Converted spatial over to use Cloner to do its various

deep and semi-shallow cloning.  I'd be very surprised if nothing
is broken as there is only so much testing I can easily do.
Also various fixes for places I forgot to call super.cloneFields().

jme3-core/src/main/java/com/jme3/animation/EffectTrack.java

@@ -129,11 +129,6 @@ public class EffectTrack implements ClonableTrack {
             return c;
         }
 
-        @Override   
-        public void cloneFields( Cloner cloner, Object original ) { 
-            this.spatial = cloner.clone(spatial);
-        }
-         
         @Override
         protected void controlRender(RenderManager rm, ViewPort vp) {
         }

jme3-core/src/main/java/com/jme3/audio/AudioNode.java

@@ -730,6 +730,8 @@ public class AudioNode extends Node implements AudioSource {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
+
         this.direction = cloner.clone(direction);
         this.velocity = cloner.clone(velocity);
 

jme3-core/src/main/java/com/jme3/effect/ParticleEmitter.java

@@ -174,6 +174,13 @@ public class ParticleEmitter extends Geometry {
 
     @Override
     public ParticleEmitter clone(boolean cloneMaterial) {
+        return (ParticleEmitter)super.clone(cloneMaterial);
+    }
+
+    /**
+     *  The old clone() method that did not use the new Cloner utility.
+     */
+    public ParticleEmitter oldClone(boolean cloneMaterial) {
         ParticleEmitter clone = (ParticleEmitter) super.clone(cloneMaterial);
         clone.shape = shape.deepClone();
 
@@ -216,6 +223,8 @@ public class ParticleEmitter extends Geometry {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
+
         this.shape = cloner.clone(shape);
         this.control = cloner.clone(control);
         this.faceNormal = cloner.clone(faceNormal);

jme3-core/src/main/java/com/jme3/effect/influencers/RadialParticleInfluencer.java

@@ -125,6 +125,8 @@ public class RadialParticleInfluencer extends DefaultParticleInfluencer {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
+
         // Change in behavior: the old origin was not cloned -pspeed
         this.origin = cloner.clone(origin);
     }

jme3-core/src/main/java/com/jme3/font/BitmapText.java

@@ -90,6 +90,8 @@ public class BitmapText extends Node {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
+
         for( int i = 0; i < textPages.length; i++ ) {
             textPages[i] = cloner.clone(textPages[i]);
         }

jme3-core/src/main/java/com/jme3/scene/AssetLinkNode.java

@@ -76,6 +76,8 @@ public class AssetLinkNode extends Node {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
+
         // This is a change in behavior because the old version did not clone
         // this list... changes to one clone would be reflected in all.
         // I think that's probably undesirable. -pspeed

jme3-core/src/main/java/com/jme3/scene/BatchNode.java

@@ -727,6 +727,8 @@ public class BatchNode extends GeometryGroupNode {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
+
         this.batches = cloner.clone(batches);
         this.tmpFloat = cloner.clone(tmpFloat);
         this.tmpFloatN = cloner.clone(tmpFloatN);

jme3-core/src/main/java/com/jme3/scene/CameraNode.java

@@ -100,6 +100,8 @@ public class CameraNode extends Node {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
+
         // A change in behavior... I think previously CameraNode was probably
         // not really cloneable... or at least its camControl would be pointing
         // to the wrong control. -pspeed

jme3-core/src/main/java/com/jme3/scene/Geometry.java

@@ -44,6 +44,7 @@ import com.jme3.math.Matrix4f;
 import com.jme3.renderer.Camera;
 import com.jme3.scene.VertexBuffer.Type;
 import com.jme3.util.clone.Cloner;
+import com.jme3.util.clone.IdentityCloneFunction;
 import com.jme3.util.TempVars;
 import java.io.IOException;
 import java.util.Queue;
@@ -492,6 +493,13 @@ public class Geometry extends Spatial {
      */
     @Override
     public Geometry clone(boolean cloneMaterial) {
+        return (Geometry)super.clone(cloneMaterial);
+    }
+
+    /**
+     *  The old clone() method that did not use the new Cloner utility.
+     */
+    public Geometry oldClone(boolean cloneMaterial) {
         Geometry geomClone = (Geometry) super.clone(cloneMaterial);
 
