Merge commit 'b5662b875f5cd93c51b53a517dc9cc6ed332bb8e'

Editor/ClusterEditor.cs

@@ -22,6 +22,8 @@ namespace NanoBrain.Unity {
         }
 
         public override void OnInspectorGUI() {
+            EditorGUI.BeginChangeCheck();
+
             // Begin horizontal split
             EditorGUILayout.BeginHorizontal();
 
@@ -45,6 +47,16 @@ namespace NanoBrain.Unity {
             EditorGUIUtility.labelWidth = prevLabelWidth;
             EditorGUILayout.EndVertical(); // end right column
             EditorGUILayout.EndHorizontal(); // end split
+
+            if (EditorGUI.EndChangeCheck()) {
+                Undo.RecordObject(target, "Edit ClusterPrefab");
+                SerializedProperty versionProp = serializedObject.FindProperty("version");
+                versionProp.intValue++;
+                serializedObject.ApplyModifiedProperties();
+                EditorUtility.SetDirty(target);
+                Debug.Log($"{name} Prefab changed, version {versionProp.intValue}");
+            }
+
         }
 
         #region Inspector

Editor/ClusterView.cs

@@ -26,15 +26,26 @@ namespace NanoBrain.Unity {
 
         public static readonly Dictionary<string, ClusterView> clusterViews = new();
         public static ClusterView GetClusterView(SerializedProperty property) {
-            string key = property.propertyPath + "_" + property.serializedObject.targetObject.GetInstanceID();//GetEntityId();
+#if UNITY_6000_0_OR_NEWER            
+            EntityId id = property.serializedObject.targetObject.GetEntityId();
+#else
+            int id = property.serializedObject.targetObject.GetInstanceID();
+#endif            
+
+            string key = property.propertyPath + "_" + id;
             if (!clusterViews.TryGetValue(key, out ClusterView clusterView))
                 clusterView = new(key);// { key = key };
             return clusterView;
         }
         public static ClusterView GetClusterView(SerializedObject serializedObject) {
-            string key = serializedObject.targetObject.GetInstanceID().ToString(); //GetEntityId().ToString();
+#if UNITY_6000_0_OR_NEWER            
+            EntityId id = serializedObject.targetObject.GetEntityId();
+#else
+            int id = serializedObject.targetObject.GetInstanceID();
+#endif            
+            string key = id.ToString();
             if (!clusterViews.TryGetValue(key, out ClusterView clusterView))
-                clusterView = new(key); // { key = key };
+                clusterView = new(key);
             return clusterView;
         }
 
@@ -202,12 +213,12 @@ namespace NanoBrain.Unity {
         #region Full Graph
 
         protected void DrawFullGraph() {
-            if (this.currentNucleus == null) {
-                Vector3 position = new(150, 210, 0);
-                DrawAllOutputs(position);
-                DrawOutputs(position);
-                return;
-            }
+            // if (this.currentNucleus == null) {
+            //     Vector3 position = new(150, 210, 0);
+            //     DrawAllOutputs(position);
+            //     DrawOutputs(position);
+            //     return;
+            // }
 
             Dag dag = GenerateGraph(this.selectedOutput);
             Dag.ComputeLayout(dag);
@@ -260,8 +271,8 @@ namespace NanoBrain.Unity {
 
         public Dag GenerateGraph(Nucleus rootNucleus) {
             Dag dag = new();
-            if (rootNucleus == null)
-                return dag;
+            // if (rootNucleus == null)
+            //     return dag;
 
             int ix = 0;
             Dag.Node receiver = new() {
@@ -270,18 +281,41 @@ namespace NanoBrain.Unity {
             };
             dag.nodes.Add(receiver);
             ix++;
+            if (rootNucleus == null)
+                DescendGraphFromRoot(ref ix, dag);
+            else
                 DescendGraph(receiver, ref ix, dag);
             return dag;
         }
 
