diff --git a/web/app/components/workflow/skill/file-tree/tree/node-menu.spec.tsx b/web/app/components/workflow/skill/file-tree/tree/node-menu.spec.tsx
index 7d1c419d45..80de905352 100644
--- a/web/app/components/workflow/skill/file-tree/tree/node-menu.spec.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/node-menu.spec.tsx
@@ -14,7 +14,6 @@ import { NODE_MENU_TYPE } from '../../constants'
 import NodeMenu from './node-menu'
 
 type MockWorkflowState = {
-  selectedNodeIds: Set<string>
   hasClipboard: () => boolean
 }
 
@@ -39,6 +38,7 @@ type RenderNodeMenuProps = {
   type?: 'root' | 'folder' | 'file'
   menuType?: 'dropdown' | 'context'
   nodeId?: string
+  actionNodeIds?: string[]
   onClose?: () => void
   onImportSkills?: () => void
 }
@@ -64,10 +64,10 @@ function createFileOperationsMock(): MockFileOperations {
 
 const mocks = vi.hoisted(() => ({
   storeState: {
-    selectedNodeIds: new Set<string>(),
     hasClipboard: () => false,
   } as MockWorkflowState,
   cutNodes: vi.fn(),
+  setFileTreeSearchTerm: vi.fn(),
   fileOperations: createFileOperationsMock(),
 }))
 
@@ -76,6 +76,7 @@ vi.mock('@/app/components/workflow/store', () => ({
   useWorkflowStore: () => ({
     getState: () => ({
       cutNodes: mocks.cutNodes,
+      setFileTreeSearchTerm: mocks.setFileTreeSearchTerm,
     }),
   }),
 }))
@@ -84,6 +85,7 @@ const renderNodeMenu = ({
   type = NODE_MENU_TYPE.FOLDER,
   menuType = 'dropdown',
   nodeId = 'node-1',
+  actionNodeIds,
   onClose = vi.fn(),
   onImportSkills,
 }: RenderNodeMenuProps = {}) => {
@@ -96,6 +98,7 @@ const renderNodeMenu = ({
               type={type}
               menuType={menuType}
               nodeId={nodeId}
+              actionNodeIds={actionNodeIds}
               onClose={onClose}
               fileInputRef={mocks.fileOperations.fileInputRef}
               folderInputRef={mocks.fileOperations.folderInputRef}
@@ -120,6 +123,7 @@ const renderNodeMenu = ({
               type={type}
               menuType={menuType}
               nodeId={nodeId}
+              actionNodeIds={actionNodeIds}
               onClose={onClose}
               fileInputRef={mocks.fileOperations.fileInputRef}
               folderInputRef={mocks.fileOperations.folderInputRef}
@@ -147,7 +151,6 @@ const renderNodeMenu = ({
 describe('NodeMenu', () => {
   beforeEach(() => {
     vi.clearAllMocks()
-    mocks.storeState.selectedNodeIds = new Set<string>()
     mocks.storeState.hasClipboard = () => false
     mocks.fileOperations = createFileOperationsMock()
   })
@@ -195,6 +198,8 @@ describe('NodeMenu', () => {
       fireEvent.click(screen.getByRole('menuitem', { name: /workflow\.skillSidebar\.menu\.newFile/i }))
       fireEvent.click(screen.getByRole('menuitem', { name: /workflow\.skillSidebar\.menu\.newFolder/i }))
 
+      expect(mocks.setFileTreeSearchTerm).toHaveBeenNthCalledWith(1, '')
+      expect(mocks.setFileTreeSearchTerm).toHaveBeenNthCalledWith(2, '')
       expect(mocks.fileOperations.handleNewFile).toHaveBeenCalledTimes(1)
       expect(mocks.fileOperations.handleNewFolder).toHaveBeenCalledTimes(1)
     })
@@ -209,9 +214,12 @@ describe('NodeMenu', () => {
       expect(clickSpy).toHaveBeenCalledTimes(2)
     })
 
-    it('should cut selected nodes and close menu when cut is clicked', () => {
-      mocks.storeState.selectedNodeIds = new Set(['file-1', 'file-2'])
-      const { onClose } = renderNodeMenu({ type: NODE_MENU_TYPE.FILE, nodeId: 'fallback-id' })
+    it('should cut explicit action node ids and close menu when cut is clicked', () => {
+      const { onClose } = renderNodeMenu({
+        type: NODE_MENU_TYPE.FILE,
+        nodeId: 'fallback-id',
+        actionNodeIds: ['file-1', 'file-2'],
+      })
 
       fireEvent.click(screen.getByRole('menuitem', { name: /workflow\.skillSidebar\.menu\.cut/i }))
 