         // This geometry is managed,
@@ -535,6 +543,10 @@ public class Geometry extends Spatial {
      */
     @Override
     public Spatial deepClone() {
+        return super.deepClone();
+    }
+
+    public Spatial oldDeepClone() {
         Geometry geomClone = clone(true);
         geomClone.mesh = mesh.deepClone();
         return geomClone;
@@ -545,9 +557,42 @@ public class Geometry extends Spatial {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
-        this.mesh = cloner.clone(mesh);
+        super.cloneFields(cloner, original);
+
+        // If this is a grouped node and if our group node is
+        // also cloned then we'll grab it's reference.
+        if( groupNode != null ) {
+            if( cloner.isCloned(groupNode) ) {
+                // Then resolve the reference
+                this.groupNode = cloner.clone(groupNode);
+            } else {
+                // We are on our own now
+                this.groupNode = null;
+                this.startIndex = -1;
+            }
+
+            // The above is based on the fact that if we were
+            // cloning the hierarchy that contained the parent
+            // group then it would have been shallow cloned before
+            // this child.  Can't really be otherwise.
+        }
+
+        this.cachedWorldMat = cloner.clone(cachedWorldMat);
+
+        // See if we are doing a shallow clone or a deep mesh clone
+        boolean shallowClone = (cloner.getCloneFunction(Mesh.class) instanceof IdentityCloneFunction);
+
+        // See if we clone the mesh using the special animation
+        // semi-deep cloning
+        if( shallowClone && mesh != null && mesh.getBuffer(Type.BindPosePosition) != null ) {
+            // Then we need to clone the mesh a little deeper
+            this.mesh = mesh.cloneForAnim();
+        } else {
+            // Do whatever the cloner wants to do about it
+            this.mesh = cloner.clone(mesh);
+        }
+
         this.material = cloner.clone(material);
-        this.groupNode = cloner.clone(groupNode);
     }
 
     @Override

jme3-core/src/main/java/com/jme3/scene/LightNode.java

@@ -100,6 +100,8 @@ public class LightNode extends Node {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
+
         // A change in behavior... I think previously LightNode was probably
         // not really cloneable... or at least its lightControl would be pointing
         // to the wrong control. -pspeed

jme3-core/src/main/java/com/jme3/scene/Mesh.java

@@ -307,7 +307,9 @@ public class Mesh implements Savable, Cloneable, JmeCloneable {
     @Override
     public Mesh jmeClone() {
         try {
-            return (Mesh)super.clone();
+            Mesh clone = (Mesh)super.clone();
+            clone.vertexArrayID = -1;
+            return clone;
         } catch (CloneNotSupportedException ex) {
             throw new AssertionError();
         }

jme3-core/src/main/java/com/jme3/scene/Node.java

@@ -697,7 +697,17 @@ public class Node extends Spatial {
     }
 
     @Override
-    public Spatial deepClone(){
+    public Spatial deepClone() {
+        Node nodeClone = (Node)super.deepClone();
+
+        // Reset the fields of the clone that should be in a 'new' state.
+        nodeClone.updateList = null;
+        nodeClone.updateListValid = false; // safe because parent is nulled out in super.clone()
+
+        return nodeClone;
+    }
+
+    public Spatial oldDeepClone(){
         Node nodeClone = (Node) super.clone();
         nodeClone.children = new SafeArrayList<Spatial>(Spatial.class);
         for (Spatial child : children){
@@ -713,6 +723,8 @@ public class Node extends Spatial {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
+
         this.children = cloner.clone(children);
 
