojoExecutionException {
+		Xpp3Dom original = readXMLFile(xmlFile);
+		if (original != null && original.equals(xmlDomTree)) {
+			this.log.info("Rad6CleanMojo.unchanged" + xmlFile.getAbsolutePath());
+			return;
+		}
+		FileWriter w = null;
+		xmlFile.getParentFile().mkdirs();
+		try {
+			w = new FileWriter(xmlFile);
+		} catch (IOException ex) {
+			throw new MojoExecutionException("Rad6Plugin.erroropeningfile", ex); //$NON-NLS-1$
+		}
+		XMLWriter writer = new PrettyPrintXMLWriter(w, "UTF-8", null);
+		Xpp3DomWriter.write(writer, xmlDomTree);
+		IOUtil.close(w);
+	}
+}
diff --git a/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/EclipseWtpComponentWriter.java b/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/EclipseWtpComponentWriter.java
index 074d009..265ed5c 100644
--- a/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/EclipseWtpComponentWriter.java
+++ b/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/EclipseWtpComponentWriter.java
@@ -122,7 +122,8 @@
         }
         writer.startElement( ELT_WB_MODULE );
 
-        writer.addAttribute( ATTR_DEPLOY_NAME, config.getProject().getArtifactId() );
+        //we should use the eclipse project name as the deploy name.
+        writer.addAttribute( ATTR_DEPLOY_NAME, this.config.getEclipseProjectName() );
 
         // deploy-path is "/" for utility and ejb projects, "/WEB-INF/classes" for webapps
         String target = "/"; //$NON-NLS-1$
@@ -153,9 +154,12 @@
         }
         else if ( "ear".equalsIgnoreCase( packaging ) ) //$NON-NLS-1$
         {
+        	
+        	String defaultApplicationXML = config.getWtpapplicationxml()?"/target/eclipseEar":"/src/main/application";
+        	
             String earSourceDirectory = IdeUtils.getPluginSetting( config.getProject(), ARTIFACT_MAVEN_EAR_PLUGIN,
                                                                    "earSourceDirectory", //$NON-NLS-1$
-                                                                   config.getProject().getBasedir()+"/src/main/application" ); //$NON-NLS-1$
+                                                                   config.getProject().getBasedir()+defaultApplicationXML); //$NON-NLS-1$
             writer.startElement( ELT_WB_RESOURCE );
             writer.addAttribute( ATTR_DEPLOY_PATH, "/" ); //$NON-NLS-1$
             writer.addAttribute( ATTR_SOURCE_PATH, IdeUtils
diff --git a/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/EclipseWtpmodulesWriter.java b/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/EclipseWtpmodulesWriter.java
index 88cc867..c978a25 100644
--- a/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/EclipseWtpmodulesWriter.java
+++ b/src/main/java/org/apache/maven/plugin/eclipse/writers/wtp/EclipseWtpmodulesWriter.java
@@ -64,7 +64,8 @@
         writer.addAttribute( ATTR_MODULE_ID, "moduleCoreId" ); //$NON-NLS-1$
 
         writer.startElement( ELT_WB_MODULE );
-        writer.addAttribute( ATTR_DEPLOY_NAME, config.getProject().getArtifactId() );
+        // we should use the configured eclipse project name.
+        writer.addAttribute( ATTR_DEPLOY_NAME, this.config.getEclipseProjectName() );
 
         writer.startElement( ELT_MODULE_TYPE );
         writeModuleTypeAccordingToPackaging( config.getProject(), writer, config.getBuildOutputDirectory() );
diff --git a/src/main/java/org/apache/maven/plugin/ide/AbstractIdeSupportMojo.java b/src/main/java/org/apache/maven/plugin/ide/AbstractIdeSupportMojo.java
index 7800bc8..561252e 100644
--- a/src/main/java/org/apache/maven/plugin/ide/AbstractIdeSupportMojo.java
+++ b/src/main/java/org/apache/maven/plugin/ide/AbstractIdeSupportMojo.java
@@ -633,10 +633,13 @@
                                 .getVersion(), art.getClassifier(), isReactorProject, Artifact.SCOPE_TEST.equals( art
                                 .getScope() ), Artifact.SCOPE_SYSTEM.equals( art.getScope() ), Artifact.SCOPE_PROVIDED
                                 .equals( art.getScope() ), art.getArtifactHandler().isAddedToClasspath(),
-                                                                   art.getFile(), art.getType(), isOsgiBundle,
-                                                                   osgiSymbolicName, dependencyDepth );
-
-                            dependencies.add( dep );
+                                art.getFile(), art.getType(), isOsgiBundle, osgiSymbolicName, dependencyDepth,
+                                getProjectNameForArifact(art));
+                            //no duplicate entries allowed. System paths can cause this problem.
+                            if ( !dependencies.contains(dep) )
+                            {
+                                dependencies.add( dep );
+                            }
                         }
 
