diff --git a/packages/app/e2e/browser/file-explorer-collapse.spec.ts b/packages/app/e2e/browser/file-explorer-collapse.spec.ts
index 705f667260..b00101c2ff 100644
--- a/packages/app/e2e/browser/file-explorer-collapse.spec.ts
+++ b/packages/app/e2e/browser/file-explorer-collapse.spec.ts
@@ -1,4 +1,6 @@
-import { test } from "../support/fixtures";
+import { writeFile } from "node:fs/promises";
+import path from "node:path";
+import { expect, test } from "../support/fixtures";
 import {
   collapseFolder,
   expandFolder,
@@ -8,6 +10,7 @@ import {
   openFileExplorer,
   openFileFromExplorer,
 } from "../support/helpers/file-explorer";
+import { delayDirectoryListingResponse } from "../support/helpers/directory-listing-gate";
 import { gotoWorkspace } from "../support/helpers/launcher";
 import { seedWorkspace, type SeededWorkspace } from "../support/helpers/seed-client";
 
@@ -49,3 +52,66 @@ test.describe("File explorer collapse", () => {
     await expectExplorerEntryVisible(page, "guide.md");
   });
 });
+
+test("Files Refresh reveals new files when a cached collapsed folder is reopened", async ({
+  page,
+}) => {
+  await gotoWorkspace(page, workspace.workspaceId);
+  await openFileExplorer(page);
+  await expandFolder(page, "docs");
+  await expectExplorerEntryVisible(page, "guide.md");
+  await collapseFolder(page, "docs");
+  await expectExplorerEntryHidden(page, "guide.md");
+  await createFileOutsidePaseo("docs/NEW.md");
+  await refreshFiles(page);
+  await expandFolder(page, "docs");
+  await expectExplorerEntryVisible(page, "guide.md");
+  await expectExplorerEntryVisible(page, "NEW.md");
+
+  await createFileOutsidePaseo("docs/NEXT.md");
+  await refreshFiles(page);
+  await expectExplorerEntryVisible(page, "NEXT.md");
+});
+
+async function refreshFiles(page: import("@playwright/test").Page): Promise<void> {
+  const refresh = page.getByRole("button", { name: "Refresh files", exact: true });
+  await refresh.click();
+  await expect(refresh).toBeEnabled();
+}
+
+async function createFileOutsidePaseo(filePath: string): Promise<void> {
+  await writeFile(path.join(workspace.repoPath, filePath), "# New output\n");
+}
+
+test("Files Refresh ignores an old reply for a folder collapsed while loading", async ({
+  page,
+}) => {
+  const reply = await delayDirectoryListingResponse(page, "docs");
+  await gotoWorkspace(page, workspace.workspaceId);
+  await openFileExplorer(page);
+  await expandFolder(page, "docs");
+  await reply.waitUntilHeld();
+  await collapseFolder(page, "docs");
+  await createFileOutsidePaseo("docs/DELAYED.md");
+  await refreshFiles(page);
+  await reply.release();
+  await expandFolder(page, "docs");
+  await expectExplorerEntryVisible(page, "DELAYED.md");
+});
+
+test("Files Refresh preserves expanded folders while their saved view is restoring", async ({
+  page,
+}) => {
+  await gotoWorkspace(page, workspace.workspaceId);
+  await openFileExplorer(page);
+  await expandFolder(page, "docs");
+  await expectExplorerEntryVisible(page, "guide.md");
+  const reply = await delayDirectoryListingResponse(page, "docs");
+  await page.reload();
+  await openFileExplorer(page);
+  await reply.waitUntilHeld();
+  await refreshFiles(page);
+  await expectExplorerEntryVisible(page, "guide.md");
+  await reply.release();
+  await expectExplorerEntryVisible(page, "guide.md");
+});
diff --git a/packages/app/e2e/support/helpers/directory-listing-gate.ts b/packages/app/e2e/support/helpers/directory-listing-gate.ts
new file mode 100644
index 0000000000..4e9dd8dc10
--- /dev/null
+++ b/packages/app/e2e/support/helpers/directory-listing-gate.ts
@@ -0,0 +1,44 @@
+import type { Page, WebSocketRoute } from "@playwright/test";
+import { daemonWsRoutePattern } from "./daemon-port";
+
+function listingResponse(message: string | Buffer) {
+  try {
+    const envelope = JSON.parse(message.toString());
+    return envelope.message?.type === "file_explorer_response" ? envelope.message.payload : null;
+  } catch {
+    return null;
+  }
+}
+
+/** Delay one real directory response after the daemon has read its contents. */
+export async function delayDirectoryListingResponse(page: Page, directoryPath: string) {
+  let held: { socket: WebSocketRoute; message: string | Buffer; requestId: string } | null = null;
+  let resolveHeld!: () => void;
+  const heldResponse = new Promise<void>((resolve) => {
+    resolveHeld = resolve;
+  });
+  await page.routeWebSocket(daemonWsRoutePattern(), (socket) => {
+    const server = socket.connectToServer();
+    socket.onMessage((message) => server.send(message));
+    server.onMessage((message) => {
+      const response = listingResponse(message);
+      if (!held && response?.mode === "list" && response.path === directoryPath) {
+        held = { socket, message, requestId: response.requestId };
+        resolveHeld();
+        return;
+      }
+      socket.send(message);
+    });
+  });
+  return {
+    waitUntilHeld: () => heldResponse,
+    release: async () => {
+      if (!held) throw new Error("Directory response must be held before release");
+      held.socket.send(held.message);
+      // Let the delivered reply update the UI before the user reopens the folder.
