diff --git a/packages/app/e2e/browser/changes-pane.spec.ts b/packages/app/e2e/browser/changes-pane.spec.ts
index 1ff6059460..3e6fecc934 100644
--- a/packages/app/e2e/browser/changes-pane.spec.ts
+++ b/packages/app/e2e/browser/changes-pane.spec.ts
@@ -16,6 +16,7 @@ interface DirtyWorkspace {
 }
 
 interface WorkspaceFixtureOptions {
+  workspaceSubdirectory?: string;
   includeDeletedFile?: boolean;
   includeNestedFolders?: boolean;
   includeRenamedFile?: boolean;
@@ -435,6 +436,76 @@ test("changes file actions open below the right-click without a reserved kebab",
   await expect(page.getByTestId("workspace-tab-file_src/use-mounted-tab-set.ts")).toBeVisible();
 });
 
+for (const { workspaceSubdirectory, filePath, content, visibleContent } of [
+  {
+    workspaceSubdirectory: ".",
+    filePath: "src/use-mounted-tab-set.ts",
+    content: AFTER,
+    visibleContent: "interface DeriveRenderMountedTabIdsInput",
+  },
+  {
+    workspaceSubdirectory: "src",
+    filePath: "src/use-mounted-tab-set.ts",
+    content: AFTER,
+    visibleContent: "interface DeriveRenderMountedTabIdsInput",
+  },
+  {
+    workspaceSubdirectory: "src",
+    filePath: "a-root-note.txt",
+    content: "root note\n",
+    visibleContent: "root note",
+  },
+]) {
+  test(`changes file actions resolve ${filePath} from project ${workspaceSubdirectory}`, async ({
+    page,
+    context,
+  }, testInfo) => {
+    const workspace = await createWorkspaceWithMountedTabDiff({
+      workspaceSubdirectory,
+      includeRootFileSortingFirst: filePath === "a-root-note.txt",
+    });
+    await context.grantPermissions(["clipboard-read", "clipboard-write"]);
+    await openWorkspaceChanges(page, workspace);
+    const panel = page.getByTestId("working-diff-panel").filter({ visible: true });
+    const header = diffHeaderForPath(panel, filePath).getByTestId(/^diff-file-\d+-toggle$/);
+    await header.click({ button: "right" });
+    await testInfo.attach("changes-file-menu", {
+      body: await page.screenshot(),
+      contentType: "image/png",
+    });
+    await test.step("Duplicate creates a copy next to the source", async () => {
+      const file = path.parse(filePath);
+      const copyPath = path.join(workspace.repoPath, file.dir, `${file.name} copy${file.ext}`);
+      await page.getByRole("menuitem", { name: "Duplicate", exact: true }).click();
+      await expect
+        .poll(() => readFileIfPresent(copyPath), { message: `Expected duplicate at ${copyPath}` })
+        .toBe(content);
+    });
+    await header.click({ button: "right" });
+    await page.getByRole("menuitem", { name: "Copy relative path", exact: true }).click();
+    await expectClipboardText(page, filePath);
+    await header.click({ button: "right" });
+    await page.getByRole("menuitem", { name: "Copy path", exact: true }).click();
+    await expectClipboardText(page, path.join(workspace.repoPath, filePath));
+
+    await header.click({ button: "right" });
+    const downloaded = page.waitForEvent("download");
+    await page.getByRole("menuitem", { name: "Download", exact: true }).click();
+    const download = await downloaded;
+    expect(download.suggestedFilename()).toBe(path.basename(filePath));
+    expect(await readFile((await download.path())!, "utf8")).toBe(content);
+
+    await header.click({ button: "right" });
+    await page.getByRole("menuitem", { name: "Open file", exact: true }).click();
+    const editor = page.getByTestId("workspace-file-pane").filter({ visible: true });
+    await expect(editor.locator(".cm-content")).toContainText(visibleContent);
+    await testInfo.attach("opened-changed-file", {
+      body: await page.screenshot(),
+      contentType: "image/png",
+    });
+  });
+}
+
 test("canvas file headers select without toggling for context menu and long press", async ({
   page,
 }) => {
@@ -1591,7 +1662,7 @@ async function createWorkspaceWithMountedTabDiff(
     );
   }
   const createdWorkspace = await client.createWorkspace({
-    source: { kind: "directory", path: repo.path },
+    source: { kind: "directory", path: path.join(repo.path, options.workspaceSubdirectory ?? ".") },
   });
   if (!createdWorkspace.workspace) {
     throw new Error(createdWorkspace.error ?? `Failed to create workspace ${repo.path}`);
diff --git a/packages/app/src/git/diff-pane.tsx b/packages/app/src/git/diff-pane.tsx
index 3dd84f256a..aef17bc47a 100644
--- a/packages/app/src/git/diff-pane.tsx
+++ b/packages/app/src/git/diff-pane.tsx
@@ -56,6 +56,7 @@ import * as Clipboard from "expo-clipboard";
 import { useFileDownload } from "@/hooks/use-file-download";
 import { useIsLocalDaemon } from "@/hooks/use-is-local-daemon";
 import { buildAbsoluteExplorerPath } from "@/utils/explorer-paths";
+import { isWorkspaceRootPath } from "@/workspace/file-open";
 import { Tooltip, TooltipTrigger, TooltipContent } from "@/components/ui/tooltip";
 import { GitActionsSplitButton } from "@/git/actions-split-button";
 import type { GitActions } from "@/git/policy";
@@ -1452,6 +1453,10 @@ function useDiffTabNavigation({
   };
 }
 