                     }
@@ -656,7 +659,14 @@
 
         return ideDeps;
     }
-
+    
+    /**
+     * Find the name of the project as used in eclipse.
+     * @param artifact The artifact to find the eclipse name for.
+     * @return The name os the eclipse project.
+     */
+    abstract public String getProjectNameForArifact(Artifact artifact) ;
+    
     /**
      * Returns the list of project artifacts. Also artifacts
      * generated from referenced projects will be added, but
diff --git a/src/main/java/org/apache/maven/plugin/ide/IdeDependency.java b/src/main/java/org/apache/maven/plugin/ide/IdeDependency.java
index 01d0fff..d39484c 100644
--- a/src/main/java/org/apache/maven/plugin/ide/IdeDependency.java
+++ b/src/main/java/org/apache/maven/plugin/ide/IdeDependency.java
@@ -20,6 +20,8 @@
 
 import java.io.File;
 
+import org.apache.maven.project.MavenProject;
+
 /**
  * @author Fabrizio Giustina
  * @version $Id$
@@ -98,6 +100,11 @@
     private boolean osgiBundle;
 
     /**
+     * How is this dependency called when it is an eclipse project. 
+     */
+    private String eclipseProjectName;
+    
+    /**
      * Creates an uninitialized instance
      */
     public IdeDependency()
@@ -120,10 +127,12 @@
      * @param osgiBundle Does this artifact contains a OSGI Manifest?
      * @param osgiSymbolicName Bundle-SymbolicName from the Manifest (if available)
      * @param dependencyDepth Depth of this dependency in the transitive dependency trail.
+     * @param eclipseProjectName The name of the project in eclipse
      */
     public IdeDependency( String groupId, String artifactId, String version, String classifier, boolean referencedProject,
                           boolean testDependency, boolean systemScoped, boolean provided, boolean addedToClasspath,
-                          File file, String type, boolean osgiBundle, String osgiSymbolicName, int dependencyDepth )
+                          File file, String type, boolean osgiBundle, String osgiSymbolicName, int dependencyDepth,
+                          String eclipseProjectName)
     {
         // group:artifact:version
         this.groupId = groupId;
@@ -143,6 +152,7 @@
         // file and type
         this.file = file;
         this.type = type;
+        this.eclipseProjectName = eclipseProjectName;
     }
 
     /**
@@ -398,6 +408,22 @@
     }
 
     /**
+     * Getter for <code>eclipseProjectName</code>.
+     * @return Returns the eclipseProjectName.
+     */
+    public String getEclipseProjectName() {
+        return this.eclipseProjectName;
+    }
+    
+    /**
+     * Setter for <code>eclipseProjectName</code>.
+     * @param eclipseProjectName The eclipseProjectName to set.
+     */
+    public void setEclipseProjectName(String eclipseProjectName) {
+        this.eclipseProjectName = eclipseProjectName;
+    }
+    
+    /**
      * @see java.lang.Object#toString()
      */
     public String toString()
@@ -412,6 +438,11 @@
     public int compareTo( Object o )
     {
         IdeDependency dep = (IdeDependency) o;
+        //in case of system scoped dependencies the files must be compared.
+        if (isSystemScoped() && dep.isSystemScoped() && getFile().equals(dep.getFile())) 
+        {
+            return 0;
+        }
         int equals = this.getGroupId().compareTo( dep.getGroupId() );
         if ( equals != 0 )
         {
@@ -427,8 +458,44 @@
         {
             return equals;
         }
-
         return 0;
     }
 
+    /**
+     * Is this dependency System scoped outside the eclipse project. This is 
+     * NOT complete because in reality the check should mean that any module 
+     * in the reactor contains the system scope locally!
+     * @return Returns this dependency is systemScoped outside the project.
+     */
+    public boolean isSystemScopedOutsideProject( MavenProject project )
+    {
+        File modulesTop = project.getBasedir();
+        while (new File(modulesTop.getParentFile(), "pom.xml").exists())
+        {
+            modulesTop = modulesTop.getParentFile();
+        }
+        return isSystemScoped() && !getFile().getAbsolutePath().startsWith(modulesTop.getAbsolutePath());
+    }
+    
+    /**
+     * {@inheritDoc}
+     */
+    public boolean equals(Object obj) 
+    {
+        return compareTo(obj) == 0;
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    public int hashCode() {
+        if (isSystemScoped()) 
+        {
+            return getFile().hashCode();
+        } 
+        else 
+        {
+            return this.getGroupId().hashCode() ^ this.getArtifactId().hashCode() ^ this.getType().hashCode();
+        }
+    }
 }
diff --git a/src/main/java/org/apache/maven/plugin/ide/IdeUtils.java b/src/main/java/org/apache/maven/plugin/ide/IdeUtils.java
index f9a68dd..45b180e 100644
--- a/src/main/java/org/apache/maven/plugin/ide/IdeUtils.java
+++ b/src/main/java/org/apache/maven/plugin/ide/IdeUtils.java
@@ -195,6 +195,18 @@
         return getProjectName( template, dep.getGroupId(), dep.getArtifactId(), dep.getVersion() );
     }
 