diff --git a/web/app/components/workflow/skill/file-tree/tree/node-menu.tsx b/web/app/components/workflow/skill/file-tree/tree/node-menu.tsx
index c6ae521466..58295ef10d 100644
--- a/web/app/components/workflow/skill/file-tree/tree/node-menu.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/node-menu.tsx
@@ -24,6 +24,7 @@ type NodeMenuProps = {
   type: NodeMenuType
   menuType: 'dropdown' | 'context'
   nodeId?: string
+  actionNodeIds?: string[]
   onClose: () => void
   fileInputRef: React.RefObject<HTMLInputElement | null>
   folderInputRef: React.RefObject<HTMLInputElement | null>
@@ -42,6 +43,7 @@ const NodeMenu = ({
   type,
   menuType,
   nodeId,
+  actionNodeIds,
   onClose,
   fileInputRef,
   folderInputRef,
@@ -57,7 +59,6 @@ const NodeMenu = ({
 }: NodeMenuProps) => {
   const { t } = useTranslation('workflow')
   const storeApi = useWorkflowStore()
-  const selectedNodeIds = useStore(s => s.selectedNodeIds)
   const hasClipboard = useStore(s => s.hasClipboard())
   const isRoot = type === NODE_MENU_TYPE.ROOT
   const isFolder = type === NODE_MENU_TYPE.FOLDER || isRoot
@@ -65,18 +66,30 @@ const NodeMenu = ({
   const currentNodeId = nodeId
 
   const handleCut = useCallback(() => {
-    const ids = selectedNodeIds.size > 0 ? [...selectedNodeIds] : (currentNodeId ? [currentNodeId] : [])
+    const ids = actionNodeIds && actionNodeIds.length > 0
+      ? actionNodeIds
+      : (currentNodeId ? [currentNodeId] : [])
     if (ids.length > 0) {
       storeApi.getState().cutNodes(ids)
       onClose()
     }
-  }, [currentNodeId, onClose, selectedNodeIds, storeApi])
+  }, [actionNodeIds, currentNodeId, onClose, storeApi])
 
   const handlePaste = useCallback(() => {
     window.dispatchEvent(new CustomEvent('skill:paste'))
     onClose()
   }, [onClose])
 
+  const handleCreateFile = useCallback(() => {
+    storeApi.getState().setFileTreeSearchTerm('')
+    onNewFile()
+  }, [onNewFile, storeApi])
+
+  const handleCreateFolder = useCallback(() => {
+    storeApi.getState().setFileTreeSearchTerm('')
+    onNewFolder()
+  }, [onNewFolder, storeApi])
+
   const showRenameDelete = isFolder ? !isRoot : true
   const Separator = menuType === 'dropdown' ? DropdownMenuSeparator : ContextMenuSeparator
 
@@ -106,14 +119,14 @@ const NodeMenu = ({
             menuType={menuType}
             icon={FileAdd}
             label={t('skillSidebar.menu.newFile')}
-            onClick={onNewFile}
+            onClick={handleCreateFile}
             disabled={isLoading}
           />
           <MenuItem
             menuType={menuType}
             icon={FolderAdd}
             label={t('skillSidebar.menu.newFolder')}
-            onClick={onNewFolder}
+            onClick={handleCreateFolder}
             disabled={isLoading}
           />
 
diff --git a/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.spec.tsx b/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.spec.tsx
index 241be57ee4..63cf90d3e9 100644
--- a/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.spec.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.spec.tsx
@@ -3,6 +3,7 @@ import { ROOT_ID } from '../../constants'
 import TreeContextMenu from './tree-context-menu'
 
 const mocks = vi.hoisted(() => ({
+  selectedNodeIds: new Set<string>(),
   clearSelection: vi.fn(),
   setSelectedNodeIds: vi.fn(),
   deselectAll: vi.fn(),
@@ -30,6 +31,7 @@ const mocks = vi.hoisted(() => ({
 vi.mock('@/app/components/workflow/store', () => ({
   useWorkflowStore: () => ({
     getState: () => ({
+      selectedNodeIds: mocks.selectedNodeIds,
       clearSelection: mocks.clearSelection,
       setSelectedNodeIds: mocks.setSelectedNodeIds,
     }),
@@ -63,11 +65,12 @@ vi.mock('../../hooks/file-tree/operations/use-file-operations', () => ({
 }))
 
 vi.mock('./node-menu', () => ({
-  default: ({ type, menuType, nodeId, onImportSkills }: { type: string, menuType: string, nodeId?: string, onImportSkills?: () => void }) => (
+  default: ({ type, menuType, nodeId, actionNodeIds, onImportSkills }: { type: string, menuType: string, nodeId?: string, actionNodeIds?: string[], onImportSkills?: () => void }) => (
     <div
       data-testid={`node-menu-${menuType}`}
       data-type={type}
       data-node-id={nodeId ?? ''}
+      data-action-node-ids={(actionNodeIds ?? []).join(',')}
     >
       {onImportSkills && (
         <button type="button" onClick={onImportSkills}>
@@ -81,6 +84,7 @@ vi.mock('./node-menu', () => ({
 describe('TreeContextMenu', () => {
   beforeEach(() => {
     vi.clearAllMocks()
+    mocks.selectedNodeIds = new Set<string>()
     mocks.fileOperations.showDeleteConfirm = false
   })
 