+        private void DescendGraphFromRoot(ref int ix, Dag dag) {
+            foreach (Nucleus nucleus in this.currentCluster.outputs) {
+                string nucleusName = nucleus.name;
+                Dag.Node node = dag.FindNode(nucleusName);
+                if (node == null) {
+                    node = new() {
+                        id = ix,
+                        nucleus = nucleus
+                    };
+                    dag.nodes.Add(node);
+                }
+                Dag.Edge edge = new() {
+                    fromId = node.id,
+                    toId = 0
+                };
+                dag.edges.Add(edge);
+                ix++;
+                DescendGraph(node, ref ix, dag);
+            }
+        }
+
         private void DescendGraph(Dag.Node receiver, ref int ix, Dag dag) {
-            Neuron receiverNeuron = receiver.nucleus as Neuron;
-            if (receiverNeuron == null)
+            if (receiver.nucleus is not Neuron receiverNeuron)
                 return;
 
             foreach (Synapse synapse in receiverNeuron.synapses) {
                 Nucleus nucleus = synapse.neuron;
-                if (nucleus.parent != null && nucleus.parent != currentNucleus.parent) {
+                if (nucleus.parent != null && currentNucleus != null && nucleus.parent != currentNucleus.parent) {
                     nucleus = nucleus.parent;
                 }
                 string nucleusName = nucleus.name;
@@ -739,13 +773,13 @@ namespace NanoBrain.Unity {
 
             Vector2 dir = to - from;
             float len = dir.magnitude;
-            if (len <= 2f * discRadius || len <= Mathf.Epsilon)
+            if (len <= Mathf.Epsilon) //len <= 2f * discRadius || )
                 // line too short
                 return;
 
             Vector2 n = dir / len; // normalized
-            Vector2 a = from + n * discRadius;
-            Vector2 b = to - n * discRadius;
+            Vector2 a = from;// + n * discRadius;
+            Vector2 b = to;// - n * discRadius;
             Handles.DrawLine(a, b);
         }
 
@@ -756,7 +790,7 @@ namespace NanoBrain.Unity {
             if (nucleus is Neuron neuron) {
                 tooltip = new(
                     $"{nucleus.name}" +
-                    $"\nValue: {neuron.outputMagnitude}");
+                    $"\nValue: {neuron.outputValue}");
             }
             else
                 tooltip = new($"{nucleus.name}");

Editor/Cluster_Drawer.cs

@@ -1,5 +1,4 @@
 using System.Collections;
-using System.Collections.Generic;
 using System.Reflection;
 using UnityEngine;
 using UnityEditor;
@@ -13,38 +12,55 @@ namespace NanoBrain.Unity {
         static Cluster_Drawer() {
             if (Application.isPlaying)
                 SceneView.duringSceneGui += OnSceneGUI;
-
-            Selection.selectionChanged += OnSelectionChanged;
-            if (clusterView != null)
-                clusterView.initialized = false;
         }
 
-        private const float padding = 4f;
-        private const float elementHeight = 64f; // height reserved for the VisualElement
-        private static ClusterView clusterView;
+        private const float graphHeight = 500f; // height reserved for the VisualElement
+        private static ClusterView currentClusterView;
         private static UnityEngine.Object selectedTarget;
 
         public override float GetPropertyHeight(SerializedProperty property, GUIContent label) {
-            if (Cluster_Drawer.clusterView == null)
-                return 0;
-
-            float height = EditorGUIUtility.singleLineHeight + padding;
+            float height = EditorGUIUtility.singleLineHeight;
+            if (Cluster_Drawer.currentClusterView == null)
+                // When no cluster is viewed
+                return height;
 
             SerializedProperty prefabProp = property.FindPropertyRelative(nameof(Cluster.prefab));
-            if (prefabProp.objectReferenceValue != null && Cluster_Drawer.clusterView.isOpen) {
-                height += padding + elementHeight;
-                height = 500;
+            if (prefabProp.objectReferenceValue != null && Cluster_Drawer.currentClusterView.isOpen) {
+                height = graphHeight;
+            }
+            else {
+                // Unclear why this is necessary,
+                // but without this, expanding the graph foldout is not possible
+                height += EditorGUIUtility.singleLineHeight;
             }
-            else
-                height = 18;
             return height;
         }
 
+        private void InstantiateCluster(SerializedProperty property, ClusterView clusterView) {
+            if (property == null || property.serializedObject == null || clusterView.initialized)
+                return;
+
+            SerializedProperty prefabProp = property.FindPropertyRelative(nameof(Cluster.prefab));
+            UnityEngine.Object targetObject = property.serializedObject.targetObject;
+            if (targetObject == null)
+                return;
+
+            Debug.Log($"Instantiate new Cluster for {targetObject.name}");
+
+            ClusterPrefab clusterPrefab = prefabProp.objectReferenceValue as ClusterPrefab;
+            Cluster cluster = new(clusterPrefab);
+            object parent = SerializedPropertyUtility.GetParentObjectAndMember(targetObject, property.propertyPath, out var memberInfo, out int outIndex);
+            if (parent != null && memberInfo is FieldInfo fieldInfo) {
+                fieldInfo.SetValue(parent, cluster);
+                EditorUtility.SetDirty(targetObject);
+            }
+            clusterView.initialized = true;
+        }
 