+      await page.evaluate(
+        () => new Promise<void>((resolve) => requestAnimationFrame(() => resolve())),
+      );
+    },
+  };
+}
diff --git a/packages/app/src/components/file-explorer-pane.tsx b/packages/app/src/components/file-explorer-pane.tsx
index 80bc9b0257..2625407d60 100644
--- a/packages/app/src/components/file-explorer-pane.tsx
+++ b/packages/app/src/components/file-explorer-pane.tsx
@@ -64,10 +64,15 @@ import { useIsLocalDaemon } from "@/hooks/use-is-local-daemon";
 import { buildWorkspaceExplorerStateKey } from "@/hooks/use-file-explorer-actions";
 import { usePanelStore, type ExpandedPathsUpdate, type SortOption } from "@/stores/panel-store";
 import { buildAbsoluteExplorerPath } from "@/utils/explorer-paths";
+import {
+  DIRECTORY_LISTING_INVALIDATED,
+  type DirectoryListingResult,
+} from "@/file-explorer/directory-listings";
 import { isHiddenExplorerPath } from "@/file-explorer/visibility";
 import {
   flattenExplorerTree,
   reconcileRestoredExpandedPaths,
+  refreshExplorerDirectories,
   restoreExpandedDirectories,
   setExpandedDirectoryPath,
   showHiddenFilesAndRestoreExpandedDirectories,
@@ -435,6 +440,7 @@ export function FileExplorerPane({
 
   const {
     requestDirectoryListing,
+    invalidateDirectoryListings,
     createEntry,
     renameEntry,
     duplicateEntry,
@@ -886,9 +892,11 @@ export function FileExplorerPane({
       refreshExplorerDirectories({
         hasWorkspaceScope,
         expandedPaths,
+        showHiddenFiles: usePanelStore.getState().explorerShowHiddenFiles,
         requestDirectoryListing,
+        invalidateDirectoryListings,
       }),
-    [expandedPaths, hasWorkspaceScope, requestDirectoryListing],
+    [invalidateDirectoryListings, expandedPaths, hasWorkspaceScope, requestDirectoryListing],
   );
   const { refetch: refetchExplorer, isFetching: isRefreshFetching } = useQuery({
     queryKey: ["fileExplorerRefresh", serverId, workspaceStateKey],
@@ -1424,7 +1432,7 @@ function toggleDirectory({
   requestDirectoryListing: (
     path: string,
     opts?: { recordHistory?: boolean; setCurrentPath?: boolean },
-  ) => Promise<ExplorerDirectory | null>;
+  ) => Promise<DirectoryListingResult>;
   setExpandedPathsForWorkspace: (workspaceStateKey: string, paths: ExpandedPathsUpdate) => void;
 }): void {
   if (!workspaceStateKey) {
@@ -1561,7 +1569,7 @@ async function initializeExplorer({
   requestDirectoryListing: (
     path: string,
     opts?: { recordHistory?: boolean; setCurrentPath?: boolean },
-  ) => Promise<ExplorerDirectory | null>;
+  ) => Promise<DirectoryListingResult>;
   setExpandedPathsForWorkspace: (workspaceStateKey: string, paths: ExpandedPathsUpdate) => void;
 }): Promise<void> {
   if (!hasWorkspaceScope || hasInitializedRef.current) {
@@ -1572,6 +1580,7 @@ async function initializeExplorer({
     recordHistory: false,
     setCurrentPath: false,
   });
+  if (rootDirectory === DIRECTORY_LISTING_INVALIDATED) return;
   if (!rootDirectory) {
     hasInitializedRef.current = false;
     return;
@@ -1593,7 +1602,10 @@ async function initializeExplorer({
   const hiddenPersistedPaths = showHiddenFiles
     ? []
     : Array.from(persistedExpandedPaths).filter(isHiddenExplorerPath);
-  const restoredPathsWithHidden = [...restoredPaths, ...hiddenPersistedPaths];
+  const restoredPathsWithHidden =
+    restoredPaths === DIRECTORY_LISTING_INVALIDATED
+      ? DIRECTORY_LISTING_INVALIDATED
+      : [...restoredPaths, ...hiddenPersistedPaths];
   setExpandedPathsForWorkspace(workspaceStateKey, (currentPaths) =>
     reconcileRestoredExpandedPaths({
       persistedExpandedPaths,
@@ -1603,39 +1615,6 @@ async function initializeExplorer({
   );
 }
 
-async function refreshExplorerDirectories({
-  hasWorkspaceScope,
-  expandedPaths,
-  requestDirectoryListing,
-}: {
-  hasWorkspaceScope: boolean;
-  expandedPaths: Set<string>;
-  requestDirectoryListing: (
-    path: string,
-    opts?: { recordHistory?: boolean; setCurrentPath?: boolean },
-  ) => Promise<ExplorerDirectory | null>;
-}): Promise<null> {
-  if (!hasWorkspaceScope) {
-    return null;
-  }
-  const showHiddenFiles = usePanelStore.getState().explorerShowHiddenFiles;
-  const directoryPaths = Array.from(expandedPaths).filter(