@@ -143,6 +147,7 @@ describe('TreeContextMenu', () => {
       expect(mocks.clearSelection).not.toHaveBeenCalled()
       expect(screen.getByTestId('node-menu-context')).toHaveAttribute('data-type', 'file')
       expect(screen.getByTestId('node-menu-context')).toHaveAttribute('data-node-id', 'file-1')
+      expect(screen.getByTestId('node-menu-context')).toHaveAttribute('data-action-node-ids', 'file-1')
       expect(mocks.useFileOperations).toHaveBeenLastCalledWith(expect.objectContaining({
         nodeId: 'file-1',
         nodeType: 'file',
@@ -150,6 +155,31 @@ describe('TreeContextMenu', () => {
       }))
     })
 
+    it('should preserve multi-selection when right-click target is already selected', () => {
+      mocks.selectedNodeIds = new Set(['file-1', 'file-2'])
+      mocks.getNode.mockReturnValue({
+        select: mocks.selectNode,
+        data: { name: 'readme.md' },
+      })
+
+      render(
+        <TreeContextMenu treeRef={{ current: { deselectAll: mocks.deselectAll, get: mocks.getNode } as never }}>
+          <div>
+            <div data-skill-tree-node-id="file-1" data-skill-tree-node-type="file" role="treeitem">
+              readme.md
+            </div>
+          </div>
+        </TreeContextMenu>,
+      )
+
+      fireEvent.contextMenu(screen.getByRole('treeitem'))
+
+      expect(mocks.deselectAll).not.toHaveBeenCalled()
+      expect(mocks.selectNode).not.toHaveBeenCalled()
+      expect(mocks.setSelectedNodeIds).not.toHaveBeenCalled()
+      expect(screen.getByTestId('node-menu-context')).toHaveAttribute('data-action-node-ids', 'file-1,file-2')
+    })
+
     it('should keep import modal mounted after root menu requests it', () => {
       render(
         <TreeContextMenu treeRef={{ current: { deselectAll: mocks.deselectAll } as never }}>
diff --git a/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.tsx b/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.tsx
index 105e60950d..f22a4f720e 100644
--- a/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.tsx
@@ -33,11 +33,13 @@ type MenuTarget = {
   nodeId: string
   type: typeof NODE_MENU_TYPE.ROOT | typeof NODE_MENU_TYPE.FOLDER | typeof NODE_MENU_TYPE.FILE
   fileName?: string
+  actionNodeIds: string[]
 }
 
 const defaultMenuTarget: MenuTarget = {
   nodeId: ROOT_ID,
   type: NODE_MENU_TYPE.ROOT,
+  actionNodeIds: [],
 }
 
 const TreeContextMenu = ({
@@ -68,13 +70,23 @@ const TreeContextMenu = ({
       return
 
     const targetNode = treeRef.current?.get(nodeId)
-    treeRef.current?.deselectAll?.()
-    targetNode?.select()
-    storeApi.getState().setSelectedNodeIds([nodeId])
+    const selectedNodeIds = storeApi.getState().selectedNodeIds
+    const targetIsInSelection = selectedNodeIds.has(nodeId)
+    const actionNodeIds = targetIsInSelection && selectedNodeIds.size > 0
+      ? [...selectedNodeIds]
+      : [nodeId]
+
+    if (!targetIsInSelection) {
+      treeRef.current?.deselectAll?.()
+      targetNode?.select()
+      storeApi.getState().setSelectedNodeIds([nodeId])
+    }
+
     setMenuTarget({
       nodeId,
       type: nodeType,
       fileName: targetNode?.data.name,
+      actionNodeIds,
     })
   }, [storeApi, treeRef])
 