         public override void OnGUI(Rect position, SerializedProperty property, GUIContent label) {
             // Not sure if this works properly with multiple Clusters in a single gameObject
-            ClusterView clusterView = Cluster_Drawer.clusterView;
-            if (Cluster_Drawer.clusterView == null)
+            ClusterView clusterView = Cluster_Drawer.currentClusterView;
+            if (Cluster_Drawer.currentClusterView == null)
                 clusterView = ClusterView.GetClusterView(property);
 
             label = EditorGUI.BeginProperty(position, label, property);
@@ -59,44 +75,34 @@ namespace NanoBrain.Unity {
             Rect fieldRect = new(position.x, position.y, position.width, EditorGUIUtility.singleLineHeight);
             EditorGUI.BeginChangeCheck();
             EditorGUI.PropertyField(fieldRect, prefabProp, label);
+            // If a new prefab has been selected
             if (EditorGUI.EndChangeCheck()) {
+                Debug.Log($"Cluster change, Event is {Event.current.type}");
+                // Ensure the changed prefab is changed in the object
                 prefabProp.serializedObject.ApplyModifiedProperties();
                 ClusterPrefab clusterPrefab = prefabProp.objectReferenceValue as ClusterPrefab;
                 if (clusterPrefab != null) {
                     Cluster newCluster = new(clusterPrefab);
-
-                    SerializedObject serializedObject = property.serializedObject;
-                    foreach (UnityEngine.Object targetObject in serializedObject.targetObjects) {
-                        var parent = SerializedPropertyUtility.GetParentObjectAndMember(targetObject, property.propertyPath, out var memberInfo, out int outIndex);
-                        if (parent != null && memberInfo is FieldInfo fieldInfo) {
-                            fieldInfo.SetValue(parent, newCluster);
-                            EditorUtility.SetDirty(targetObject);
-                        }
+                    SetInstance(property, newCluster);
                 }
+                else {
+                    // No prefab selected -> no cluster instance
+                    SetInstance(property, new());
                 }
             }
 
+            // If a brain has been selected
             if (prefabProp.objectReferenceValue != null) {
                 // Graph is not shown when multi-editing
                 if (property.serializedObject.targetObjects.Length == 1) {
                     UnityEngine.Object targetObject = property.serializedObject.targetObject;
                     Cluster_Drawer.selectedTarget = targetObject;
 
-                    Cluster cluster;
-                    if (clusterView.initialized || Application.isPlaying) {
-                        cluster = SerializedPropertyUtility.GetManagedObjectForProperty(targetObject, property.propertyPath) as Cluster;
-                    }
-                    else {
-                        Debug.Log("New cluster instance");
-                        // This does not work properly yet it seems
-                        ClusterPrefab clusterPrefab = prefabProp.objectReferenceValue as ClusterPrefab;
-                        cluster = new(clusterPrefab);
-                        object parent = SerializedPropertyUtility.GetParentObjectAndMember(targetObject, property.propertyPath, out var memberInfo, out int outIndex);
-                        if (parent != null && memberInfo is FieldInfo fieldInfo) {
-                            fieldInfo.SetValue(parent, cluster);
-                            EditorUtility.SetDirty(targetObject);
-                        }
-                        clusterView.initialized = true;
+                    Cluster cluster = SerializedPropertyUtility.GetManagedObjectForProperty(targetObject, property.propertyPath) as Cluster;
+                    if (cluster.version != cluster.prefab.version) {
+                        // Debug.Log($"prefab version: {cluster.prefab.version} cluster version: {cluster.version}");
+                        clusterView.initialized = false;
+                        EditorApplication.delayCall += () => InstantiateCluster(property, clusterView);
                     }
 
                     // foldout header rect
@@ -107,12 +113,12 @@ namespace NanoBrain.Unity {
                         // content rect below header
                         Rect drawRect = new(fieldRect.x, headerRect.yMax + 2f, fieldRect.width, 450f);
 
-                        if (clusterView.currentCluster == null || clusterView.currentCluster != cluster) {
+                        if (cluster is not null && (clusterView.currentCluster == null || clusterView.currentCluster != cluster)) {
                             clusterView.currentCluster = cluster;
                             clusterView.currentNucleus = cluster.defaultOutput;
                             clusterView.selectedOutput = clusterView.currentNucleus;
                         }
-                        Cluster_Drawer.clusterView = clusterView;
+                        Cluster_Drawer.currentClusterView = clusterView;
                         clusterView.Render(drawRect);
                         //Debug.Log(prefab.cluster.defaultOutput.outputMagnitude);
                     }
@@ -123,6 +129,17 @@ namespace NanoBrain.Unity {
             EditorGUI.EndProperty();
         }
 