-    (path) => showHiddenFiles || !isHiddenExplorerPath(path),
-  );
-  if (!directoryPaths.includes(".")) {
-    directoryPaths.unshift(".");
-  }
-  await Promise.all(
-    directoryPaths.map((path) =>
-      requestDirectoryListing(path, {
-        recordHistory: false,
-        setCurrentPath: false,
-      }),
-    ),
-  );
-  return null;
-}
-
 function getErrorRecoveryPath(state: AgentFileExplorerState | undefined): string {
   if (!state) {
     return ".";
diff --git a/packages/app/src/file-explorer/directory-listings.test.ts b/packages/app/src/file-explorer/directory-listings.test.ts
new file mode 100644
index 0000000000..8e56b39b2b
--- /dev/null
+++ b/packages/app/src/file-explorer/directory-listings.test.ts
@@ -0,0 +1,180 @@
+import { describe, expect, it } from "vitest";
+import type { AgentFileExplorerState, ExplorerDirectory } from "@/stores/session-store";
+import {
+  refreshExplorerDirectories,
+  restoreExpandedDirectories,
+  showHiddenFilesAndRestoreExpandedDirectories,
+  reconcileRestoredExpandedPaths,
+} from "./tree";
+import {
+  DIRECTORY_LISTING_INVALIDATED,
+  invalidateExplorerDirectoryListings,
+  loadExplorerDirectory,
+} from "./directory-listings";
+
+function directory(path: string, names: string[]): ExplorerDirectory {
+  return {
+    path,
+    entries: names.map((name) => ({
+      path: `${path}/${name}`,
+      name,
+      kind: "file",
+      size: 0,
+      modifiedAt: "2026-01-01T00:00:00.000Z",
+    })),
+  };
+}
+
+function deferred<T>() {
+  let resolve!: (value: T) => void;
+  let reject!: (error: Error) => void;
+  const promise = new Promise<T>((yes, no) => {
+    resolve = yes;
+    reject = no;
+  });
+  return { promise, resolve, reject };
+}
+
+function explorer() {
+  let state: AgentFileExplorerState = {
+    listingGeneration: 0,
+    directories: new Map([[".", directory(".", ["docs"])]]),
+    isLoading: false,
+    lastError: null,
+    pendingRequest: null,
+    currentPath: ".",
+    history: ["."],
+    lastVisitedPath: ".",
+    selectedEntryPath: null,
+  };
+  const updateState = (update: (state: AgentFileExplorerState) => AgentFileExplorerState) => {
+    state = update(state);
+    return state;
+  };
+  return {
+    state: () => state,
+    load: (path: string, result: Promise<ExplorerDirectory>) =>
+      loadExplorerDirectory({
+        path,
+        updateState,
+        listDirectory: () => result,
+        fallbackError: "Directory listing failed",
+        options: { recordHistory: false, setCurrentPath: false },
+      }),
+    refresh: (retained: readonly string[]) =>
+      invalidateExplorerDirectoryListings(updateState, retained),
+  };
+}
+
+describe("directory listings across Refresh", () => {
+  it("ignores an earlier reply for a collapsed folder while the fresh root is loading", async () => {
+    const model = explorer();
+    const old = deferred<ExplorerDirectory>();
+    const oldLoad = model.load("docs", old.promise);
+    model.refresh(["."]);
+    const fresh = deferred<ExplorerDirectory>();
+    const freshLoad = model.load(".", fresh.promise);
+    old.resolve(directory("docs", ["OLD.md"]));
+
+    await expect(oldLoad).resolves.toBe(DIRECTORY_LISTING_INVALIDATED);
+    expect(model.state().directories.has("docs")).toBe(false);
+    expect(model.state().isLoading).toBe(true);
+    expect(model.state().pendingRequest?.path).toBe(".");
+
+    const root = directory(".", ["docs", "NEW.md"]);
+    fresh.resolve(root);
+    await expect(freshLoad).resolves.toEqual(root);
+    expect(model.state().directories.get(".")).toEqual(root);
+    expect(model.state().isLoading).toBe(false);
+  });
+
+  it("does not let a pre-refresh reply replace a newer listing of the same folder", async () => {
+    const model = explorer();
+    const old = deferred<ExplorerDirectory>();
+    const oldLoad = model.load("docs", old.promise);
+    model.refresh([".", "docs"]);
+    const fresh = directory("docs", ["NEW.md"]);
+    await model.load("docs", Promise.resolve(fresh));
+    old.resolve(directory("docs", ["OLD.md"]));
+
+    await expect(oldLoad).resolves.toBe(DIRECTORY_LISTING_INVALIDATED);
+    expect(model.state().directories.get("docs")).toEqual(fresh);
