Shift and Drag copying should now work correctly. [This was one of those stupid little one line bugs that was so much fun to track down that I decided to spend a few hours on it)

Linking groups should now work better than it did, but still a bit of work to do on getting the rotations of all the parts after linking right. 
Added part of dalien's #301 patch (xml loading/saving related parts with some small changes)

OpenSim/Region/Application/OpenSimMain.cs

@@ -333,6 +333,8 @@ namespace OpenSim
                     m_log.Error("  alert [First] [Last] [Message] - send an alert to a user. Case sensitive.");
                     m_log.Error("  alert general [Message] - send an alert to all users.");
                     m_log.Error("backup - trigger a simulator backup");
+                    m_log.Error("load-xml [filename] - load prims from XML");
+                    m_log.Error("save-xml [filename] - save prims to XML");
                     m_log.Error("script - manually trigger scripts? or script commands?");
                     m_log.Error("show uptime - show simulator startup and uptime.");
                     m_log.Error("show users - show info about connected users.");

OpenSim/Region/Environment/Scenes/Scene.PacketHandlers.cs

@@ -508,15 +508,15 @@ namespace OpenSim.Region.Environment.Scenes
 
         public void UpdatePrimSinglePosition(uint localID, LLVector3 pos, IClientAPI remoteClient)
         {
-            Primitive prim = null;
+            bool hasPrim = false;
             foreach (EntityBase ent in Entities.Values)
             {
                 if (ent is SceneObjectGroup)
                 {
-                    //prim = ((SceneObject)ent).HasChildPrim(localID);
+                    hasPrim = ((SceneObjectGroup)ent).HasChildPrim(localID);
-                    if (prim != null)
+                    if (hasPrim != false)
                     {
-                        prim.UpdateSinglePosition(pos);
+                        ((SceneObjectGroup)ent).UpdateSinglePosition(pos, localID);
                         break;
                     }
                 }

OpenSim/Region/Environment/Scenes/Scene.cs

@@ -610,6 +610,8 @@ namespace OpenSim.Region.Environment.Scenes
                 {
                     SceneObjectGroup obj = new SceneObjectGroup(this,
                                 this.m_regionHandle, aPrimNode.OuterXml);
+                    //if we want this to be a import method then we need new uuids for the object to avoid any clashes
+                    //obj.RegenerateFullIDs(); 
                     AddEntity(obj);
                     primCount++;
                 }

OpenSim/Region/Environment/Scenes/SceneObjectGroup.cs

@@ -251,11 +251,11 @@ namespace OpenSim.Region.Environment.Scenes
         public new SceneObjectGroup Copy()
         {
             SceneObjectGroup dupe = (SceneObjectGroup)this.MemberwiseClone();
+            dupe.m_parts = new Dictionary<LLUUID, SceneObjectPart>();
             dupe.m_parts.Clear();
             dupe.AbsolutePosition = new LLVector3(AbsolutePosition.X, AbsolutePosition.Y, AbsolutePosition.Z);
             dupe.m_scene = m_scene;
             dupe.m_regionHandle = this.m_regionHandle;
-
             dupe.CopyRootPart(this.m_rootPart);
 
             List<SceneObjectPart> partList = new List<SceneObjectPart>(this.m_parts.Values);
@@ -291,6 +291,7 @@ namespace OpenSim.Region.Environment.Scenes
         public void CopyPart(SceneObjectPart part)
         {
             SceneObjectPart newPart = part.Copy(m_scene.PrimIDAllocate());
+            newPart.SetParent(this);
             this.m_parts.Add(newPart.UUID, newPart);
             this.SetPartAsNonRoot(newPart);
         }
@@ -431,6 +432,9 @@ namespace OpenSim.Region.Environment.Scenes
         public void LinkToGroup(SceneObjectGroup objectGroup)
         {
             SceneObjectPart linkPart = objectGroup.m_rootPart;
+            Axiom.Math.Vector3 oldGroupPosition = new Vector3(linkPart.GroupPosition.X, linkPart.GroupPosition.Y, linkPart.GroupPosition.Z);
+            Axiom.Math.Quaternion oldRootRotation = new Quaternion(linkPart.RotationOffset.W, linkPart.RotationOffset.X, linkPart.RotationOffset.Y, linkPart.RotationOffset.Z);
+
             linkPart.OffsetPosition = linkPart.GroupPosition - this.AbsolutePosition;
             linkPart.GroupPosition = this.AbsolutePosition;
 