@@ -107,6 +119,7 @@ const TreeContextMenu = ({
             menuType="context"
             type={menuTarget.type}
             nodeId={menuTarget.nodeId}
+            actionNodeIds={menuTarget.actionNodeIds}
             onClose={handleMenuClose}
             fileInputRef={fileOperations.fileInputRef}
             folderInputRef={fileOperations.folderInputRef}
diff --git a/web/app/components/workflow/skill/file-tree/tree/tree-node.spec.tsx b/web/app/components/workflow/skill/file-tree/tree/tree-node.spec.tsx
index 78d301b258..da29172ae1 100644
--- a/web/app/components/workflow/skill/file-tree/tree/tree-node.spec.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/tree-node.spec.tsx
@@ -6,6 +6,7 @@ import TreeNode from './tree-node'
 type MockWorkflowSelectorState = {
   dirtyContents: Set<string>
   isCutNode: (nodeId: string) => boolean
+  selectedNodeIds: Set<string>
 }
 
 type NodeState = {
@@ -24,6 +25,7 @@ type NodeState = {
 const workflowState = vi.hoisted(() => ({
   dirtyContents: new Set<string>(),
   cutNodeIds: new Set<string>(),
+  selectedNodeIds: new Set<string>(),
   dragOverFolderId: null as string | null,
 }))
 
@@ -69,6 +71,7 @@ vi.mock('@/app/components/workflow/store', () => ({
   useStore: (selector: (state: MockWorkflowSelectorState) => unknown) => selector({
     dirtyContents: workflowState.dirtyContents,
     isCutNode: (nodeId: string) => workflowState.cutNodeIds.has(nodeId),
+    selectedNodeIds: workflowState.selectedNodeIds,
   }),
   useWorkflowStore: () => ({
     getState: () => ({
@@ -114,15 +117,17 @@ vi.mock('./node-menu', () => ({
   default: ({
     type,
     menuType,
+    actionNodeIds,
     onClose,
     onDeleteClick,
   }: {
     type: string
     menuType: string
+    actionNodeIds?: string[]
     onClose: () => void
     onDeleteClick?: () => void
   }) => (
-    <div data-testid={`node-menu-${menuType}`} data-type={type}>
+    <div data-testid={`node-menu-${menuType}`} data-type={type} data-action-node-ids={(actionNodeIds ?? []).join(',')}>
       <button type="button" onClick={onClose}>close-menu</button>
       <button type="button" onClick={onDeleteClick}>delete-item</button>
     </div>
@@ -179,6 +184,7 @@ describe('TreeNode', () => {
 
     workflowState.dirtyContents.clear()
     workflowState.cutNodeIds.clear()
+    workflowState.selectedNodeIds = new Set<string>()
     workflowState.dragOverFolderId = null
 
     dndMocks.isDragOver = false
@@ -202,6 +208,7 @@ describe('TreeNode', () => {
     })
 
     it('should render selected open folder with folder expansion aria state', () => {
+      workflowState.selectedNodeIds = new Set(['folder-1', 'folder-2'])
       const props = buildProps({
         id: 'folder-1',
         name: 'src',
@@ -216,6 +223,8 @@ describe('TreeNode', () => {
       expect(treeItem).toHaveAttribute('aria-selected', 'true')
       expect(treeItem).toHaveAttribute('aria-expanded', 'true')
       expect(treeItem).toHaveClass('bg-state-base-active')
+      fireEvent.click(screen.getByRole('button', { name: /workflow\.skillSidebar\.menu\.moreActions/i }))
+      expect(screen.getByTestId('node-menu-dropdown')).toHaveAttribute('data-action-node-ids', 'folder-1,folder-2')
     })
 
     it('should apply drag-over, blinking, and cut styles when states are active', () => {
diff --git a/web/app/components/workflow/skill/file-tree/tree/tree-node.tsx b/web/app/components/workflow/skill/file-tree/tree/tree-node.tsx
index 57321855a6..99f2ddfbfd 100644
--- a/web/app/components/workflow/skill/file-tree/tree/tree-node.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/tree-node.tsx
@@ -3,7 +3,7 @@
 import type { NodeRendererProps } from 'react-arborist'
 import type { TreeNodeData } from '../../type'
 import * as React from 'react'
-import { useCallback, useEffect, useRef } from 'react'
+import { useCallback, useEffect, useMemo, useRef } from 'react'
 import { useTranslation } from 'react-i18next'
 import {
   DropdownMenu,
@@ -32,7 +32,13 @@ const TreeNode = ({ node, style, dragHandle, treeChildren }: TreeNodeProps) => {
   const isSelected = node.isSelected
   const isDirty = useStore(s => s.dirtyContents.has(node.data.id))
   const isCut = useStore(s => s.isCutNode(node.data.id))
+  const selectedNodeIds = useStore(s => s.selectedNodeIds)
   const storeApi = useWorkflowStore()
+  const actionNodeIds = useMemo(() => {
+    if (node.isSelected && selectedNodeIds.size > 0)
+      return [...selectedNodeIds]
+    return [node.data.id]
+  }, [node.data.id, node.isSelected, selectedNodeIds])
 