+  });
+
+  it("ignores errors from requests invalidated by Refresh", async () => {
+    const model = explorer();
+    const old = deferred<ExplorerDirectory>();
+    const oldLoad = model.load("docs", old.promise);
+    model.refresh(["."]);
+    const fresh = deferred<ExplorerDirectory>();
+    const freshLoad = model.load(".", fresh.promise);
+    old.reject(new Error("Old request failed"));
+
+    await expect(oldLoad).resolves.toBe(DIRECTORY_LISTING_INVALIDATED);
+    expect(model.state().lastError).toBeNull();
+    expect(model.state().isLoading).toBe(true);
+    fresh.resolve(directory(".", ["docs"]));
+    await freshLoad;
+  });
+
+  it("keeps expanded listings visible and discards collapsed listings on Refresh", async () => {
+    const model = explorer();
+    const docs = directory("docs", ["guide.md"]);
+    await model.load("docs", Promise.resolve(docs));
+    await model.load("assets", Promise.resolve(directory("assets", ["logo.png"])));
+    model.refresh([".", "docs"]);
+
+    expect(model.state().directories.get("docs")).toEqual(docs);
+    expect(model.state().directories.has("assets")).toBe(false);
+    expect(model.state().currentPath).toBe(".");
+    expect(model.state().history).toEqual(["."]);
+  });
+});
+
+it.each([false, true])(
+  "preserves saved expansion when Refresh invalidates restoration (hidden: %s)",
+  async (hidden) => {
+    const model = explorer();
+    const folder = hidden ? ".hidden" : "docs";
+    const root: ExplorerDirectory = {
+      path: ".",
+      entries: [
+        {
+          name: folder,
+          path: folder,
+          kind: "directory",
+          size: 0,
+          modifiedAt: "2026-01-01T00:00:00.000Z",
+        },
+      ],
+    };
+    const saved = new Set([".", folder]);
+    const pending = deferred<ExplorerDirectory>();
+    const input = {
+      rootDirectory: root,
+      persistedExpandedPaths: saved,
+      requestDirectoryListing: (path: string) => model.load(path, pending.promise),
+    };
+    const restoration = hidden
+      ? showHiddenFilesAndRestoreExpandedDirectories({ ...input, showHiddenFiles: () => {} })
+      : restoreExpandedDirectories({ ...input, showHiddenFiles: false });
+    const fresh = directory(folder, ["NEW.md"]);
+    await refreshExplorerDirectories({
+      hasWorkspaceScope: true,
+      expandedPaths: saved,
+      showHiddenFiles: hidden,
+      invalidateDirectoryListings: model.refresh,
+      requestDirectoryListing: (path) =>
+        model.load(path, Promise.resolve(path === "." ? root : fresh)),
+    });
+    pending.resolve(directory(folder, ["OLD.md"]));
+    const restored = await restoration;
+    const expanded = reconcileRestoredExpandedPaths({
+      persistedExpandedPaths: saved,
+      currentExpandedPaths: saved,
+      restoredExpandedPaths: restored,
+    });
+    expect(model.state().directories.get(folder)).toEqual(fresh);
+    expect(expanded).toEqual([".", folder]);
+  },
+);
diff --git a/packages/app/src/file-explorer/directory-listings.ts b/packages/app/src/file-explorer/directory-listings.ts
new file mode 100644
index 0000000000..4d52aaf782
--- /dev/null
+++ b/packages/app/src/file-explorer/directory-listings.ts
@@ -0,0 +1,91 @@
+import type { AgentFileExplorerState, ExplorerDirectory } from "@/stores/session-store";
+
+export const DIRECTORY_LISTING_INVALIDATED = Symbol("directory-listing-invalidated");
+export type DirectoryListingResult =
+  | ExplorerDirectory
+  | null
+  | typeof DIRECTORY_LISTING_INVALIDATED;
+
+type UpdateExplorerState = (
+  update: (state: AgentFileExplorerState) => AgentFileExplorerState,
+) => AgentFileExplorerState | null;
+
+function pushHistory(history: string[], path: string): string[] {
+  const normalizedHistory = history.length === 0 ? ["."] : history;
+  return normalizedHistory.at(-1) === path ? normalizedHistory : [...normalizedHistory, path];
+}
+
+export async function loadExplorerDirectory({
+  path,
+  options,
+  updateState,
+  listDirectory,
+  fallbackError,
+}: {
+  path: string;
+  options?: { recordHistory?: boolean; setCurrentPath?: boolean };
+  updateState: UpdateExplorerState;
+  listDirectory: () => Promise<ExplorerDirectory>;