+        private static void SetInstance(SerializedProperty property, Cluster newCluster) {
+            SerializedObject serializedObject = property.serializedObject;
+            foreach (UnityEngine.Object targetObject in serializedObject.targetObjects) {
+                object parent = SerializedPropertyUtility.GetParentObjectAndMember(targetObject, property.propertyPath, out var memberInfo, out int outIndex);
+                if (parent != null && memberInfo is FieldInfo fieldInfo) {
+                    fieldInfo.SetValue(parent, newCluster);
+                    EditorUtility.SetDirty(targetObject);
+                }
+            }
+        }
+
         private static void OnSceneGUI(SceneView sceneView) {
             if (Application.isPlaying == false || selectedTarget == null)
                 return;
@@ -134,29 +151,21 @@ namespace NanoBrain.Unity {
                 gameObject = g;
 
             Handles.color = Color.yellow;
-            if (Cluster_Drawer.clusterView.selectedSynapseNeuron != null) {
-                foreach (Cluster sibling in Cluster_Drawer.clusterView.selectedSynapseNeuron.parent.instances) {
-                    Neuron siblingNeuron = sibling.GetNeuron(Cluster_Drawer.clusterView.selectedSynapseNeuron.name);
+            if (Cluster_Drawer.currentClusterView.selectedSynapseNeuron != null) {
+                foreach (Cluster sibling in Cluster_Drawer.currentClusterView.selectedSynapseNeuron.parent.instances) {
+                    Neuron siblingNeuron = sibling.GetNeuron(Cluster_Drawer.currentClusterView.selectedSynapseNeuron.name);
                     Vector3 worldVector = gameObject.transform.TransformVector(siblingNeuron.outputValue);
                     Handles.DrawLine(gameObject.transform.position, gameObject.transform.position + worldVector);
                 }
             }
             else {
-                if (Cluster_Drawer.clusterView.currentNucleus is Neuron currentNeuron) {
+                if (Cluster_Drawer.currentClusterView.currentNucleus is Neuron currentNeuron) {
                     Vector3 worldVector = gameObject.transform.TransformVector(currentNeuron.outputValue);
                     Handles.DrawLine(gameObject.transform.position, gameObject.transform.position + worldVector);
                 }
             }
         }
 
-        private static void OnSelectionChanged() {
-            UnityEngine.Object active = Selection.activeObject;
-            if (active == null)
-                return;
-
-            foreach (ClusterView clusterView in ClusterView.clusterViews.Values)
-                clusterView.initialized = false;            
-        }
     }
 
     public static class SerializedPropertyUtility {

Editor/Dag.cs

@@ -28,6 +28,9 @@ namespace NanoBrain.Unity {
                     name = name[..colonPos];
             }
             foreach (Node node in this.nodes) {
+                if (node.nucleus == null)
+                    continue;
+                    
                 string nodeName = node.nucleus.name;
                 if (justBaseName) {
                     int colonPos = nodeName.IndexOf(":");
@@ -43,6 +46,144 @@ namespace NanoBrain.Unity {
         public static Node GetNodeById(Dag dag, int id) => dag.nodes.FirstOrDefault(x => x.id == id);
 