+    /**
+     * Use the project name template to create an eclipse project.
+     *  
+     * @param template Template for the project name
+     * @param artifact the artifact to create the project name for
+     * @return the created ide project name
+     */
+    public static String getProjectName( String template, Artifact artifact )
+    {
+        return getProjectName( template, artifact.getGroupId(), artifact.getArtifactId(), artifact.getVersion() );
+    }
+    
     public static String getProjectName( String template, MavenProject project )
     {
         return getProjectName( template, project.getGroupId(), project.getArtifactId(), project.getVersion() );
diff --git a/src/test/java/org/apache/maven/plugin/eclipse/EclipsePluginTest.java b/src/test/java/org/apache/maven/plugin/eclipse/EclipsePluginTest.java
index e870f9b..729eb78 100644
--- a/src/test/java/org/apache/maven/plugin/eclipse/EclipsePluginTest.java
+++ b/src/test/java/org/apache/maven/plugin/eclipse/EclipsePluginTest.java
@@ -342,6 +342,10 @@
         testProject( "project-32" );
     }
     
+    public void testProject34() throws Exception
+    {
+        testProject( "project-34" );
+    }
     
     /**
      * MECLIPSE-287 : dependencies with and without classifiers
diff --git a/src/test/resources/m2repo/eclipsetest/multymodule-1/1.0/multymodule-1-1.0.jar b/src/test/resources/m2repo/eclipsetest/multymodule-1/1.0/multymodule-1-1.0.jar
new file mode 100644
index 0000000..e51013e
--- /dev/null
+++ b/src/test/resources/m2repo/eclipsetest/multymodule-1/1.0/multymodule-1-1.0.jar
@@ -0,0 +1 @@
+-testfile-not a valid jar-
\ No newline at end of file
diff --git a/src/test/resources/m2repo/eclipsetest/multymodule-1/1.0/multymodule-1-1.0.pom b/src/test/resources/m2repo/eclipsetest/multymodule-1/1.0/multymodule-1-1.0.pom
new file mode 100644
index 0000000..0e4e900
--- /dev/null
+++ b/src/test/resources/m2repo/eclipsetest/multymodule-1/1.0/multymodule-1-1.0.pom
@@ -0,0 +1,55 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>eclipsetest</groupId>
+		<artifactId>master-test</artifactId>
+		<version>1.0</version>
+	</parent>
+	<packaging>jar</packaging>
+	<groupId>eclipsetest</groupId>
+	<artifactId>multymodule-1</artifactId>
+	<version>1.0</version>
+	<name>multymodule-1</name>
+	<dependencies>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>multymodule-4</artifactId>
+			<version>1.0</version>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>refproject-compile</artifactId>
+			<version>1.0</version>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>refproject-test</artifactId>
+			<version>1.0</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>refproject-provided</artifactId>
+			<version>1.0</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>refproject-optional</artifactId>
+			<version>1.0</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>refproject-sysdep</artifactId>
+			<version>1.0</version>
+			<scope>system</scope>
+			<systemPath>${basedir}/refproject-sysdep.jar</systemPath>
+		</dependency>
+	</dependencies>
+	<distributionManagement>
+		<status>verified</status>
+	</distributionManagement>
+</project>
diff --git a/src/test/resources/m2repo/eclipsetest/multymodule-2/1.0/multymodule-2-1.0.pom b/src/test/resources/m2repo/eclipsetest/multymodule-2/1.0/multymodule-2-1.0.pom
new file mode 100644
index 0000000..6679876
--- /dev/null
+++ b/src/test/resources/m2repo/eclipsetest/multymodule-2/1.0/multymodule-2-1.0.pom
@@ -0,0 +1,64 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>eclipsetest</groupId>
+		<artifactId>master-test</artifactId>
+		<version>1.0</version>
+	</parent>
+	<packaging>war</packaging>
+	<groupId>eclipsetest</groupId>
+	<artifactId>module-2</artifactId>
+	<version>1.0</version>
+	<name>module-2</name>
+	<dependencies>
+		<dependency>
+			<!-- module -->
+			<groupId>eclipsetest</groupId>
+			<artifactId>module-1</artifactId>
+			<version>1.0</version>
+		</dependency>
+		<dependency>
+			<!-- module -->
+			<groupId>eclipsetest</groupId>
+			<artifactId>module-1</artifactId>
+			<version>1.0</version>
+			<type>test-jar</type>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-compile</artifactId>
+			<version>1.0</version>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-test</artifactId>