+  fallbackError: string;
+}): Promise<DirectoryListingResult> {
+  const shouldSetCurrentPath = options?.setCurrentPath ?? true;
+  const shouldRecordHistory = options?.recordHistory ?? shouldSetCurrentPath;
+  const initial = updateState((state) => ({
+    ...state,
+    isLoading: true,
+    lastError: null,
+    pendingRequest: { path, mode: "list" },
+    ...(shouldSetCurrentPath
+      ? {
+          currentPath: path,
+          history: shouldRecordHistory ? pushHistory(state.history, path) : state.history,
+          lastVisitedPath: path,
+        }
+      : {}),
+  }));
+  if (!initial) return null;
+  const generation = initial.listingGeneration;
+  try {
+    const directory = await listDirectory();
+    let accepted = false;
+    updateState((state) => {
+      if (state.listingGeneration !== generation) return state;
+      accepted = true;
+      const directories = new Map(state.directories);
+      directories.set(directory.path, directory);
+      return { ...state, directories, isLoading: false, lastError: null, pendingRequest: null };
+    });
+    return accepted ? directory : DIRECTORY_LISTING_INVALIDATED;
+  } catch (error) {
+    let invalidated = false;
+    updateState((state) => {
+      if (state.listingGeneration !== generation) {
+        invalidated = true;
+        return state;
+      }
+      return {
+        ...state,
+        isLoading: false,
+        lastError: error instanceof Error ? error.message : fallbackError,
+        pendingRequest: null,
+      };
+    });
+    return invalidated ? DIRECTORY_LISTING_INVALIDATED : null;
+  }
+}
+
+/** Refresh invalidates earlier replies as well as listings of collapsed folders. */
+export function invalidateExplorerDirectoryListings(
+  updateState: UpdateExplorerState,
+  retainedPaths: readonly string[],
+): void {
+  const retained = new Set(retainedPaths);
+  updateState((state) => ({
+    ...state,
+    listingGeneration: state.listingGeneration + 1,
+    directories: new Map([...state.directories].filter(([path]) => retained.has(path))),
+    isLoading: false,
+    pendingRequest: null,
+    lastError: null,
+  }));
+}
diff --git a/packages/app/src/file-explorer/tree.test.ts b/packages/app/src/file-explorer/tree.test.ts
index e3df026c0d..82d4bcc61a 100644
--- a/packages/app/src/file-explorer/tree.test.ts
+++ b/packages/app/src/file-explorer/tree.test.ts
@@ -1,9 +1,10 @@
 import { describe, expect, it } from "vitest";
-import type { ExplorerEntry } from "@/stores/session-store";
+import type { ExplorerDirectory, ExplorerEntry } from "@/stores/session-store";
 import {
   MAX_AUTO_EXPANDED_DIRECTORY_DEPTH,
   flattenExplorerTree,
   reconcileRestoredExpandedPaths,
+  refreshExplorerDirectories,
   restoreExpandedDirectories,
   setExpandedDirectoryPath,
   showHiddenFilesAndRestoreExpandedDirectories,
@@ -195,3 +196,76 @@ describe("file explorer tree", () => {
     await expect(restoration).resolves.toEqual([".", ".hidden"]);
   });
 });
+
+describe("refreshExplorerDirectories", () => {
+  function makeListing(path: string, names: string[]): ExplorerDirectory {
+    return {
+      path,
+      entries: names.map((name) => ({
+        name,
+        path: path === "." ? name : `${path}/${name}`,
+        kind: "file" as const,
+        size: 0,
+        modifiedAt: "2026-01-01T00:00:00.000Z",
+      })),
+    };
+  }
+
+  function createExplorer(disk: Record<string, string[]>, cached: Record<string, string[]>) {
+    const directories = new Map(
+      Object.entries(cached).map(([path, names]) => [path, makeListing(path, names)]),
+    );
+    return {
+      directories,
+      requestDirectoryListing: async (path: string) => {
+        const listing = makeListing(path, disk[path] ?? []);
+        directories.set(path, listing);
+        return listing;
+      },
+      invalidateDirectoryListings: (retainedPaths: readonly string[]) => {
+        const retained = new Set(retainedPaths);
+        for (const path of directories.keys()) if (!retained.has(path)) directories.delete(path);
+      },
+    };
+  }
+
+  it("does not keep a stale listing for a collapsed folder", async () => {
+    // docs/ was expanded and collapsed earlier, then NEW.md was created in it.