         public static void ComputeLayout(Dag dag) {
+            BuildAdjacencyAndPredecessors(dag, out Dictionary<int, List<int>> adjacency, out Dictionary<int, List<int>> predecessors);
+            List<int> order = TopologicalOrder(adjacency, dag.nodes.Select(n => n.id));
+            Dictionary<int, int> column = ComputeLongestPathColumns(adjacency, order, dag.nodes.Select(n => n.id));
+
+            CreateDummiesAndEdges(dag, column, out List<Node> allNodes, out Dictionary<int, int> allColumns, out List<Edge> newEdges);
+
+            List<List<int>> columns = GroupColumns(allColumns);
+            PlaceNodes(allNodes, columns);
+
+            // update dag with new lists (dummies included)
+            dag.edges = newEdges;
+            dag.nodes = allNodes;
+        }
+
+        // Helper: build adjacency and predecessor lists
+        private static void BuildAdjacencyAndPredecessors(Dag dag, out Dictionary<int, List<int>> adjacency, out Dictionary<int, List<int>> predecessors) {
+            adjacency = dag.nodes.ToDictionary(n => n.id, n => new List<int>());
+            predecessors = dag.nodes.ToDictionary(n => n.id, n => new List<int>());
+            foreach (Edge edge in dag.edges) {
+                if (!adjacency.ContainsKey(edge.fromId) || !adjacency.ContainsKey(edge.toId))
+                    continue;
+                adjacency[edge.fromId].Add(edge.toId);
+                predecessors[edge.toId].Add(edge.fromId);
+            }
+        }
+
+        // Helper: compute topological order (returns empty list if cycle present)
+        private static List<int> TopologicalOrder(Dictionary<int, List<int>> adjacency, IEnumerable<int> nodeIds) {
+            Dictionary<int, int> inDegree = nodeIds.ToDictionary(id => id, _ => 0);
+            foreach (KeyValuePair<int, List<int>> keyValue in adjacency)
+                foreach (int to in keyValue.Value) if (inDegree.ContainsKey(to))
+                    inDegree[to]++;
+
+            Queue<int> queue = new(inDegree.Where(keyValue => keyValue.Value == 0).Select(kv => kv.Key));
+            List<int> topo = new();
+            while (queue.Count > 0) {
+                int nodeId = queue.Dequeue();
+                topo.Add(nodeId);
+                foreach (int adjacentNodeId in adjacency[nodeId]) {
+                    if (!inDegree.ContainsKey(adjacentNodeId))
+                        continue;
+                    inDegree[adjacentNodeId]--;
+                    if (inDegree[adjacentNodeId] == 0)
+                        queue.Enqueue(adjacentNodeId);
+                }
+            }
+            return topo;
+        }
+
+        // Helper: longest-path-from-sinks column assignment (deterministic)
+        private static Dictionary<int, int> ComputeLongestPathColumns(Dictionary<int, List<int>> adjacency, List<int> order, IEnumerable<int> nodeIds) {
+            Dictionary<int, int> column = nodeIds.ToDictionary(id => id, _ => 0);
+            foreach (int nodeId in Enumerable.Reverse(order)) {
+                foreach (int child in adjacency[nodeId]) {
+                    int cand = column[child] + 1;
+                    if (cand > column[nodeId])
+                        column[nodeId] = cand;
+                }
+            }
+            return column;
+        }
+
+        // Helper: replace long edges with dummy node chains and return augmented node/column/edge lists
+        private static void CreateDummiesAndEdges(Dag dag, Dictionary<int, int> column, out List<Node> allNodes, out Dictionary<int, int> allColumns, out List<Edge> newEdges) {
+            allColumns = new Dictionary<int, int>(column);
+            allNodes = new List<Node>(dag.nodes);
+            newEdges = new List<Edge>();
+            int nextDummyId = -1;
+
+            foreach (Edge edge in dag.edges) {
+                if (!column.ContainsKey(edge.fromId) || !column.ContainsKey(edge.toId)) {
+                    newEdges.Add(edge);
+                    continue;
+                }
+
+                int columnFrom = column[edge.fromId];
+                int columnTo = column[edge.toId];
+                int span = Mathf.Abs(columnTo - columnFrom);
+                if (span <= 1) {
+                    newEdges.Add(edge);
+                    continue;
+                }
+
+                int prev = edge.fromId;
+                int direction = columnTo > columnFrom ? 1 : -1;
+                for (int step = 1; step < span; step++) {
+                    int dummyCol = columnFrom + step * direction;
+                    int dummyId = nextDummyId--;
+                    Node dummy = new() {
+                        id = dummyId,
+                        position = Vector2.zero
+                    };
+                    // System.Reflection.FieldInfo field = typeof(Node).GetField("isDummy");
+                    // if (field != null) field.SetValue(dummy, true);
+                    allNodes.Add(dummy);
+                    allColumns[dummyId] = dummyCol;
+
+                    Edge newDummyEdge = new() {
+                        fromId = prev,
+                        toId = dummyId
+                    };
+                    newEdges.Add(newDummyEdge);
+                    prev = dummyId;
+                }
+                Edge newEdge = new() {
+                    fromId = prev,
+                    toId = edge.toId
+                };
+                newEdges.Add(newEdge);
+            }
+        }
+
+        // Helper: group columns into ordered list of lists
+        private static List<List<int>> GroupColumns(Dictionary<int, int> allColumns) {
+            return allColumns.GroupBy(kv => kv.Value).OrderBy(g => g.Key).Select(g => g.Select(x => x.Key).ToList()).ToList();
+        }
+
+        // Helper: place nodes vertically within each column
+        private static void PlaceNodes(List<Node> allNodes, List<List<int>> columns) {
+            float hSpacing = 100f;
+            float totalHeight = 400f;
+            for (int columnIx = 0; columnIx < columns.Count; columnIx++) {
+                List<int> nodeList = columns[columnIx];
+                float spacing = totalHeight / Mathf.Max(1, nodeList.Count);
+                float margin = 10 + spacing / 2;
+                for (int i = 0; i < nodeList.Count; i++) {
+                    int id = nodeList[i];
+                    Node node = allNodes.FirstOrDefault(n => n.id == id);
+                    if (node == null)
+                        continue;
+                    float x = (hSpacing * 1.5f) + columnIx * hSpacing;
+                    float y = margin + i * spacing;
+                    node.position = new Vector2(x, y);
+                }
+            }
+        }
+
+        public static void ComputeLayoutKahn(Dag dag) {
             Dictionary<int, List<int>> adjacency = dag.nodes.ToDictionary(n => n.id, n => new List<int>());
             Dictionary<int, int> outdegree = dag.nodes.ToDictionary(node => node.id, n => 0);
             foreach (Edge edge in dag.edges) {
@@ -99,29 +240,6 @@ namespace NanoBrain.Unity {
                 Select(g => g.Select(x => x.Key).ToList()).
                 ToList();
 