+			<version>1.0</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-provided</artifactId>
+			<version>1.0</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-optional</artifactId>
+			<version>1.0</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-sysdep</artifactId>
+			<version>1.0</version>
+			<scope>system</scope>
+			<systemPath>${basedir}/direct-sysdep.jar</systemPath>
+		</dependency>
+	</dependencies>
+	<distributionManagement>
+		<status>verified</status>
+	</distributionManagement>
+</project>
diff --git a/src/test/resources/m2repo/eclipsetest/multymodule-2/1.0/multymodule-2-1.0.war b/src/test/resources/m2repo/eclipsetest/multymodule-2/1.0/multymodule-2-1.0.war
new file mode 100644
index 0000000..e51013e
--- /dev/null
+++ b/src/test/resources/m2repo/eclipsetest/multymodule-2/1.0/multymodule-2-1.0.war
@@ -0,0 +1 @@
+-testfile-not a valid jar-
\ No newline at end of file
diff --git a/src/test/resources/m2repo/eclipsetest/multymodule-4/1.0/multymodule-4-1.0.jar b/src/test/resources/m2repo/eclipsetest/multymodule-4/1.0/multymodule-4-1.0.jar
new file mode 100644
index 0000000..e51013e
--- /dev/null
+++ b/src/test/resources/m2repo/eclipsetest/multymodule-4/1.0/multymodule-4-1.0.jar
@@ -0,0 +1 @@
+-testfile-not a valid jar-
\ No newline at end of file
diff --git a/src/test/resources/m2repo/eclipsetest/multymodule-4/1.0/multymodule-4-1.0.pom b/src/test/resources/m2repo/eclipsetest/multymodule-4/1.0/multymodule-4-1.0.pom
new file mode 100644
index 0000000..405fbd1
--- /dev/null
+++ b/src/test/resources/m2repo/eclipsetest/multymodule-4/1.0/multymodule-4-1.0.pom
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>eclipsetest</groupId>
+		<artifactId>master-test</artifactId>
+		<version>1.0</version>
+	</parent>
+	<packaging>jar</packaging>
+	<groupId>eclipsetest</groupId>
+	<artifactId>multymodule-4</artifactId>
+	<version>1.0</version>
+	<name>multymodule-4</name>
+	<dependencies>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>refproject-compile</artifactId>
+			<version>1.0</version>
+		</dependency>
+	</dependencies>
+	<distributionManagement>
+		<status>verified</status>
+	</distributionManagement>
+</project>
diff --git a/src/test/resources/projects/project-05/expected/.wtpmodules b/src/test/resources/projects/project-05/expected/.wtpmodules
index 374ff8f..580db97 100644
--- a/src/test/resources/projects/project-05/expected/.wtpmodules
+++ b/src/test/resources/projects/project-05/expected/.wtpmodules
@@ -5,7 +5,7 @@
       <property name="context-root" value="contextName"/>
     </module-type>
     <wb-resource deploy-path="/" source-path="/src/main/webapp"/>
-    <dependent-module deploy-path="/WEB-INF/lib" handle="module:/classpath/var/M2_REPO/maven/maven-core/98.0/maven-core-98.0.jar">
+    <dependent-module archiveName="maven-core.jar" deploy-path="/WEB-INF/lib" handle="module:/classpath/var/M2_REPO/maven/maven-core/98.0/maven-core-98.0.jar">
       <dependency-type>uses</dependency-type>
     </dependent-module>
     <wb-resource deploy-path="/WEB-INF/classes" source-path="src/main/java"/>
diff --git a/src/test/resources/projects/project-08/expected/.wtpmodules b/src/test/resources/projects/project-08/expected/.wtpmodules
index f389d9f..ebe44e9 100644
--- a/src/test/resources/projects/project-08/expected/.wtpmodules
+++ b/src/test/resources/projects/project-08/expected/.wtpmodules
@@ -5,8 +5,8 @@
       <property name="context-root" value="maven-eclipse-plugin-test-project-8"/>
     </module-type>
     <wb-resource deploy-path="/" source-path="/src/main/webapp"/>
-    <dependent-module deploy-path="/WEB-INF/lib" handle="module:/classpath/lib/sysdep.jar">
+    <dependent-module archiveName="sysdep.jar" deploy-path="/WEB-INF/lib" handle="module:/classpath/lib/sysdep.jar">
       <dependency-type>uses</dependency-type>
     </dependent-module>
   </wb-module>
-</project-modules>
\ No newline at end of file
+</project-modules>
diff --git a/src/test/resources/projects/project-34/multymodule-1/expected/.project b/src/test/resources/projects/project-34/multymodule-1/expected/.project
new file mode 100644
index 0000000..a155912
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-1/expected/.project
@@ -0,0 +1,15 @@
+<projectDescription>
+  <name>multymodule-1-1.0</name>
+  <comment/>
+  <projects>
+    <project>multymodule-4-1.0</project>