+    const explorer = createExplorer(
+      { ".": ["docs"], docs: ["README.md", "NEW.md"] },
+      { ".": ["docs"], docs: ["README.md"] },
+    );
+
+    await refreshExplorerDirectories({
+      hasWorkspaceScope: true,
+      expandedPaths: new Set(["."]),
+      showHiddenFiles: false,
+      requestDirectoryListing: explorer.requestDirectoryListing,
+      invalidateDirectoryListings: explorer.invalidateDirectoryListings,
+    });
+
+    // Expanding docs/ only fetches when it has no cached listing.
+    expect(explorer.directories.has("docs")).toBe(false);
+    expect(explorer.directories.get(".")?.entries.map((entry) => entry.name)).toEqual(["docs"]);
+  });
+
+  it("refreshes expanded folders and keeps their listings", async () => {
+    const explorer = createExplorer(
+      { ".": ["src"], src: ["a.ts", "b.ts"] },
+      { ".": ["src"], src: ["a.ts"] },
+    );
+
+    await refreshExplorerDirectories({
+      hasWorkspaceScope: true,
+      expandedPaths: new Set([".", "src"]),
+      showHiddenFiles: false,
+      requestDirectoryListing: explorer.requestDirectoryListing,
+      invalidateDirectoryListings: explorer.invalidateDirectoryListings,
+    });
+
+    expect(explorer.directories.get("src")?.entries.map((entry) => entry.name)).toEqual([
+      "a.ts",
+      "b.ts",
+    ]);
+  });
+});
diff --git a/packages/app/src/file-explorer/tree.ts b/packages/app/src/file-explorer/tree.ts
index 8b75ae7b25..4402cd82bc 100644
--- a/packages/app/src/file-explorer/tree.ts
+++ b/packages/app/src/file-explorer/tree.ts
@@ -1,5 +1,6 @@
 import type { ExplorerDirectory, ExplorerEntry } from "@/stores/session-store";
 import type { SortOption } from "@/stores/panel-store/state";
+import { DIRECTORY_LISTING_INVALIDATED, type DirectoryListingResult } from "./directory-listings";
 import { filterVisibleExplorerEntries, isHiddenExplorerPath } from "./visibility";
 
 export const MAX_AUTO_EXPANDED_DIRECTORY_DEPTH = 5;
@@ -16,11 +17,13 @@ interface FlattenExplorerTreeInput {
   showHiddenFiles: boolean;
 }
 
+type RestoredExpandedPaths = string[] | typeof DIRECTORY_LISTING_INVALIDATED;
+
 interface RestoreExpandedDirectoriesInput {
   rootDirectory: ExplorerDirectory;
   persistedExpandedPaths: ReadonlySet<string>;
   showHiddenFiles: boolean;
-  requestDirectoryListing: (path: string) => Promise<ExplorerDirectory | null>;
+  requestDirectoryListing: (path: string) => Promise<DirectoryListingResult>;
 }
 
 interface ShowHiddenFilesAndRestoreExpandedDirectoriesInput extends Omit<
@@ -33,7 +36,7 @@ interface ShowHiddenFilesAndRestoreExpandedDirectoriesInput extends Omit<
 interface ReconcileRestoredExpandedPathsInput {
   persistedExpandedPaths: ReadonlySet<string>;
   currentExpandedPaths: ReadonlySet<string>;
-  restoredExpandedPaths: string[];
+  restoredExpandedPaths: RestoredExpandedPaths;
 }
 
 interface SetExpandedDirectoryPathInput {
@@ -85,7 +88,7 @@ export async function restoreExpandedDirectories({
   persistedExpandedPaths,
   showHiddenFiles,
   requestDirectoryListing,
-}: RestoreExpandedDirectoriesInput): Promise<string[]> {
+}: RestoreExpandedDirectoriesInput): Promise<RestoredExpandedPaths> {
   const restoredPaths = ["."];
   const restoredPathSet = new Set(restoredPaths);
   let parentDirectories = [rootDirectory];
@@ -110,9 +113,11 @@ export async function restoreExpandedDirectories({
     const requestedDirectories = await Promise.all(
       pathsToRequest.map((path) => requestDirectoryListing(path)),
     );
+    if (requestedDirectories.includes(DIRECTORY_LISTING_INVALIDATED))
+      return DIRECTORY_LISTING_INVALIDATED;
     parentDirectories = [];
     for (const directory of requestedDirectories) {
-      if (!directory) {
+      if (!directory || directory === DIRECTORY_LISTING_INVALIDATED) {
         continue;
       }
       restoredPaths.push(directory.path);
@@ -128,7 +133,7 @@ export function showHiddenFilesAndRestoreExpandedDirectories({
   persistedExpandedPaths,
   showHiddenFiles,
   requestDirectoryListing,
-}: ShowHiddenFilesAndRestoreExpandedDirectoriesInput): Promise<string[]> {
+}: ShowHiddenFilesAndRestoreExpandedDirectoriesInput): Promise<RestoredExpandedPaths> {
   showHiddenFiles();
   return restoreExpandedDirectories({
     rootDirectory,
@@ -143,6 +148,8 @@ export function reconcileRestoredExpandedPaths({
   currentExpandedPaths,
   restoredExpandedPaths,
 }: ReconcileRestoredExpandedPathsInput): string[] {
+  if (restoredExpandedPaths === DIRECTORY_LISTING_INVALIDATED)
+    return Array.from(currentExpandedPaths);