@@ -450,20 +454,39 @@ namespace OpenSim.Region.Environment.Scenes
             {
                 if (part.UUID != objectGroup.m_rootPart.UUID)
                 {
-                    this.LinkNonRootPart(part);
+                    this.LinkNonRootPart(part, oldGroupPosition, oldRootRotation);
                 }
             }
 
             m_scene.EventManager.OnBackup -= objectGroup.ProcessBackup;
             m_scene.DeleteEntity(objectGroup.UUID);
+            objectGroup.DeleteParts();
             this.ScheduleGroupForFullUpdate();
         }
 
-        private void LinkNonRootPart(SceneObjectPart part)
+        private void LinkNonRootPart(SceneObjectPart part, Vector3 oldGroupPosition, Quaternion oldGroupRotation)
         {
             part.SetParent(this);
             part.ParentID = this.m_rootPart.LocalID;
             this.m_parts.Add(part.UUID, part);
+
+            Vector3 axiomOldPos = new Vector3(part.OffsetPosition.X, part.OffsetPosition.Y, part.OffsetPosition.Z);
+            axiomOldPos = oldGroupRotation * axiomOldPos;
+            axiomOldPos += oldGroupPosition;
+            LLVector3 oldAbsolutePosition = new LLVector3(axiomOldPos.x, axiomOldPos.y, axiomOldPos.z);
+            part.OffsetPosition = oldAbsolutePosition - this.AbsolutePosition;
+
+            Quaternion axiomRootRotation = new Quaternion(m_rootPart.RotationOffset.W, m_rootPart.RotationOffset.X, m_rootPart.RotationOffset.Y, m_rootPart.RotationOffset.Z);
+
+            Vector3 axiomPos = new Vector3(part.OffsetPosition.X, part.OffsetPosition.Y, part.OffsetPosition.Z);
+            axiomPos = axiomRootRotation.Inverse() * axiomPos;
+            part.OffsetPosition = new LLVector3(axiomPos.x, axiomPos.y, axiomPos.z);
+
+            Quaternion axiomPartRotation = new Quaternion(part.RotationOffset.W, part.RotationOffset.X, part.RotationOffset.Y, part.RotationOffset.Z);
+
+            axiomPartRotation = oldGroupRotation * axiomPartRotation;
+            axiomPartRotation = axiomRootRotation.Inverse() * axiomPartRotation;
+            part.RotationOffset = new LLQuaternion(axiomPartRotation.x, axiomPartRotation.y, axiomPartRotation.z, axiomPartRotation.w);
         }
 
         /// <summary>
@@ -669,7 +692,7 @@ namespace OpenSim.Region.Environment.Scenes
         public void UpdateGroupPosition(LLVector3 pos)
         {
             this.AbsolutePosition = pos;
-
+            this.ScheduleGroupForTerseUpdate();
         }
 
         /// <summary>
@@ -720,6 +743,7 @@ namespace OpenSim.Region.Environment.Scenes
             pos.X = newPos.X;
             pos.Y = newPos.Y;
             pos.Z = newPos.Z;
+            this.ScheduleGroupForTerseUpdate();
         }
         #endregion
 
@@ -859,7 +883,7 @@ namespace OpenSim.Region.Environment.Scenes
         /// <param name="part"></param>
         internal void SendPartFullUpdate(IClientAPI remoteClient, SceneObjectPart part)
         {
-            if (m_rootPart == part)
+            if (m_rootPart.UUID == part.UUID)
             {
                 part.SendFullUpdateToClient(remoteClient, AbsolutePosition);
             }
@@ -876,7 +900,7 @@ namespace OpenSim.Region.Environment.Scenes
         /// <param name="part"></param>
         internal void SendPartTerseUpdate(IClientAPI remoteClient, SceneObjectPart part)
         {
-            if (m_rootPart == part)
+            if (m_rootPart.UUID == part.UUID)
             {
                 part.SendTerseUpdateToClient(remoteClient, AbsolutePosition);
             }
@@ -932,6 +956,14 @@ namespace OpenSim.Region.Environment.Scenes
             }
         }
 
+        public void RegenerateFullIDs()
+        {
+            foreach (SceneObjectPart part in this.m_parts.Values)
+            {
+                part.UUID = LLUUID.Random();
+            }
+        }
+
         public LLUUID GetPartsFullID(uint localID)
         {
             SceneObjectPart part = this.GetChildPrim(localID);
@@ -984,6 +1016,12 @@ namespace OpenSim.Region.Environment.Scenes
             }
         }
 
+        public void DeleteParts()
+        {
+            this.m_rootPart = null;
+            this.m_parts.Clear();
+        }
+
         public override void SetText(string text, Vector3 color, double alpha)
         {
             Text = text;