         // Only the outer cloning thing knows whether this should be nulled

jme3-core/src/main/java/com/jme3/scene/Spatial.java

@@ -48,6 +48,7 @@ import com.jme3.renderer.queue.RenderQueue.Bucket;
 import com.jme3.renderer.queue.RenderQueue.ShadowMode;
 import com.jme3.scene.control.Control;
 import com.jme3.util.clone.Cloner;
+import com.jme3.util.clone.IdentityCloneFunction;
 import com.jme3.util.clone.JmeCloneable;
 import com.jme3.util.SafeArrayList;
 import com.jme3.util.TempVars;
@@ -1263,12 +1264,42 @@ public abstract class Spatial implements Savable, Cloneable, Collidable, Cloneab
      * Note that meshes of geometries are not cloned explicitly, they
      * are shared if static, or specially cloned if animated.
      *
-     * All controls will be cloned using the Control.cloneForSpatial method
-     * on the clone.
-     *
      * @see Mesh#cloneForAnim()
      */
-    public Spatial clone(boolean cloneMaterial) {
+    public Spatial clone( boolean cloneMaterial ) {
+
+        // Setup the cloner for the type of cloning we want to do.
+        Cloner cloner = new Cloner();
+
+        // First, we definitely do not want to clone our own parent
+        cloner.setClonedValue(parent, null);
+
+        // If we aren't cloning materials then we will make sure those
+        // aren't cloned also
+        if( !cloneMaterial ) {
+            cloner.setCloneFunction(Material.class, new IdentityCloneFunction<Material>());
+        }
+
+        // By default the meshes are not cloned.  The geometry
+        // may choose to selectively force them to be cloned but
+        // normally they will be shared
+        cloner.setCloneFunction(Mesh.class, new IdentityCloneFunction<Mesh>());
+
+        // Clone it!
+        Spatial clone = cloner.clone(this);
+
+        // Because we've nulled the parent out we need to make sure
+        // the transforms and stuff get refreshed.
+        clone.setTransformRefresh();
+        clone.setLightListRefresh();
+
+        return clone;
+    }
+
+    /**
+     *  The old clone() method that did not use the new Cloner utility.
+     */
+    public Spatial oldClone(boolean cloneMaterial) {
         try {
             Spatial clone = (Spatial) super.clone();
             if (worldBound != null) {
@@ -1344,7 +1375,22 @@ public abstract class Spatial implements Savable, Cloneable, Collidable, Cloneab
      *
      * @see Spatial#clone()
      */
-    public abstract Spatial deepClone();
+    public Spatial deepClone() {
+        // Setup the cloner for the type of cloning we want to do.
+        Cloner cloner = new Cloner();
+
+        // First, we definitely do not want to clone our own parent
+        cloner.setClonedValue(parent, null);
+
+        Spatial clone = cloner.clone(this);
+
+        // Because we've nulled the parent out we need to make sure
+        // the transforms and stuff get refreshed.
+        clone.setTransformRefresh();
+        clone.setLightListRefresh();
+
+        return clone;
+    }
 
     /**
      *  Called internally by com.jme3.util.clone.Cloner.  Do not call directly.
@@ -1381,13 +1427,15 @@ public abstract class Spatial implements Savable, Cloneable, Collidable, Cloneab
         // to avoid all of the nasty cloneForSpatial() fixup style code that
         // used to inject stuff into the clone's user data.  By using cloner
         // to clone the user data we get this automatically.
-        userData = (HashMap<String, Savable>)userData.clone();
-        for( Map.Entry<String, Savable> e : userData.entrySet() ) {
-            Savable value = e.getValue();
-            if( value instanceof Cloneable ) {
-                // Note: all JmeCloneable objects are also Cloneable so this
-                // catches both cases.
-                e.setValue(cloner.clone(value));
+        if( userData != null ) {
+            userData = (HashMap<String, Savable>)userData.clone();
+            for( Map.Entry<String, Savable> e : userData.entrySet() ) {
+                Savable value = e.getValue();
+                if( value instanceof Cloneable ) {
+                    // Note: all JmeCloneable objects are also Cloneable so this
+                    // catches both cases.
+                    e.setValue(cloner.clone(value));
+                }
             }
         }
     }

jme3-core/src/main/java/com/jme3/scene/instancing/InstancedGeometry.java

@@ -349,6 +349,8 @@ public class InstancedGeometry extends Geometry {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
+
         this.globalInstanceData = cloner.clone(globalInstanceData);
         this.transformInstanceData = cloner.clone(transformInstanceData);
         this.geometries = cloner.clone(geometries);

jme3-core/src/main/java/com/jme3/scene/instancing/InstancedNode.java

@@ -350,6 +350,8 @@ public class InstancedNode extends GeometryGroupNode {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
+
         this.control = cloner.clone(control);
         this.lookUp = cloner.clone(lookUp);
 

jme3-terrain/src/main/java/com/jme3/terrain/geomipmap/NormalRecalcControl.java

@@ -84,6 +84,7 @@ public class NormalRecalcControl extends AbstractControl {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
         this.terrain = cloner.clone(terrain);
     }
 

jme3-terrain/src/main/java/com/jme3/terrain/geomipmap/TerrainLodControl.java

@@ -314,6 +314,8 @@ public class TerrainLodControl extends AbstractControl {
 
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
+
         this.lodCalculator = cloner.clone(lodCalculator);
 
         try {

jme3-terrain/src/main/java/com/jme3/terrain/geomipmap/TerrainPatch.java

@@ -961,6 +961,7 @@ public class TerrainPatch extends Geometry {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
 
         this.stepScale = cloner.clone(stepScale);
         this.offset = cloner.clone(offset);

jme3-terrain/src/main/java/com/jme3/terrain/geomipmap/TerrainQuad.java

@@ -1813,6 +1813,8 @@ public class TerrainQuad extends Node implements Terrain {
      */
     @Override
     public void cloneFields( Cloner cloner, Object original ) {
+        super.cloneFields(cloner, original);
+
         this.stepScale = cloner.clone(stepScale);
         this.offset = cloner.clone(offset);