-            // Same code without using Linq
-            // Build layers dictionary: layerIndex -> List<int> nodeIds
-            // Dictionary<int, List<int>> layersDict = new();
-            // foreach (KeyValuePair<int, int> kv in layer) {
-            //     int nodeId = kv.Key;
-            //     int layerIndex = kv.Value;
-            //     if (!layersDict.TryGetValue(layerIndex, out List<int> list)) {
-            //         list = new List<int>();
-            //         layersDict[layerIndex] = list;
-            //     }
-            //     list.Add(nodeId);
-            // }
-
-            // // Determine sorted layer indices
-            // List<int> layerIndices = new(layersDict.Keys);
-            // layerIndices.Sort(); // ascending order
-
-            // // Build final List<List<int>> in sorted order
-            // List<List<int>> layers = new();
-            // foreach (int idx in layerIndices) {
-            //     layers.Add(layersDict[idx]);
-            // }
-
             float hSpacing = 100f;
             float totalHeight = 400f;
 
@@ -136,14 +254,11 @@ namespace NanoBrain.Unity {
                     if (node == null)
                         continue;
                     float x = (hSpacing * 1.5f) + columnIx * hSpacing;
-                    //float y = 400 - totalHeight / 2f + i * vSpacing;
                     float y = margin + i * spacing;
-                    // Debug.Log($"({li}, {i}) -> {x}, {y}");
                     node.position = new Vector2(x, y);
                 }
             }
 
-            //Repaint();
         }
     }
 }

Runtime/Scripts/Core/Cluster.cs

@@ -72,6 +72,10 @@ namespace NanoBrain {
 
         #region Init
 
+        public Cluster() {
+            this.name = "Empty Cluster";
+        }
+
         /// <summary>
         /// Instantiate a new copy of a ClusterPrefab in the given parent
         /// </summary>
@@ -451,7 +455,7 @@ namespace NanoBrain {
         /// </summary>
         public virtual Neuron defaultOutput {//=> this.nuclei[0] as Nucleus;
             get {
-                if (this.nuclei.Count > 0)
+                if (this.nuclei != null && this.nuclei.Count > 0)
                     return this.nuclei[0] as Neuron;
                 return null;
             }
@@ -471,6 +475,9 @@ namespace NanoBrain {
             get {
                 if (this._outputs == null || this._outputs.Count == 0) {
                     this._outputs = new();
+                    if (this.nuclei == null)
+                        return this._outputs;
+
                     foreach (Nucleus nucleus in this.nuclei) {
                         if (nucleus is Neuron neuron && neuron.receivers.Count == 0)
                             this._outputs.Add(neuron);

Runtime/Scripts/Core/Neuron.cs

@@ -32,7 +32,10 @@ namespace NanoBrain {
         public Neuron(Cluster parent, string name) {
             this.parent = parent;
             this.name = name;
-            this.parent?.nuclei.Add(this);
+            if (this.parent != null) {
+                this.parent.nuclei ??= new();
+                this.parent.nuclei.Add(this);
+            }
         }
 
         #region Serialization

Runtime/Scripts/ScriptableObjects/ClusterPrefab.cs

@@ -1,4 +1,3 @@
-using System.Collections.Generic;
 using UnityEngine;
 
 namespace NanoBrain.Unity {
@@ -17,25 +16,43 @@ namespace NanoBrain.Unity {
         //[HideInInspector]
         public int version;
 