   // Sync react-arborist drag state to Zustand for DragActionTooltip
   const prevIsDraggingRef = useRef(node.isDragging)
@@ -181,6 +187,7 @@ const TreeNode = ({ node, style, dragHandle, treeChildren }: TreeNodeProps) => {
               menuType="dropdown"
               type={isFolder ? 'folder' : 'file'}
               nodeId={node.data.id}
+              actionNodeIds={actionNodeIds}
               onClose={handleMenuClose}
               fileInputRef={fileOperations.fileInputRef}
               folderInputRef={fileOperations.folderInputRef}
diff --git a/web/app/components/workflow/skill/hooks/file-tree/operations/use-modify-operations.spec.tsx b/web/app/components/workflow/skill/hooks/file-tree/operations/use-modify-operations.spec.tsx
index 6cdfe18097..d5afb4962b 100644
--- a/web/app/components/workflow/skill/hooks/file-tree/operations/use-modify-operations.spec.tsx
+++ b/web/app/components/workflow/skill/hooks/file-tree/operations/use-modify-operations.spec.tsx
@@ -19,6 +19,7 @@ const mocks = vi.hoisted(() => ({
   toastSuccess: vi.fn<(message: string) => void>(),
   toastError: vi.fn<(message: string) => void>(),
   getAllDescendantFileIds: vi.fn<(nodeId: string, nodes: TreeNodeData[]) => string[]>(),
+  isDescendantOf: vi.fn<(potentialDescendantId: string | null | undefined, ancestorId: string | null | undefined, nodes: TreeNodeData[]) => boolean>(),
 }))
 
 vi.mock('@/service/use-app-asset', () => ({
@@ -34,6 +35,7 @@ vi.mock('../data/use-skill-tree-collaboration', () => ({
 
 vi.mock('../../../utils/tree-utils', () => ({
   getAllDescendantFileIds: mocks.getAllDescendantFileIds,
+  isDescendantOf: mocks.isDescendantOf,
 }))
 
 vi.mock('@/app/components/base/ui/toast', () => ({
@@ -75,19 +77,27 @@ const createTreeRef = (targetNode: NodeApi<TreeNodeData> | null) => {
 const createStoreApi = () => {
   const closeTab = vi.fn<(fileId: string) => void>()
   const clearDraftContent = vi.fn<(fileId: string) => void>()
+  const clearFileMetadata = vi.fn<(fileId: string) => void>()
+  const clearClipboard = vi.fn<() => void>()
   const state = {
+    clipboard: null,
     closeTab,
     clearDraftContent,
-  } as Pick<SkillEditorSliceShape, 'closeTab' | 'clearDraftContent'>
+    clearFileMetadata,
+    clearClipboard,
+  } as Pick<SkillEditorSliceShape, 'clipboard' | 'closeTab' | 'clearDraftContent' | 'clearFileMetadata' | 'clearClipboard'>
 
   const storeApi = {
     getState: () => state,
   } as unknown as StoreApi<SkillEditorSliceShape>
 
   return {
+    state,
     storeApi,
     closeTab,
     clearDraftContent,
+    clearFileMetadata,
+    clearClipboard,
   }
 }
 
@@ -97,6 +107,7 @@ describe('useModifyOperations', () => {
     mocks.deletePending = false
     mocks.deleteMutateAsync.mockResolvedValue(undefined)
     mocks.getAllDescendantFileIds.mockReturnValue([])
+    mocks.isDescendantOf.mockReturnValue(false)
   })
 
   // Scenario: loading state should match mutation pending status.
@@ -197,13 +208,17 @@ describe('useModifyOperations', () => {
   // Scenario: successful deletes should close tabs/drafts and emit collaboration updates.
   describe('Delete success', () => {
     it('should delete file node, clear descendants and current file tabs, and show file success toast', async () => {
-      const { storeApi, closeTab, clearDraftContent } = createStoreApi()
+      const { storeApi, closeTab, clearDraftContent, clearFileMetadata, clearClipboard, state } = createStoreApi()
       const onClose = vi.fn()
       const { node } = createNodeApi('file', 'file-7')
       const treeData: AppAssetTreeResponse = {
         children: [createTreeNodeData('root-folder', 'folder')],
       }
       mocks.getAllDescendantFileIds.mockReturnValue(['desc-1', 'desc-2'])
+      state.clipboard = {
+        operation: 'cut',
+        nodeIds: new Set(['file-7']),
+      }
 
       const { result } = renderHook(() => useModifyOperations({
         nodeId: 'file-7',
@@ -235,6 +250,10 @@ describe('useModifyOperations', () => {
       expect(clearDraftContent).toHaveBeenNthCalledWith(1, 'desc-1')
       expect(clearDraftContent).toHaveBeenNthCalledWith(2, 'desc-2')
       expect(clearDraftContent).toHaveBeenNthCalledWith(3, 'file-7')
+      expect(clearFileMetadata).toHaveBeenNthCalledWith(1, 'desc-1')
+      expect(clearFileMetadata).toHaveBeenNthCalledWith(2, 'desc-2')
+      expect(clearFileMetadata).toHaveBeenNthCalledWith(3, 'file-7')
+      expect(clearClipboard).toHaveBeenCalledTimes(1)
 