   const reconciledPaths = new Set(restoredExpandedPaths);
 
   for (const path of persistedExpandedPaths) {
@@ -205,7 +212,7 @@ function sortExplorerEntries(entries: ExplorerEntry[], sortOption: SortOption):
 /** Load and expand the path to a directory selected outside the tree. */
 export async function revealExplorerDirectory(input: {
   directoryPath: string;
-  requestDirectoryListing: (path: string) => Promise<ExplorerDirectory | null>;
+  requestDirectoryListing: (path: string) => Promise<DirectoryListingResult>;
   expandPaths: (paths: string[]) => void;
   showHiddenFiles: () => void;
 }): Promise<void> {
@@ -218,7 +225,51 @@ export async function revealExplorerDirectory(input: {
     }
   }
   for (const path of paths) {
-    if (!(await input.requestDirectoryListing(path))) return;
+    const directory = await input.requestDirectoryListing(path);
+    if (!directory || directory === DIRECTORY_LISTING_INVALIDATED) return;
   }
   input.expandPaths(paths);
 }
+
+/**
+ * Files Refresh: re-lists the expanded directories (and the root), and drops the cached
+ * listing of every other directory. Expanding a directory only fetches when it has no
+ * cached listing, so keeping a collapsed directory's old listing would show it as it was
+ * before the refresh.
+ */
+export async function refreshExplorerDirectories({
+  hasWorkspaceScope,
+  expandedPaths,
+  showHiddenFiles,
+  requestDirectoryListing,
+  invalidateDirectoryListings,
+}: {
+  hasWorkspaceScope: boolean;
+  expandedPaths: Set<string>;
+  showHiddenFiles: boolean;
+  requestDirectoryListing: (
+    path: string,
+    opts?: { recordHistory?: boolean; setCurrentPath?: boolean },
+  ) => Promise<DirectoryListingResult>;
+  invalidateDirectoryListings: (retainedPaths: readonly string[]) => void;
+}): Promise<null> {
+  if (!hasWorkspaceScope) {
+    return null;
+  }
+  const directoryPaths = Array.from(expandedPaths).filter(
+    (path) => showHiddenFiles || !isHiddenExplorerPath(path),
+  );
+  if (!directoryPaths.includes(".")) {
+    directoryPaths.unshift(".");
+  }
+  invalidateDirectoryListings(directoryPaths);
+  await Promise.all(
+    directoryPaths.map((path) =>
+      requestDirectoryListing(path, {
+        recordHistory: false,
+        setCurrentPath: false,
+      }),
+    ),
+  );
+  return null;
+}
diff --git a/packages/app/src/hooks/use-file-explorer-actions.ts b/packages/app/src/hooks/use-file-explorer-actions.ts
index d54131eb4a..82edab6a13 100644
--- a/packages/app/src/hooks/use-file-explorer-actions.ts
+++ b/packages/app/src/hooks/use-file-explorer-actions.ts
@@ -1,16 +1,18 @@
 import { useCallback, useMemo } from "react";
 import { useTranslation } from "react-i18next";
-import {
-  useSessionStore,
-  type AgentFileExplorerState,
-  type ExplorerDirectory,
-} from "@/stores/session-store";
+import { useSessionStore, type AgentFileExplorerState } from "@/stores/session-store";
 import { usePanelStore } from "@/stores/panel-store";
 import { revealExplorerDirectory } from "@/file-explorer/tree";
+import {
+  loadExplorerDirectory,
+  type DirectoryListingResult,
+  invalidateExplorerDirectoryListings,
+} from "@/file-explorer/directory-listings";
 import { parentExplorerPath } from "@/utils/explorer-paths";
 
 function createExplorerState(): AgentFileExplorerState {
   return {
+    listingGeneration: 0,
     directories: new Map(),
     isLoading: false,
     lastError: null,
@@ -22,15 +24,6 @@ function createExplorerState(): AgentFileExplorerState {
   };
 }
 
-function pushHistory(history: string[], path: string): string[] {
-  const normalizedHistory = history.length === 0 ? ["."] : history;
-  const last = normalizedHistory[normalizedHistory.length - 1];
-  if (last === path) {
-    return normalizedHistory;
-  }
-  return [...normalizedHistory, path];
-}
-
 export interface FileExplorerWorkspaceScope {
   workspaceId?: string | null;
   workspaceRoot?: string | null;
@@ -75,16 +68,21 @@ export function useFileExplorerActions(params: { serverId: string } & FileExplor
   );
 
   const updateExplorerState = useCallback(
-    (updater: (prev: AgentFileExplorerState) => AgentFileExplorerState) => {
+    (
+      updater: (prev: AgentFileExplorerState) => AgentFileExplorerState,
+    ): AgentFileExplorerState | null => {
       if (!workspaceStateKey) {
-        return;
+        return null;
       }
+      let updated: AgentFileExplorerState | null = null;
       setFileExplorer(serverId, (prev) => {
         const next = new Map(prev);
         const current = next.get(workspaceStateKey) ?? createExplorerState();