-        /// <summary>
-        /// Call this function to ensure that there is at least one nucleus
-        /// </summary>
-        /// his is an invariant and should be ensured before the nucleus is used
-        /// because output requires it.
-        public void EnsureInitialization() {
-            this.cluster.prefab = this;
-            this.cluster.name = this.name;
-            this.cluster.nuclei ??= new List<Nucleus>();
-            if (this.cluster.nuclei.Count <= 0)
-                new Neuron(this.cluster, "Output"); // Every cluster should have at least 1 neuron
-            this.cluster.instanceCount = 1;
-        }
+// #if UNITY_EDITOR
+//         private bool queuedIncrement = false;
 
-#if UNITY_EDITOR
-        private void OnValidate() {
-            version++;
-        }
-#endif
+//         private void OnValidate() {
+//             Debug.Log("Validating...");
+//             if (queuedIncrement) {
+//                 Debug.Log("Re-entry");
+//                 return; // avoid re-entrancy
+//             }
+
+//             queuedIncrement = true;
+
+//             // Defer so Unity finishes its internal serialization/validate cycle first
+//             UnityEditor.EditorApplication.update += IncrementVersion;
+//         }
+//         private void IncrementVersion() {
+//             UnityEditor.EditorApplication.update -= IncrementVersion;
+//             Debug.Log("updating version...");
+//             // Ensure object still exists and hasn't been destroyed
+//             if (this == null) {
+//                 queuedIncrement = false;
+//                 return;
+//             }
+
+//             // Record for Undo and mark dirty so change persists
+//             UnityEditor.Undo.RecordObject(this, $"Increment {name} version");
+//             version++;
+//             UnityEditor.EditorUtility.SetDirty(this);
+//             Debug.Log($"{name} Prefab changed, version {version}");
+
+//             // Optional: force Inspector repaint
+//             //UnityEditor.EditorUtility.SetDirty(this);
+//             // clear the flag
+//             queuedIncrement = false;
+
+//         }
+// #endif
     }
 
 }

Samples/Braitenberg/Brains/Braitenberg 1.asset

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Samples/Braitenberg/Brains/Braitenberg 2a.asset

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Samples/Braitenberg/Brains/Braitenberg 2b.asset

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Samples/Braitenberg/Brains/Braitenberg 3a.asset

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Samples/Braitenberg/Brains/Braitenberg 3b.asset

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Samples/Braitenberg/Brains/Braitenberg 4a.asset

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     m_RemovedComponents: []
     m_RemovedGameObjects: []
     m_AddedGameObjects: []

Samples/Braitenberg/Prefabs/Vehicle.prefab

@@ -59,15 +59,9 @@ MonoBehaviour:
     _synapses: []
     combinator: 0
     _activator: 0
-    curve:
-      serializedVersion: 2
-      m_Curve: []
-      m_PreInfinity: 2
-      m_PostInfinity: 2
-      m_RotationOrder: 4
-    curveMax: 0
     persistOutput: 0
     lastUpdate: 0
+    breakOnUpdate: 0
     _receivers: []
   useOcclusion: 1
   sensitivityAngle: 90
@@ -225,15 +219,9 @@ MonoBehaviour:
     _synapses: []
     combinator: 0
     _activator: 0
-    curve:
-      serializedVersion: 2
-      m_Curve: []
-      m_PreInfinity: 2
-      m_PostInfinity: 2
-      m_RotationOrder: 4
-    curveMax: 0
     persistOutput: 0
     lastUpdate: 0
+    breakOnUpdate: 0
     _receivers: []
   references:
     version: 2
@@ -427,15 +415,9 @@ MonoBehaviour:
     _synapses: []
     combinator: 0
     _activator: 0
-    curve:
-      serializedVersion: 2
-      m_Curve: []
-      m_PreInfinity: 2
-      m_PostInfinity: 2
-      m_RotationOrder: 4
-    curveMax: 0
     persistOutput: 0
     lastUpdate: 0
+    breakOnUpdate: 0
     _receivers: []
   references:
     version: 2
@@ -540,15 +522,9 @@ MonoBehaviour:
     _synapses: []
     combinator: 0
     _activator: 0
-    curve:
-      serializedVersion: 2
-      m_Curve: []
-      m_PreInfinity: 2
-      m_PostInfinity: 2
-      m_RotationOrder: 4
-    curveMax: 0
     persistOutput: 0
     lastUpdate: 0
+    breakOnUpdate: 0
     _receivers: []
   useOcclusion: 1
   sensitivityAngle: 90
@@ -666,7 +642,7 @@ BoxCollider:
   m_LayerOverridePriority: 0
   m_IsTrigger: 0
   m_ProvidesContacts: 0
-  m_Enabled: 0
+  m_Enabled: 1
   serializedVersion: 3
   m_Size: {x: 1, y: 1, z: 1}
   m_Center: {x: 0, y: 0, z: 0}
@@ -749,11 +725,24 @@ MonoBehaviour:
   m_Script: {fileID: 11500000, guid: a8d53357b6673864d91bbc5c595d48b9, type: 3}
   m_Name: 
   m_EditorClassIdentifier: Assembly-CSharp::Breitenberg.Vehicle
-  brain: {fileID: 11400000, guid: c2d142058a073d6fdba2c8fab05834e3, type: 2}
+  brain:
+    name: 
+    parent:
+      rid: -2
+    prefab: {fileID: 0}
+    version: 0
+    instances: []
+    instanceCount: 0
+    nuclei: []
   motorLeft: {fileID: 2164057505425015568}
   motorRight: {fileID: 7548586118443431667}
   sensorLeft: {fileID: 93666564301131443}
   sensorRight: {fileID: 6470252300495393990}
+  references:
+    version: 2
+    RefIds:
+    - rid: -2
+      type: {class: , ns: , asm: }
 --- !u!1 &6750002523281406744
 GameObject:
   m_ObjectHideFlags: 0

