diff --git a/maven-plugin-tools-annotations/pom.xml b/maven-plugin-tools-annotations/pom.xml
index 5ac0ecc..0c832fb 100644
--- a/maven-plugin-tools-annotations/pom.xml
+++ b/maven-plugin-tools-annotations/pom.xml
@@ -71,6 +71,12 @@
       <artifactId>asm-commons</artifactId>
       <version>3.3.1</version>
     </dependency>
+
+    <dependency>
+      <groupId>com.thoughtworks.qdox</groupId>
+      <artifactId>qdox</artifactId>
+    </dependency>
+
   </dependencies>
 
 </project>
diff --git a/maven-plugin-tools-annotations/src/main/java/org/apache/maven/tools/plugin/annotations/JavaAnnotationsMojoDescriptorExtractor.java b/maven-plugin-tools-annotations/src/main/java/org/apache/maven/tools/plugin/annotations/JavaAnnotationsMojoDescriptorExtractor.java
index 0fa534c..235e0d9 100644
--- a/maven-plugin-tools-annotations/src/main/java/org/apache/maven/tools/plugin/annotations/JavaAnnotationsMojoDescriptorExtractor.java
+++ b/maven-plugin-tools-annotations/src/main/java/org/apache/maven/tools/plugin/annotations/JavaAnnotationsMojoDescriptorExtractor.java
@@ -18,6 +18,8 @@ package org.apache.maven.tools.plugin.annotations;
  * under the License.
  */
 
+import com.thoughtworks.qdox.JavaDocBuilder;
+import com.thoughtworks.qdox.model.JavaClass;
 import org.apache.maven.artifact.DependencyResolutionRequiredException;
 import org.apache.maven.plugin.descriptor.DuplicateParameterException;
 import org.apache.maven.plugin.descriptor.InvalidPluginDescriptorException;
@@ -43,6 +45,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 
 /**
  * @author Olivier Lamy
@@ -76,9 +79,11 @@ public class JavaAnnotationsMojoDescriptorExtractor
 
             mojoAnnotationsScannerRequest.setDependencies( request.getProject().getCompileClasspathElements() );
 
-            List<MojoAnnotatedClass> mojoAnnotatedClasses =
+            Map<String, MojoAnnotatedClass> mojoAnnotatedClasses =
                 mojoAnnotationsScanner.scan( mojoAnnotationsScannerRequest );
 
+            JavaClass[] javaClasses = discoverClasses( request );
+
             return toMojoDescriptors( mojoAnnotatedClasses, request );
         }
         catch ( DependencyResolutionRequiredException e )
@@ -87,6 +92,28 @@ public class JavaAnnotationsMojoDescriptorExtractor
         }
     }
 
+    protected JavaClass[] discoverClasses( final PluginToolsRequest request )
+    {
+        JavaDocBuilder builder = new JavaDocBuilder();
+        builder.setEncoding( request.getEncoding() );
+
+        MavenProject project = request.getProject();
+
+        for ( String source : (List<String>) project.getCompileSourceRoots() )
+        {
+            builder.addSourceTree( new File( source ) );
+        }
+
+        // TODO be more dynamic
+        File generatedPlugin = new File( project.getBasedir(), "target/generated-sources/plugin" );
+        if ( !project.getCompileSourceRoots().contains( generatedPlugin.getAbsolutePath() ) )
+        {
+            builder.addSourceTree( generatedPlugin );
+        }
+
+        return builder.getClasses();
+    }
+
     private List<File> toFiles( List<String> directories )
     {
         if ( directories == null )
@@ -101,18 +128,19 @@ public class JavaAnnotationsMojoDescriptorExtractor
         return files;
     }
 
-    private List<MojoDescriptor> toMojoDescriptors( List<MojoAnnotatedClass> mojoAnnotatedClasses,
+    private List<MojoDescriptor> toMojoDescriptors( Map<String, MojoAnnotatedClass> mojoAnnotatedClasses,
                                                     PluginToolsRequest request )
         throws DuplicateParameterException
     {
         List<MojoDescriptor> mojoDescriptors = new ArrayList<MojoDescriptor>( mojoAnnotatedClasses.size() );
-        for ( MojoAnnotatedClass mojoAnnotatedClass : mojoAnnotatedClasses )
+        for ( MojoAnnotatedClass mojoAnnotatedClass : mojoAnnotatedClasses.values() )
         {
             MojoDescriptor mojoDescriptor = new MojoDescriptor();
 