+  </projects>
+  <buildSpec>
+    <buildCommand>
+      <name>org.eclipse.jdt.core.javabuilder</name>
+    </buildCommand>
+  </buildSpec>
+  <natures>
+    <nature>org.eclipse.jdt.core.javanature</nature>
+  </natures>
+</projectDescription>
\ No newline at end of file
diff --git a/src/test/resources/projects/project-34/multymodule-1/expected/target/generated-resources/eclipse/META-INF/MANIFEST.MF b/src/test/resources/projects/project-34/multymodule-1/expected/target/generated-resources/eclipse/META-INF/MANIFEST.MF
new file mode 100644
index 0000000..e202401
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-1/expected/target/generated-resources/eclipse/META-INF/MANIFEST.MF
@@ -0,0 +1,5 @@
+Manifest-Version: 1.0
+Class-Path: refproject-compile-1.0.jar refproject-sysdep.jar multymodu
+ le-4-1.0.jar refproject-optional-1.0.jar deps-refproject-compile-1.0.
+ jar
+
diff --git a/src/test/resources/projects/project-34/multymodule-1/pom.xml b/src/test/resources/projects/project-34/multymodule-1/pom.xml
new file mode 100644
index 0000000..9b69ffa
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-1/pom.xml
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>eclipsetest</groupId>
+		<artifactId>master-test</artifactId>
+		<version>1.0</version>
+	</parent>
+	<packaging>jar</packaging>
+	<groupId>eclipsetest</groupId>
+	<artifactId>multymodule-1</artifactId>
+	<version>1.0</version>
+	<name>multymodule-1</name>
+	<dependencies>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>multymodule-4</artifactId>
+			<version>1.0</version>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>refproject-compile</artifactId>
+			<version>1.0</version>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>refproject-test</artifactId>
+			<version>1.0</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>refproject-provided</artifactId>
+			<version>1.0</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>refproject-optional</artifactId>
+			<version>1.0</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>refproject-sysdep</artifactId>
+			<version>1.0</version>
+			<scope>system</scope>
+			<systemPath>${basedir}/refproject-sysdep.jar</systemPath>
+		</dependency>
+	</dependencies>
+</project>
diff --git a/src/test/resources/projects/project-34/multymodule-1/src/main/java/DummyClass.txt b/src/test/resources/projects/project-34/multymodule-1/src/main/java/DummyClass.txt
new file mode 100644
index 0000000..9ade9c1
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-1/src/main/java/DummyClass.txt
@@ -0,0 +1,7 @@
+/**
+ * @author <a href="mailto:trygvis@inamo.no">Trygve Laugst&oslash;l</a>
+ * @version $Id: DummyClass.txt 359507 2005-12-28 13:14:19Z fgiust $
+ */
+public class DummyClass
+{
+}
diff --git a/src/test/resources/projects/project-34/multymodule-2/expected/.classpath b/src/test/resources/projects/project-34/multymodule-2/expected/.classpath
new file mode 100644
index 0000000..dc23684
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-2/expected/.classpath
@@ -0,0 +1,16 @@
+<classpath>
+  <classpathentry kind="src" path="src/main/java"/>
+  <classpathentry kind="output" path="target/classes"/>
+  <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+  <classpathentry kind="var" path="M2_REPO/eclipsetest/direct-optional/1.0/direct-optional-1.0.jar"/>
+  <classpathentry kind="var" path="M2_REPO/eclipsetest/deps-direct-compile/1.0/deps-direct-compile-1.0.jar"/>
+  <classpathentry kind="src" path="/multymodule-4-1.0"/>
+  <classpathentry kind="var" path="M2_REPO/eclipsetest/direct-test/1.0/direct-test-1.0.jar"/>
+  <classpathentry kind="var" path="M2_REPO/eclipsetest/refproject-compile/1.0/refproject-compile-1.0.jar"/>
+  <classpathentry kind="var" path="M2_REPO/eclipsetest/deps-refproject-compile/1.0/deps-refproject-compile-1.0.jar"/>
+  <classpathentry kind="lib" path="/tmp/maven-eclipse-plugin-trunk/target/test-classes/projects/project-34/multymodule-1/refproject-sysdep.jar"/>
+  <classpathentry kind="src" path="/multymodule-1-1.0"/>
+  <classpathentry kind="lib" path="direct-sysdep.jar"/>
+  <classpathentry kind="var" path="M2_REPO/eclipsetest/direct-provided/1.0/direct-provided-1.0.jar"/>
+  <classpathentry kind="var" path="M2_REPO/eclipsetest/direct-compile/1.0/direct-compile-1.0.jar"/>
+</classpath>