       expect(mocks.toastSuccess).toHaveBeenCalledWith('workflow.skillSidebar.menu.fileDeleted')
       expect(result.current.showDeleteConfirm).toBe(false)
@@ -242,12 +261,17 @@ describe('useModifyOperations', () => {
     })
 
     it('should delete folder node and skip closing the folder tab itself', async () => {
-      const { storeApi, closeTab, clearDraftContent } = createStoreApi()
+      const { storeApi, closeTab, clearDraftContent, clearFileMetadata, clearClipboard, state } = createStoreApi()
       const { node } = createNodeApi('folder', 'folder-9')
       const treeData: AppAssetTreeResponse = {
         children: [createTreeNodeData('root-folder', 'folder')],
       }
       mocks.getAllDescendantFileIds.mockReturnValue(['file-in-folder'])
+      mocks.isDescendantOf.mockReturnValueOnce(true)
+      state.clipboard = {
+        operation: 'cut',
+        nodeIds: new Set(['nested-folder']),
+      }
 
       const { result } = renderHook(() => useModifyOperations({
         nodeId: 'folder-9',
@@ -266,6 +290,9 @@ describe('useModifyOperations', () => {
       expect(closeTab).toHaveBeenCalledWith('file-in-folder')
       expect(clearDraftContent).toHaveBeenCalledTimes(1)
       expect(clearDraftContent).toHaveBeenCalledWith('file-in-folder')
+      expect(clearFileMetadata).toHaveBeenCalledTimes(1)
+      expect(clearFileMetadata).toHaveBeenCalledWith('file-in-folder')
+      expect(clearClipboard).toHaveBeenCalledTimes(1)
       expect(closeTab).not.toHaveBeenCalledWith('folder-9')
       expect(clearDraftContent).not.toHaveBeenCalledWith('folder-9')
       expect(mocks.toastSuccess).toHaveBeenCalledWith('workflow.skillSidebar.menu.deleted')
@@ -276,7 +303,7 @@ describe('useModifyOperations', () => {
   describe('Delete errors', () => {
     it('should show folder delete error toast on failure', async () => {
       mocks.deleteMutateAsync.mockRejectedValueOnce(new Error('delete failed'))
-      const { storeApi, closeTab, clearDraftContent } = createStoreApi()
+      const { storeApi, closeTab, clearDraftContent, clearFileMetadata, clearClipboard } = createStoreApi()
       const onClose = vi.fn()
       const { node } = createNodeApi('folder', 'folder-err')
       const treeData: AppAssetTreeResponse = {
@@ -299,6 +326,8 @@ describe('useModifyOperations', () => {
       expect(mocks.emitTreeUpdate).not.toHaveBeenCalled()
       expect(closeTab).not.toHaveBeenCalled()
       expect(clearDraftContent).not.toHaveBeenCalled()
+      expect(clearFileMetadata).not.toHaveBeenCalled()
+      expect(clearClipboard).not.toHaveBeenCalled()
       expect(mocks.toastError).toHaveBeenCalledWith('workflow.skillSidebar.menu.deleteError')
       expect(result.current.showDeleteConfirm).toBe(false)
       expect(onClose).toHaveBeenCalledTimes(1)
diff --git a/web/app/components/workflow/skill/hooks/file-tree/operations/use-modify-operations.ts b/web/app/components/workflow/skill/hooks/file-tree/operations/use-modify-operations.ts
index ad07a18c3d..0afe042aa2 100644
--- a/web/app/components/workflow/skill/hooks/file-tree/operations/use-modify-operations.ts
+++ b/web/app/components/workflow/skill/hooks/file-tree/operations/use-modify-operations.ts
@@ -11,7 +11,7 @@ import { useCallback, useState } from 'react'
 import { useTranslation } from 'react-i18next'
 import { toast } from '@/app/components/base/ui/toast'
 import { useDeleteAppAssetNode } from '@/service/use-app-asset'
-import { getAllDescendantFileIds } from '../../../utils/tree-utils'
+import { getAllDescendantFileIds, isDescendantOf } from '../../../utils/tree-utils'
 import { useSkillTreeUpdateEmitter } from '../data/use-skill-tree-collaboration'
 
 type UseModifyOperationsOptions = {
@@ -61,19 +61,31 @@ export function useModifyOperations({
       const descendantFileIds = treeData?.children
         ? getAllDescendantFileIds(nodeId, treeData.children)
         : []
+      const affectedFileIds = Array.from(new Set(
+        isFolder ? descendantFileIds : [...descendantFileIds, nodeId],
+      ))
 
       await deleteNodeAsync({ appId, nodeId })
       emitTreeUpdate()
 