             //mojoDescriptor.setRole( mojoAnnotatedClass.getClassName() );
             //mojoDescriptor.setRoleHint( "default" );
             mojoDescriptor.setImplementation( mojoAnnotatedClass.getClassName() );
+            mojoDescriptor.setLanguage( "java" );
 
             MojoAnnotationContent mojo = mojoAnnotatedClass.getMojo();
 
@@ -138,7 +166,6 @@ public class JavaAnnotationsMojoDescriptorExtractor
             mojoDescriptor.setOnlineRequired( mojo.requiresOnline() );
 
             mojoDescriptor.setPhase( mojo.defaultPhase().id() );
-            mojoDescriptor.setLanguage( "java" );
 
             for ( ParameterAnnotationContent parameterAnnotationContent : mojoAnnotatedClass.getParameters() )
             {
diff --git a/maven-plugin-tools-annotations/src/main/java/org/apache/maven/tools/plugin/annotations/scanner/DefaultMojoAnnotationsScanner.java b/maven-plugin-tools-annotations/src/main/java/org/apache/maven/tools/plugin/annotations/scanner/DefaultMojoAnnotationsScanner.java
index 0a861aa..ee53ffe 100644
--- a/maven-plugin-tools-annotations/src/main/java/org/apache/maven/tools/plugin/annotations/scanner/DefaultMojoAnnotationsScanner.java
+++ b/maven-plugin-tools-annotations/src/main/java/org/apache/maven/tools/plugin/annotations/scanner/DefaultMojoAnnotationsScanner.java
@@ -41,7 +41,7 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -55,22 +55,21 @@ public class DefaultMojoAnnotationsScanner
 {
     private Reflector reflector = new Reflector();
 
-    public List<MojoAnnotatedClass> scan( MojoAnnotationsScannerRequest request )
+    public Map<String, MojoAnnotatedClass> scan( MojoAnnotationsScannerRequest request )
         throws ExtractionException
     {
-        List<MojoAnnotatedClass> mojoAnnotatedClasses = new ArrayList<MojoAnnotatedClass>();
+        Map<String, MojoAnnotatedClass> mojoAnnotatedClasses = new HashMap<String, MojoAnnotatedClass>();
         try
         {
             for ( File classDirectory : request.getClassesDirectories() )
             {
                 if ( classDirectory.exists() && classDirectory.isDirectory() )
                 {
-                    mojoAnnotatedClasses.addAll( scanDirectory( classDirectory, request.getIncludePatterns() ) );
+                    mojoAnnotatedClasses.putAll( scanDirectory( classDirectory, request.getIncludePatterns() ) );
                     // TODO scan sources to get @since and @deprecated and description of classes and fields.
                 }
             }
 
-
             //TODO scan dependencies to get super class annotations if exist request.getDependencies()
 
             return mojoAnnotatedClasses;
@@ -81,10 +80,10 @@ public class DefaultMojoAnnotationsScanner
         }
     }
 
-    protected List<MojoAnnotatedClass> scanDirectory( File classDirectory, List<String> includePatterns )
+    protected Map<String, MojoAnnotatedClass> scanDirectory( File classDirectory, List<String> includePatterns )
         throws IOException, ExtractionException
     {
-        List<MojoAnnotatedClass> mojoAnnotatedClasses = new ArrayList<MojoAnnotatedClass>();
+        Map<String, MojoAnnotatedClass> mojoAnnotatedClasses = new HashMap<String, MojoAnnotatedClass>();
         DirectoryScanner scanner = new DirectoryScanner();
         scanner.setBasedir( classDirectory );
         scanner.addDefaultExcludes();
@@ -110,7 +109,8 @@ public class DefaultMojoAnnotationsScanner
                     analyzeVisitors( mojoClassVisitor );
                     if ( isMojoAnnnotatedClassCandidate( mojoClassVisitor.getMojoAnnotatedClass() ) != null )
                     {
-                        mojoAnnotatedClasses.add( mojoClassVisitor.getMojoAnnotatedClass() );
+                        mojoAnnotatedClasses.put( mojoClassVisitor.getMojoAnnotatedClass().getClassName(),
+                                                  mojoClassVisitor.getMojoAnnotatedClass() );
                     }
 