Samples/Braitenberg/Scripts/LightSensor.cs

@@ -15,7 +15,11 @@ namespace NanoBrain.Braitenberg {
         protected override float SampleSensor() {
             float sum = 0f;
             // Get all active lights in scene (Point lights only)
+#if UNITY_6000_0_OR_NEWER
+            Light[] lights = FindObjectsByType<Light>();
+#else            
             Light[] lights = FindObjectsByType<Light>(FindObjectsSortMode.None);
+#endif            
             Vector3 pos = transform.position;
             Vector3 forward = transform.forward;
 

Samples/Braitenberg/Scripts/Motor.cs

@@ -27,7 +27,7 @@ namespace NanoBrain.Braitenberg {
                 return;
                 
             this.speed = motorNeuron.outputValue.z;
-            //Debug.DrawRay(this.transform.position, this.transform.forward * this.speed, Color.magenta);
+            Debug.DrawRay(this.transform.position, this.transform.forward * this.speed, Color.blue);
 
             float desiredRpm = speed * 60; // target wheel RPM
             float currentRpm = wheelCollider.rpm;

Samples/Braitenberg/Scripts/Sensor.cs

@@ -2,8 +2,11 @@ using System.Collections;
 using UnityEngine;
 
 namespace NanoBrain.Braitenberg {
-    using Unity;
 
+    /// <summary>
+    /// A non-directional sensor
+    /// </summary>
+    /// The sensor has a field of view, but the signal returned does not include a direction
     public class Sensor : MonoBehaviour {
         [Tooltip("Max distance sensor detects anything")]
         public float sensorRange = 10f;
@@ -60,7 +63,7 @@ namespace NanoBrain.Braitenberg {
                 float angle = Mathf.Lerp(-halfAngle, halfAngle, t);
                 Vector3 dir = Quaternion.AngleAxis(angle, this.transform.up) * this.transform.forward;
 
-                Debug.DrawRay(this.transform.position, dir * sensorRange);
+                //Debug.DrawRay(this.transform.position, dir * sensorRange);
                 if (Physics.Raycast(this.transform.position, dir, out RaycastHit hit, sensorRange, senseLayer)) {
                     // Strength inversely proportional to distance, clamped to [0,1]
                     float str = 1f - (hit.distance / sensorRange);

Samples/Braitenberg/Scripts/Vehicle.cs

@@ -15,8 +15,8 @@ namespace NanoBrain.Braitenberg {
         public Sensor sensorRight;
 
         void FixedUpdate() {
-            //     //Debug.Log($"L: {sensorLeft.output} R: {sensorRight.output}");
-            //     //Debug.Log($"L: {motorLeft.speed} R: {motorRight.speed}");
+            // Debug.Log($"L: {sensorLeft.output} R: {sensorRight.output}");
+            // Debug.Log($"L: {motorLeft.speed} R: {motorRight.speed}");
             //     Debug.Log($"L: {motorLeft.wheelCollider.rpm} R: {motorRight.wheelCollider.rpm}");
         }
     }