\ No newline at end of file
diff --git a/src/test/resources/projects/project-34/multymodule-2/expected/.project b/src/test/resources/projects/project-34/multymodule-2/expected/.project
new file mode 100644
index 0000000..242e307
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-2/expected/.project
@@ -0,0 +1,16 @@
+<projectDescription>
+  <name>multymodule-2-1.0</name>
+  <comment/>
+  <projects>
+    <project>multymodule-4-1.0</project>
+    <project>multymodule-1-1.0</project>
+  </projects>
+  <buildSpec>
+    <buildCommand>
+      <name>org.eclipse.jdt.core.javabuilder</name>
+    </buildCommand>
+  </buildSpec>
+  <natures>
+    <nature>org.eclipse.jdt.core.javanature</nature>
+  </natures>
+</projectDescription>
\ No newline at end of file
diff --git a/src/test/resources/projects/project-34/multymodule-2/expected/pom.xml b/src/test/resources/projects/project-34/multymodule-2/expected/pom.xml
new file mode 100644
index 0000000..99c6109
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-2/expected/pom.xml
@@ -0,0 +1,61 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>eclipsetest</groupId>
+		<artifactId>master-test</artifactId>
+		<version>1.0</version>
+	</parent>
+	<packaging>war</packaging>
+	<groupId>eclipsetest</groupId>
+	<artifactId>multymodule-2</artifactId>
+	<version>1.0</version>
+	<name>multymodule-2</name>
+	<dependencies>
+		<dependency>
+			<!-- module -->
+			<groupId>eclipsetest</groupId>
+			<artifactId>multymodule-1</artifactId>
+			<version>1.0</version>
+		</dependency>
+		<dependency>
+			<!-- module -->
+			<groupId>eclipsetest</groupId>
+			<artifactId>multymodule-1</artifactId>
+			<version>1.0</version>
+			<type>test-jar</type>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-compile</artifactId>
+			<version>1.0</version>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-test</artifactId>
+			<version>1.0</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-provided</artifactId>
+			<version>1.0</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-optional</artifactId>
+			<version>1.0</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-sysdep</artifactId>
+			<version>1.0</version>
+			<scope>system</scope>
+			<systemPath>${basedir}/direct-sysdep.jar</systemPath>
+		</dependency>
+	</dependencies>
+</project>
diff --git a/src/test/resources/projects/project-34/multymodule-2/expected/src/main/webapp/META-INF/MANIFEST.MF b/src/test/resources/projects/project-34/multymodule-2/expected/src/main/webapp/META-INF/MANIFEST.MF
new file mode 100644
index 0000000..d2448ea
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-2/expected/src/main/webapp/META-INF/MANIFEST.MF
@@ -0,0 +1,5 @@
+Manifest-Version: 1.0
+Class-Path: direct-optional-1.0.jar deps-direct-compile-1.0.jar multym
+ odule-4-1.0.jar refproject-compile-1.0.jar deps-refproject-compile-1.
+ 0.jar refproject-sysdep.jar direct-sysdep.jar direct-compile-1.0.jar
+
diff --git a/src/test/resources/projects/project-34/multymodule-2/pom.xml b/src/test/resources/projects/project-34/multymodule-2/pom.xml
new file mode 100644
index 0000000..99c6109
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-2/pom.xml
@@ -0,0 +1,61 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>eclipsetest</groupId>
+		<artifactId>master-test</artifactId>
+		<version>1.0</version>
+	</parent>
+	<packaging>war</packaging>
+	<groupId>eclipsetest</groupId>
+	<artifactId>multymodule-2</artifactId>
+	<version>1.0</version>
+	<name>multymodule-2</name>
+	<dependencies>
+		<dependency>
+			<!-- module -->
+			<groupId>eclipsetest</groupId>
+			<artifactId>multymodule-1</artifactId>
+			<version>1.0</version>
+		</dependency>
+		<dependency>
+			<!-- module -->
+			<groupId>eclipsetest</groupId>
+			<artifactId>multymodule-1</artifactId>
+			<version>1.0</version>
+			<type>test-jar</type>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-compile</artifactId>
+			<version>1.0</version>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-test</artifactId>
+			<version>1.0</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-provided</artifactId>
+			<version>1.0</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-optional</artifactId>
+			<version>1.0</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>direct-sysdep</artifactId>
+			<version>1.0</version>