-      descendantFileIds.forEach((fileId) => {
+      affectedFileIds.forEach((fileId) => {
         storeApi.getState().closeTab(fileId)
         storeApi.getState().clearDraftContent(fileId)
+        storeApi.getState().clearFileMetadata(fileId)
       })
 
-      // Also close and clear the node itself if it's a file
-      if (!isFolder) {
-        storeApi.getState().closeTab(nodeId)
-        storeApi.getState().clearDraftContent(nodeId)
+      const clipboard = storeApi.getState().clipboard
+      if (clipboard) {
+        const shouldClearClipboard = [...clipboard.nodeIds].some((clipboardNodeId) => {
+          if (clipboardNodeId === nodeId)
+            return true
+          if (!isFolder || !treeData?.children)
+            return false
+          return isDescendantOf(clipboardNodeId, nodeId, treeData.children)
+        })
+
+        if (shouldClearClipboard)
+          storeApi.getState().clearClipboard()
       }
 
       toast.success(
diff --git a/web/app/components/workflow/skill/hooks/file-tree/operations/use-paste-operation.spec.tsx b/web/app/components/workflow/skill/hooks/file-tree/operations/use-paste-operation.spec.tsx
index e2f2f8f33f..a4c48b1269 100644
--- a/web/app/components/workflow/skill/hooks/file-tree/operations/use-paste-operation.spec.tsx
+++ b/web/app/components/workflow/skill/hooks/file-tree/operations/use-paste-operation.spec.tsx
@@ -35,6 +35,7 @@ type WorkflowStoreState = {
     nodeIds: Set<string>
   } | null
   selectedTreeNodeId: string | null
+  cutNodes: (nodeIds: string[]) => void
   clearClipboard: () => void
 }
 
@@ -48,6 +49,7 @@ const mocks = vi.hoisted(() => ({
   workflowState: {
     clipboard: null,
     selectedTreeNodeId: null,
+    cutNodes: vi.fn<(nodeIds: string[]) => void>(),
     clearClipboard: vi.fn<() => void>(),
   } as WorkflowStoreState,
   appStoreState: {
@@ -123,6 +125,7 @@ describe('usePasteOperation', () => {
     vi.clearAllMocks()
     mocks.workflowState.clipboard = null
     mocks.workflowState.selectedTreeNodeId = null
+    mocks.workflowState.cutNodes = vi.fn()
     mocks.appStoreState.appDetail = { id: 'app-1' }
     mocks.movePending = false
     mocks.moveMutateAsync.mockResolvedValue(undefined)
@@ -303,10 +306,37 @@ describe('usePasteOperation', () => {
       })
 
       expect(mocks.workflowState.clearClipboard).not.toHaveBeenCalled()
+      expect(mocks.workflowState.cutNodes).not.toHaveBeenCalled()
       expect(mocks.emitTreeUpdate).not.toHaveBeenCalled()
       expect(mocks.toastError).toHaveBeenCalledWith('workflow.skillSidebar.menu.moveError')
     })
 
+    it('should keep failed node ids in clipboard and still refresh tree when paste partially succeeds', async () => {
+      mocks.workflowState.clipboard = {
+        operation: 'cut',
+        nodeIds: new Set(['node-ok', 'node-fail']),
+      }
+      mocks.moveMutateAsync
+        .mockResolvedValueOnce(undefined)
+        .mockRejectedValueOnce(new Error('move failed'))
+      const treeRef = createTreeRef('target')
+      const treeData: AppAssetTreeResponse = {
+        children: [createTreeNode('node-ok', 'file'), createTreeNode('node-fail', 'file')],
+      }
+
+      const { result } = renderHook(() => usePasteOperation({ treeRef, treeData }))
+
+      await act(async () => {
+        await result.current.handlePaste()
+      })
+
+      expect(mocks.moveMutateAsync).toHaveBeenCalledTimes(2)
+      expect(mocks.workflowState.clearClipboard).not.toHaveBeenCalled()
+      expect(mocks.workflowState.cutNodes).toHaveBeenCalledWith(['node-fail'])
+      expect(mocks.emitTreeUpdate).toHaveBeenCalledTimes(1)
+      expect(mocks.toastError).toHaveBeenCalledWith('workflow.skillSidebar.menu.moveError')
+    })
+
     it('should prevent re-entrant paste while a paste is in progress', async () => {
       mocks.workflowState.clipboard = {
         operation: 'cut',
diff --git a/web/app/components/workflow/skill/hooks/file-tree/operations/use-paste-operation.ts b/web/app/components/workflow/skill/hooks/file-tree/operations/use-paste-operation.ts
index 0c2099ac0e..017e436726 100644
--- a/web/app/components/workflow/skill/hooks/file-tree/operations/use-paste-operation.ts
+++ b/web/app/components/workflow/skill/hooks/file-tree/operations/use-paste-operation.ts
@@ -84,20 +84,37 @@ export function usePasteOperation({
       isPastingRef.current = true
 
