fix(search): include workspace root with submodules (#2524)

apps/backend/internal/agentctl/server/process/workspace_content_search.go

@@ -84,7 +84,7 @@ func (m *Manager) contentSearchTrackers() []*WorkspaceTracker {
 		}
 		return trackers
 	}
-	if root != nil && root.RepositoryName() != "" {
+	if root != nil && root.gitIndexPath != "" {
 		trackers = append(trackers, root)
 	}
 	trackers = append(trackers, repositories...)

apps/backend/internal/agentctl/server/process/workspace_files.go

@@ -81,8 +81,9 @@ func (wt *WorkspaceTracker) getFileListClass(ctx context.Context, class subproc.
 	// --cached: include tracked files
 	// --others: include untracked files
 	// --exclude-standard: respect .gitignore
+	// --stage: expose tracked file modes so submodule Gitlinks can be excluded
 	out, runErr, execCtxErr := subproc.RunGitOutputAfterAcquire(ctx, class, gitCommandTimeout, func(execCtx context.Context) *exec.Cmd {
-		cmd := subproc.NewGitCommand(execCtx, "ls-files", "--cached", "--others", "--exclude-standard")
+		cmd := subproc.NewGitCommand(execCtx, "ls-files", "--cached", "--others", "--exclude-standard", "--stage")
 		cmd.Dir = wt.workDir
 		return cmd
 	})
@@ -94,6 +95,12 @@ func (wt *WorkspaceTracker) getFileListClass(ctx context.Context, class subproc.
 	lines := strings.Split(string(out), "\n")
 	for _, line := range lines {
 		line = strings.TrimSpace(line)
+		if metadata, path, tracked := strings.Cut(line, "\t"); tracked {
+			if strings.HasPrefix(metadata, "160000 ") {
+				continue
+			}
+			line = strings.TrimSpace(path)
+		}
 		if line == "" || isRootOwnershipMarkerPath(line) {
 			continue
 		}
@@ -1010,7 +1017,7 @@ func (m *Manager) SearchWorkspaceFileResults(query string, limit int) []types.Fi
 	}
 
 	candidates := make([]fileSearchCandidate, 0)
-	if root != nil && root.RepositoryName() != "" {
+	if root != nil && root.gitIndexPath != "" {
 		candidates = appendTrackerFileSearchCandidates(candidates, root)
 	}
 	for _, tracker := range repositories {