+			<scope>system</scope>
+			<systemPath>${basedir}/direct-sysdep.jar</systemPath>
+		</dependency>
+	</dependencies>
+</project>
diff --git a/src/test/resources/projects/project-34/multymodule-2/src/main/java/DummyClass.txt b/src/test/resources/projects/project-34/multymodule-2/src/main/java/DummyClass.txt
new file mode 100644
index 0000000..9ade9c1
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-2/src/main/java/DummyClass.txt
@@ -0,0 +1,7 @@
+/**
+ * @author <a href="mailto:trygvis@inamo.no">Trygve Laugst&oslash;l</a>
+ * @version $Id: DummyClass.txt 359507 2005-12-28 13:14:19Z fgiust $
+ */
+public class DummyClass
+{
+}
diff --git a/src/test/resources/projects/project-34/multymodule-3/expected/.project b/src/test/resources/projects/project-34/multymodule-3/expected/.project
new file mode 100644
index 0000000..7944b14
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-3/expected/.project
@@ -0,0 +1,9 @@
+<projectDescription>
+  <name>multymodule-3-1.0</name>
+  <comment/>
+  <projects>
+    <project>multymodule-2-1.0</project>
+  </projects>
+  <buildSpec/>
+  <natures/>
+</projectDescription>
\ No newline at end of file
diff --git a/src/test/resources/projects/project-34/multymodule-3/expected/target/application.xml b/src/test/resources/projects/project-34/multymodule-3/expected/target/application.xml
new file mode 100644
index 0000000..a80e711
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-3/expected/target/application.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE application PUBLIC
+	"-//Sun Microsystems, Inc.//DTD J2EE Application 1.3//EN"
+	"http://java.sun.com/dtd/application_1_3.dtd">
+<application>
+  <display-name>multymodule-3</display-name>
+  <module>
+    <web>
+      <web-uri>multymodule-2-1.0.war</web-uri>
+      <context-root>/multymodule-2-1.0</context-root>
+    </web>
+  </module>
+</application>
\ No newline at end of file
diff --git a/src/test/resources/projects/project-34/multymodule-3/expected/target/eclipseEar/META-INF/.modulemaps b/src/test/resources/projects/project-34/multymodule-3/expected/target/eclipseEar/META-INF/.modulemaps
new file mode 100644
index 0000000..e4b502a
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-3/expected/target/eclipseEar/META-INF/.modulemaps
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<modulemap:EARProjectMap xmlns:xmi="http://www.omg.org/XMI" xmlns:application="application.xmi" xmi:version="2.0" xmlns:modulemap="modulemap.xmi" xmi:id="EARProjectMap_24763620">
+  <mappings projectName="multymodule-2-1.0" xmi:id="ModuleMapping_26542488">
+    <module xmi:type="application:WebModule" href="META-INF/application.xml#WebModule_26542488"/>
+  </mappings>
+</modulemap:EARProjectMap>
\ No newline at end of file
diff --git a/src/test/resources/projects/project-34/multymodule-3/expected/target/eclipseEar/META-INF/application.xml b/src/test/resources/projects/project-34/multymodule-3/expected/target/eclipseEar/META-INF/application.xml
new file mode 100644
index 0000000..8833430
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-3/expected/target/eclipseEar/META-INF/application.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<application xmlns="http://java.sun.com/xml/ns/j2ee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/application_1_4.xsd" id="Application_ID" version="1.4">
+  <description/>
+  <display-name>multymodule-3-1.0</display-name>
+  <module id="WebModule_26542488">
+    <web>
+      <web-uri>multymodule-2-1.0.war</web-uri>
+      <context-root>multymodule-2-1.0</context-root>
+    </web>
+  </module>
+</application>
\ No newline at end of file
diff --git a/src/test/resources/projects/project-34/multymodule-3/expected/target/eclipseEar/META-INF/test-file.txt b/src/test/resources/projects/project-34/multymodule-3/expected/target/eclipseEar/META-INF/test-file.txt
new file mode 100644
index 0000000..ea3ff8c
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-3/expected/target/eclipseEar/META-INF/test-file.txt
@@ -0,0 +1 @@
+empty test file
\ No newline at end of file
diff --git a/src/test/resources/projects/project-34/multymodule-3/pom.xml b/src/test/resources/projects/project-34/multymodule-3/pom.xml
new file mode 100644
index 0000000..61c7cda
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-3/pom.xml
