src/components/NodeContextMenu.tsx

@@ -62,6 +62,7 @@ export default function NodeContextMenu({
   const graphsById = useGraphsStore((s) => (s as { graphsById: Map<string, GraphModel> }).graphsById);
   const addTreeNode = useGraphLayersTreeStore(store => store.add);
   const removeTreeNode = useGraphLayersTreeStore(store => store.remove);
+  const moveTreeNode = useGraphLayersTreeStore(store => store.move);
   const setCut = useCutStore(store => store.setCut);
   const clearCut = useCutStore(store => store.clearCut);
 
@@ -165,6 +166,22 @@ export default function NodeContextMenu({
           }
         }
 
+        // Update navigation tree: reparent tree nodes from source graph to target graph.
+        // A tree node belongs to the source graph when its tree parent matches sourceGraphId
+        // (or is a root node when sourceGraphId is 'main').
+        const treeState = useGraphLayersTreeStore.getState();
+        const effectiveSourceParent = cutState.sourceGraphId === 'main' ? undefined : cutState.sourceGraphId ?? undefined;
+        const newTreeParent = graphContextValue.graphId === 'main' ? undefined : graphContextValue.graphId;
+
+        for (const nodeId of cutState.cutNodeIds) {
+          if (treeState.nodesFlatById.has(nodeId)) {
+            const nodeTreeParent = treeState.parentIdByChildId.get(nodeId);
+            if (nodeTreeParent === effectiveSourceParent) {
+              moveTreeNode(nodeId, newTreeParent);
+            }
+          }
+        }
+
         clearCut();
         break;
       }

src/stores/TreeStore.tsx

@@ -10,6 +10,7 @@ export interface TreeStore {
   tree: TreeDataNode[];
   add: (childNode: NodeContext, parentNodeId: string | undefined) => void;
   remove: (nodeId: string) => void;
+  move: (nodeId: string, newParentId: string | undefined) => void;
   reset: () => void;
 }
 
@@ -90,6 +91,44 @@ export const useGraphLayersTreeStore = create<TreeStore>()((set) => ({
       tree: createTree([...state.rootNodes], nodesFlatById)
     }
   }),
+  move: (nodeId, newParentId) => set((state) => {
+    const node = state.nodesFlatById.get(nodeId);
+    if (!node) return state;
+
+    const nodesFlatById = new Map(state.nodesFlatById);
+    const parentIdByChildId = new Map(state.parentIdByChildId);
+    let rootNodes = [...state.rootNodes];
+
+    // Remove from old parent
+    const oldParentId = state.parentIdByChildId.get(nodeId);
+    if (oldParentId !== undefined) {
+      const oldParent = nodesFlatById.get(oldParentId);
+      if (oldParent) {
+        oldParent.children = oldParent.children?.filter(n => n.key !== nodeId) ?? [];
+      }
+      parentIdByChildId.delete(nodeId);
+    } else {
+      rootNodes = rootNodes.filter(n => n.key !== nodeId);
+    }
+
+    // Add to new parent
+    if (newParentId !== undefined) {
+      const newParent = nodesFlatById.get(newParentId);
+      if (newParent) {
+        newParent.children = newParent.children ? [...newParent.children, node] : [node];
+        parentIdByChildId.set(nodeId, newParentId);
+      }
+    } else {
+      rootNodes = [...rootNodes, node];
+    }
+
+    return {
+      nodesFlatById,
+      parentIdByChildId,
+      rootNodes,
+      tree: createTree(rootNodes, nodesFlatById),
+    };
+  }),
   reset: () => set({
     nodesFlatById: new Map<React.Key, TreeDataNode>(),
     parentIdByChildId: new Map<React.Key, string>(),