+function resolveChangesFileRoot(status: CheckoutStatusPayload | null, cwd: string): string {
+  return status?.repoRoot ?? cwd;
+}
+
 export function ChangesSurface({
   serverId,
   workspaceId,
@@ -1631,14 +1636,30 @@ export function ChangesSurface({
     }),
     [appSettings.monoFontFamily, codeFontSize, effectiveLayout, wrapLines],
   );
-  const downloadFile = useFileDownload({ serverId, workspaceId, workspaceRoot: cwd });
+  const fileRoot = resolveChangesFileRoot(status, cwd);
+  const isRootWorkspace = isWorkspaceRootPath({ path: fileRoot, workspaceRoot: cwd });
+  const resolveFilePath = useCallback(
+    (path: string) => buildAbsoluteExplorerPath({ workspaceRoot: fileRoot, entryPath: path }),
+    [fileRoot],
+  );
+  const resolveFileTargetPath = useCallback(
+    (path: string) => (isRootWorkspace ? path : resolveFilePath(path)),
+    [isRootWorkspace, resolveFilePath],
+  );
+  const handleOpenFile = useCallback(
+    (path: string) => onOpenFile?.(resolveFileTargetPath(path)),
+    [onOpenFile, resolveFileTargetPath],
+  );
+  const handleAddToChat = useCallback(
+    (path: string) => onAddToChat?.(resolveFileTargetPath(path)),
+    [onAddToChat, resolveFileTargetPath],
+  );
+  const downloadFile = useFileDownload({ serverId, workspaceId, workspaceRoot: fileRoot });
   const handleCopyPath = useCallback(
     (path: string) => {
-      void Clipboard.setStringAsync(
-        buildAbsoluteExplorerPath({ workspaceRoot: cwd, entryPath: path }),
-      );
+      void Clipboard.setStringAsync(resolveFilePath(path));
     },
-    [cwd],
+    [resolveFilePath],
   );
   const handleCopyRelativePath = useCallback((path: string) => {
     void Clipboard.setStringAsync(path);
@@ -1652,7 +1673,7 @@ export function ChangesSurface({
         await openDesktopTarget({
           editorId: fileManagerTarget.id,
           workspacePath: cwd,
-          filePath: buildAbsoluteExplorerPath({ workspaceRoot: cwd, entryPath: path }),
+          filePath: resolveFilePath(path),
         });
       } catch (cause) {
         toast.error(
@@ -1660,7 +1681,7 @@ export function ChangesSurface({
         );
       }
     },
-    [cwd, fileManagerTarget, t, toast],
+    [cwd, fileManagerTarget, resolveFilePath, t, toast],
   );
   const handleDownloadPath = useCallback(
     (path: string) => {
@@ -1674,7 +1695,7 @@ export function ChangesSurface({
         return;
       }
       try {
-        const payload = await client.duplicateFileEntry({ cwd, path });
+        const payload = await client.duplicateFileEntry({ cwd: fileRoot, path });
         if (!payload.success) {
           toast.error(payload.error ?? t("workspace.fileExplorer.errors.duplicateFailed"));
         }
@@ -1682,7 +1703,7 @@ export function ChangesSurface({
         toast.error(cause instanceof Error ? cause.message : String(cause));
       }
     },
-    [client, cwd, t, toast],
+    [client, fileRoot, t, toast],
   );
   const onRevertPath = useDiscardChangesAction({ serverId, cwd, diffMode });
   const [localFocusRequest, setLocalFocusRequest] = useState<{
@@ -1718,9 +1739,9 @@ export function ChangesSurface({
       focusPath: documentFocusRequest?.path,
       focusRequestId: documentFocusRequest?.revision,
       workspaceFileDragScope: workspaceId ? { serverId, workspaceId } : undefined,
-      onOpenFile,
+      onOpenFile: onOpenFile ? handleOpenFile : undefined,
       onOpenToSide,
-      onAddToChat,
+      onAddToChat: onAddToChat ? handleAddToChat : undefined,
       onCopyPath: handleCopyPath,
       onCopyRelativePath: handleCopyRelativePath,
       onReveal: fileManagerTarget ? handleRevealPath : undefined,
@@ -1736,8 +1757,10 @@ export function ChangesSurface({
       serverId,
       workspaceId,
       onOpenFile,
+      handleOpenFile,
       onOpenToSide,
       onAddToChat,
+      handleAddToChat,
       handleCopyPath,
       handleCopyRelativePath,
       handleDownloadPath,