@@ -0,0 +1,40 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>eclipsetest</groupId>
+		<artifactId>master-test</artifactId>
+		<version>1.0</version>
+	</parent>
+	<packaging>ear</packaging>
+	<groupId>eclipsetest</groupId>
+	<artifactId>multymodule-3</artifactId>
+	<version>1.0</version>
+	<name>multymodule-3</name>
+	<build>
+		<plugins>
+			<plugin>
+				<artifactId>maven-ear-plugin</artifactId>
+				<configuration>
+					<defaultLibBundleDir>lib</defaultLibBundleDir>
+					<modules>
+						<webModule>
+							<groupId>${groupId}</groupId>
+							<artifactId>multymodule-2</artifactId>
+							<contextRoot>/multymodule-2-${project.version}</contextRoot>
+						</webModule>
+					</modules>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+	<dependencies>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>multymodule-2</artifactId>
+			<version>1.0</version>
+			<type>war</type>
+		</dependency>
+	</dependencies>
+</project>
diff --git a/src/test/resources/projects/project-34/multymodule-3/src/main/application/META-INF/test-file.txt b/src/test/resources/projects/project-34/multymodule-3/src/main/application/META-INF/test-file.txt
new file mode 100644
index 0000000..ea3ff8c
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-3/src/main/application/META-INF/test-file.txt
@@ -0,0 +1 @@
+empty test file
\ No newline at end of file
diff --git a/src/test/resources/projects/project-34/multymodule-4/expected/.project b/src/test/resources/projects/project-34/multymodule-4/expected/.project
new file mode 100644
index 0000000..863a276
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-4/expected/.project
@@ -0,0 +1,13 @@
+<projectDescription>
+  <name>multymodule-4-1.0</name>
+  <comment/>
+  <projects/>
+  <buildSpec>
+    <buildCommand>
+      <name>org.eclipse.jdt.core.javabuilder</name>
+    </buildCommand>
+  </buildSpec>
+  <natures>
+    <nature>org.eclipse.jdt.core.javanature</nature>
+  </natures>
+</projectDescription>
\ No newline at end of file
diff --git a/src/test/resources/projects/project-34/multymodule-4/pom.xml b/src/test/resources/projects/project-34/multymodule-4/pom.xml
new file mode 100644
index 0000000..1caca09
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-4/pom.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>eclipsetest</groupId>
+		<artifactId>master-test</artifactId>
+		<version>1.0</version>
+	</parent>
+	<packaging>jar</packaging>
+	<groupId>eclipsetest</groupId>
+	<artifactId>multymodule-4</artifactId>
+	<version>1.0</version>
+	<name>multymodule-4</name>
+	<dependencies>
+		<dependency>
+			<groupId>eclipsetest</groupId>
+			<artifactId>refproject-compile</artifactId>
+			<version>1.0</version>
+		</dependency>
+	</dependencies>
+</project>
diff --git a/src/test/resources/projects/project-34/multymodule-4/src/main/java/DummyClass.txt b/src/test/resources/projects/project-34/multymodule-4/src/main/java/DummyClass.txt
new file mode 100644
index 0000000..9ade9c1
--- /dev/null
+++ b/src/test/resources/projects/project-34/multymodule-4/src/main/java/DummyClass.txt
@@ -0,0 +1,7 @@
+/**
+ * @author <a href="mailto:trygvis@inamo.no">Trygve Laugst&oslash;l</a>
+ * @version $Id: DummyClass.txt 359507 2005-12-28 13:14:19Z fgiust $
+ */
+public class DummyClass
+{
+}
diff --git a/src/test/resources/projects/project-34/pom.xml b/src/test/resources/projects/project-34/pom.xml
new file mode 100644
index 0000000..23c9054
--- /dev/null
+++ b/src/test/resources/projects/project-34/pom.xml
@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <packaging>pom</packaging>
+  <groupId>eclipsetest</groupId>
+  <artifactId>master-test</artifactId>
+  <version>1.0</version>
+  <name>master</name>
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-eclipse-plugin</artifactId>
+        <version>test</version>
+        <configuration>
+          <workspace>${basedir}</workspace>
+          <projectNameTemplate>[artifactId]-[version]</projectNameTemplate>
+          <wtpContextName>${artifactId}-${version}</wtpContextName>
+          <wtpmanifest>true</wtpmanifest>
+          <wtpapplicationxml>true</wtpapplicationxml>
+        </configuration>
+      </plugin>
+    </plugins>
+  </build>
+  <modules>
+    <module>multymodule-1</module>
+    <module>multymodule-2</module>
+    <module>multymodule-3</module>
+  </modules>
+</project>