-        next.set(workspaceStateKey, updater(current));
+        updated = updater(current);
+        next.set(workspaceStateKey, updated);
         return next;
       });
+      return updated;
     },
     [serverId, setFileExplorer, workspaceStateKey],
   );
@@ -93,80 +91,23 @@ export function useFileExplorerActions(params: { serverId: string } & FileExplor
     async (
       path: string,
       options?: { recordHistory?: boolean; setCurrentPath?: boolean },
-    ): Promise<ExplorerDirectory | null> => {
+    ): Promise<DirectoryListingResult> => {
       if (!workspaceStateKey) {
         return null;
       }
       const normalizedPath = path && path.length > 0 ? path : ".";
-      const shouldSetCurrentPath = options?.setCurrentPath ?? true;
-      const shouldRecordHistory = options?.recordHistory ?? shouldSetCurrentPath;
-
-      updateExplorerState((state) => ({
-        ...state,
-        isLoading: true,
-        lastError: null,
-        pendingRequest: { path: normalizedPath, mode: "list" },
-        ...(shouldSetCurrentPath
-          ? {
-              currentPath: normalizedPath,
-              history: shouldRecordHistory
-                ? pushHistory(state.history, normalizedPath)
-                : state.history,
-              lastVisitedPath: normalizedPath,
-            }
-          : {}),
-      }));
-
-      if (!normalizedWorkspaceRoot) {
-        updateExplorerState((state) => ({
-          ...state,
-          isLoading: false,
-          lastError: t("workspace.fileExplorer.states.unavailable"),
-          pendingRequest: null,
-        }));
-        return null;
-      }
-
-      if (!client) {
-        updateExplorerState((state) => ({
-          ...state,
-          isLoading: false,
-          lastError: t("workspace.terminal.hostDisconnected"),
-          pendingRequest: null,
-        }));
-        return null;
-      }
-
-      try {
-        const directory = await client.listDirectory(normalizedWorkspaceRoot, normalizedPath);
-        updateExplorerState((state) => {
-          const nextState: AgentFileExplorerState = {
-            ...state,
-            isLoading: false,
-            lastError: null,
-            pendingRequest: null,
-            directories: state.directories,
-          };
-
-          const directories = new Map(state.directories);
-          directories.set(directory.path, directory);
-          nextState.directories = directories;
-
-          return nextState;
-        });
-        return directory;
-      } catch (error) {
-        updateExplorerState((state) => ({
-          ...state,
-          isLoading: false,
-          lastError:
-            error instanceof Error
-              ? error.message
-              : t("workspace.fileExplorer.errors.failedToListDirectory"),
-          pendingRequest: null,
-        }));
-        return null;
-      }
+      return loadExplorerDirectory({
+        path: normalizedPath,
+        options,
+        updateState: updateExplorerState,
+        fallbackError: t("workspace.fileExplorer.errors.failedToListDirectory"),
+        listDirectory: async () => {
+          if (!normalizedWorkspaceRoot)
+            throw new Error(t("workspace.fileExplorer.states.unavailable"));
+          if (!client) throw new Error(t("workspace.terminal.hostDisconnected"));
+          return client.listDirectory(normalizedWorkspaceRoot, normalizedPath);
+        },
+      });
     },
     [client, normalizedWorkspaceRoot, t, updateExplorerState, workspaceStateKey],
   );
@@ -308,10 +249,17 @@ export function useFileExplorerActions(params: { serverId: string } & FileExplor
     [updateExplorerState],
   );
 
+  const invalidateDirectoryListings = useCallback(
+    (retainedPaths: readonly string[]) =>
+      invalidateExplorerDirectoryListings(updateExplorerState, retainedPaths),
+    [updateExplorerState],
+  );
+
   return {
     workspaceStateKey,
     revealDirectory,
     requestDirectoryListing,
+    invalidateDirectoryListings,
     requestFileDownloadToken,
     requestFileBytes,
     createEntry,
diff --git a/packages/app/src/stores/session-store.ts b/packages/app/src/stores/session-store.ts
index 911573762f..001ad8eed6 100644
--- a/packages/app/src/stores/session-store.ts
+++ b/packages/app/src/stores/session-store.ts
@@ -260,6 +260,7 @@ interface ExplorerRequestState {
 }
 
 export interface AgentFileExplorerState {
+  listingGeneration: number;
   directories: Map<string, ExplorerDirectory>;
   isLoading: boolean;
   lastError: string | null;