                 }
diff --git a/maven-plugin-tools-annotations/src/main/java/org/apache/maven/tools/plugin/annotations/scanner/MojoAnnotationsScanner.java b/maven-plugin-tools-annotations/src/main/java/org/apache/maven/tools/plugin/annotations/scanner/MojoAnnotationsScanner.java
index c3a6179..2bf9d9a 100644
--- a/maven-plugin-tools-annotations/src/main/java/org/apache/maven/tools/plugin/annotations/scanner/MojoAnnotationsScanner.java
+++ b/maven-plugin-tools-annotations/src/main/java/org/apache/maven/tools/plugin/annotations/scanner/MojoAnnotationsScanner.java
@@ -26,6 +26,7 @@ import org.apache.maven.tools.plugin.extractor.ExtractionException;
 
 import java.util.Arrays;
 import java.util.List;
+import java.util.Map;
 
 /**
  * @author Olivier Lamy
@@ -41,6 +42,6 @@ public interface MojoAnnotationsScanner
     static final List<String> acceptedFieldLevelAnnotationClasses =
         Arrays.asList( Parameter.class.getName(), Component.class.getName() );
 
-    List<MojoAnnotatedClass> scan( MojoAnnotationsScannerRequest request )
+    Map<String, MojoAnnotatedClass> scan( MojoAnnotationsScannerRequest request )
         throws ExtractionException;
 }
diff --git a/maven-plugin-tools-annotations/src/test/java/org/apache/maven/tools/plugin/annotations/TestAnnotationsReader.java b/maven-plugin-tools-annotations/src/test/java/org/apache/maven/tools/plugin/annotations/TestAnnotationsReader.java
index 1bc5e7d..12b0a15 100644
--- a/maven-plugin-tools-annotations/src/test/java/org/apache/maven/tools/plugin/annotations/TestAnnotationsReader.java
+++ b/maven-plugin-tools-annotations/src/test/java/org/apache/maven/tools/plugin/annotations/TestAnnotationsReader.java
@@ -34,6 +34,7 @@ import java.io.File;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 
 /**
  * @author Olivier Lamy
@@ -50,13 +51,13 @@ public class TestAnnotationsReader
         request.setClassesDirectories( Collections.singletonList( new File( "target/test-classes" ) ) );
         request.setIncludePatterns( Arrays.asList( "**/FooMojo.class" ) );
 
-        List<MojoAnnotatedClass> mojoAnnotatedClasses = mojoAnnotationsScanner.scan( request );
+        Map<String, MojoAnnotatedClass> mojoAnnotatedClasses = mojoAnnotationsScanner.scan( request );
 
         System.out.println( "mojoAnnotatedClasses:" + mojoAnnotatedClasses );
 
         Assertions.assertThat( mojoAnnotatedClasses ).isNotNull().isNotEmpty().hasSize( 1 );
 
-        MojoAnnotatedClass mojoAnnotatedClass = mojoAnnotatedClasses.get( 0 );
+        MojoAnnotatedClass mojoAnnotatedClass = mojoAnnotatedClasses.values().iterator().next();
 
         assertEquals( FooMojo.class.getName(), mojoAnnotatedClass.getClassName() );
         assertEquals( AbstractMojo.class.getName(), mojoAnnotatedClass.getParentClassName() );
diff --git a/maven-plugin-tools-java/pom.xml b/maven-plugin-tools-java/pom.xml
index 91196ab..4eb2d67 100644
--- a/maven-plugin-tools-java/pom.xml
+++ b/maven-plugin-tools-java/pom.xml
@@ -66,7 +66,6 @@
     <dependency>
       <groupId>com.thoughtworks.qdox</groupId>
       <artifactId>qdox</artifactId>
-      <version>1.11</version>
     </dependency>
 
     <dependency>
diff --git a/pom.xml b/pom.xml
index e9934a6..6dec851 100644
--- a/pom.xml
+++ b/pom.xml
@@ -229,6 +229,12 @@
         <version>1.0-alpha-9-stable-1</version>
       </dependency>
 
+      <dependency>
+        <groupId>com.thoughtworks.qdox</groupId>
+        <artifactId>qdox</artifactId>
+        <version>1.11</version>
+      </dependency>
+
       <dependency>
         <groupId>org.apache.maven.plugin-testing</groupId>
         <artifactId>maven-plugin-testing-harness</artifactId>