       try {
-        await Promise.all(
-          nodeIdsArray.map(nodeId =>
-            moveNodeAsync({
+        const results = await Promise.allSettled(
+          nodeIdsArray.map(async (nodeId) => {
+            await moveNodeAsync({
               appId,
               nodeId,
               payload: { parent_id: targetParentId },
-            }),
-          ),
+            })
+            return nodeId
+          }),
         )
 
-        storeApi.getState().clearClipboard()
-        emitTreeUpdate()
+        const succeededNodeIds = results.flatMap(result =>
+          result.status === 'fulfilled' ? [result.value] : [],
+        )
+        const failedNodeIds = results.flatMap((result, index) =>
+          result.status === 'rejected' ? [nodeIdsArray[index]] : [],
+        )
 
-        toast.success(t('skillSidebar.menu.moved'))
+        if (succeededNodeIds.length > 0)
+          emitTreeUpdate()
+
+        if (failedNodeIds.length === 0) {
+          storeApi.getState().clearClipboard()
+          toast.success(t('skillSidebar.menu.moved'))
+          return
+        }
+
+        if (succeededNodeIds.length > 0)
+          storeApi.getState().cutNodes(failedNodeIds)
+
+        toast.error(t('skillSidebar.menu.moveError'))
       }
       catch {
         toast.error(t('skillSidebar.menu.moveError'))
diff --git a/web/app/components/workflow/skill/skill-body/sidebar-search-add.spec.tsx b/web/app/components/workflow/skill/skill-body/sidebar-search-add.spec.tsx
index 759a8f4a36..30993e7229 100644
--- a/web/app/components/workflow/skill/skill-body/sidebar-search-add.spec.tsx
+++ b/web/app/components/workflow/skill/skill-body/sidebar-search-add.spec.tsx
@@ -133,6 +133,7 @@ describe('SidebarSearchAdd', () => {
 
     it('should call create handlers when clicking new file and new folder actions', () => {
       // Arrange
+      mocks.storeState.fileTreeSearchTerm = 'agent'
       render(<SidebarSearchAdd />)
       fireEvent.click(screen.getByRole('button', { name: /common\.operation\.add/i }))
 
@@ -141,6 +142,8 @@ describe('SidebarSearchAdd', () => {
       fireEvent.click(screen.getByRole('menuitem', { name: /workflow\.skillSidebar\.menu\.newFolder/i }))
 
       // Assert
+      expect(mocks.setFileTreeSearchTerm).toHaveBeenNthCalledWith(1, '')
+      expect(mocks.setFileTreeSearchTerm).toHaveBeenNthCalledWith(2, '')
       expect(mocks.fileOperations.handleNewFile).toHaveBeenCalledTimes(1)
       expect(mocks.fileOperations.handleNewFolder).toHaveBeenCalledTimes(1)
     })
diff --git a/web/app/components/workflow/skill/skill-body/sidebar-search-add.tsx b/web/app/components/workflow/skill/skill-body/sidebar-search-add.tsx
index 624e3c97af..8fc94093db 100644
--- a/web/app/components/workflow/skill/skill-body/sidebar-search-add.tsx
+++ b/web/app/components/workflow/skill/skill-body/sidebar-search-add.tsx
@@ -57,6 +57,16 @@ const SidebarSearchAdd = () => {
     onClose: handleMenuClose,
   })
 
+  const handleCreateFile = useCallback(() => {
+    storeApi.getState().setFileTreeSearchTerm('')
+    handleNewFile()
+  }, [handleNewFile, storeApi])
+
+  const handleCreateFolder = useCallback(() => {
+    storeApi.getState().setFileTreeSearchTerm('')
+    handleNewFolder()
+  }, [handleNewFolder, storeApi])
+
   return (
     <div className="flex items-center gap-1 p-2">
       <SearchInput
@@ -101,14 +111,14 @@ const SidebarSearchAdd = () => {
             menuType="dropdown"
             icon={FileAdd}
             label={t('skillSidebar.menu.newFile')}
-            onClick={handleNewFile}
+            onClick={handleCreateFile}
             disabled={isLoading}
           />
           <MenuItem
             menuType="dropdown"
             icon={FolderAdd}
             label={t('skillSidebar.menu.newFolder')}
-            onClick={handleNewFolder}
+            onClick={handleCreateFolder}
             disabled={isLoading}
           />