apps/backend/internal/agentctl/server/process/workspace_search_submodule_test.go

@@ -0,0 +1,98 @@
+package process
+
+import (
+	"context"
+	"reflect"
+	"testing"
+
+	"github.com/kandev/kandev/internal/agentctl/server/config"
+)
+
+func TestManagerSearchWorkspaceFileResultsIncludesRootAndSubmodule(t *testing.T) {
+	mgr := setupWorkspaceSearchSubmoduleGraph(t)
+	updateWorkspaceSearchFileLists(mgr)
+
+	results := mgr.SearchWorkspaceFileResults("search-target", 20)
+	got := make([]string, 0, len(results))
+	for _, result := range results {
+		got = append(got, result.RepositoryName+"|"+result.Path)
+	}
+	want := []string{
+		"|root-search-target.txt",
+		"vendor/lib|vendor/lib/child-search-target.txt",
+	}
+	if !reflect.DeepEqual(got, want) {
+		t.Fatalf("search results = %v, want %v", got, want)
+	}
+}
+
+func TestManagerSearchWorkspaceFileResultsExcludesSubmoduleGitlink(t *testing.T) {
+	mgr := setupWorkspaceSearchSubmoduleGraph(t)
+	updateWorkspaceSearchFileLists(mgr)
+
+	for _, result := range mgr.SearchWorkspaceFileResults("lib", 20) {
+		if result.RepositoryName == "" && result.Path == "vendor/lib" {
+			t.Fatalf("root search returned submodule Gitlink as a file: %+v", result)
+		}
+	}
+
+	childFound := false
+	for _, result := range mgr.SearchWorkspaceFileResults("child-search-target", 20) {
+		if result.RepositoryName == "vendor/lib" && result.Path == "vendor/lib/child-search-target.txt" {
+			childFound = true
+			break
+		}
+	}
+	if !childFound {
+		t.Fatal("real file inside child scope was not searchable")
+	}
+}
+
+func TestManagerSearchWorkspaceContentIncludesRootAndSubmodule(t *testing.T) {
+	mgr := setupWorkspaceSearchSubmoduleGraph(t)
+
+	response, err := mgr.SearchWorkspaceContent(context.Background(), "shared-content-needle", 20)
+	if err != nil {
+		t.Fatalf("SearchWorkspaceContent: %v", err)
+	}
+	got := make([]string, 0, len(response.Results))
+	for _, result := range response.Results {
+		got = append(got, result.RepositoryName+"|"+result.Path)
+	}
+	want := []string{
+		"|root-search-target.txt",
+		"vendor/lib|child-search-target.txt",
+	}
+	if !reflect.DeepEqual(got, want) {
+		t.Fatalf("content search results = %v, want %v", got, want)
+	}
+}
+
+func setupWorkspaceSearchSubmoduleGraph(t *testing.T) *Manager {
+	t.Helper()
+	parent, parentCleanup := setupTestRepo(t)
+	t.Cleanup(parentCleanup)
+	child, childCleanup := setupTestRepo(t)
+	t.Cleanup(childCleanup)
+
+	writeFile(t, parent, "root-search-target.txt", "shared-content-needle\n")
+	writeFile(t, child, "child-search-target.txt", "shared-content-needle\n")
+	runGit(t, child, "add", ".")
+	runGit(t, child, "commit", "-m", "add search fixture")
+	runGit(t, parent, "-c", "protocol.file.allow=always", "submodule", "add", child, "vendor/lib")
+	runGit(t, parent, "add", ".")
+	runGit(t, parent, "commit", "-m", "add submodule search fixture")
+	runGit(t, parent, "push", "origin", "main")
+
+	mgr := NewManager(&config.InstanceConfig{WorkDir: parent}, newTestLogger(t))
+	t.Cleanup(mgr.stopWorkspaceTrackers)
+	return mgr
+}
+
+func updateWorkspaceSearchFileLists(mgr *Manager) {
+	root, repositories := mgr.snapshotTrackers()
+	root.updateFiles(context.Background())
+	for _, tracker := range repositories {
+		tracker.updateFiles(context.Background())
+	}
+}

apps/backend/internal/github/service_pr_unwatched_test.go

@@ -169,9 +169,19 @@ func TestRefreshStaleWorkspaceWatches_HealsUnwatchedRow(t *testing.T) {
 	// hands it to the background goroutine; the join it uses needs the real
 	// tasks schema, so drive the goroutine directly.
 	svc.refreshStaleWorkspaceWatches(testWorkspaceID, map[string]struct{}{"task-1": {}})
-	awaitTaskPRUpdated(t, updated)
-	// Drain the goroutine before the in-memory DB closes. Stop() cancels
-	// stopCtx, so it has to come after the write we just observed.
+	unwatchedUpdate := awaitTaskPRUpdated(t, updated)
+	if unwatchedUpdate.PRNumber != 1293 {
+		t.Fatalf("first background update PR = %d, want unwatched PR 1293", unwatchedUpdate.PRNumber)
+	}
+	// The same goroutine updates the watched PR after the unwatched row. Wait
+	// for that write too: canceling it via Stop can make sqlite discard the
+	// sole :memory: connection and leave the final assertion without a schema.
+	watchedUpdate := awaitTaskPRUpdated(t, updated)
+	if watchedUpdate.PRNumber != 1299 {
+		t.Fatalf("second background update PR = %d, want watched PR 1299", watchedUpdate.PRNumber)
+	}
+	// Drain the goroutine before the in-memory DB closes. Both observable writes
+	// have completed, so Stop has no database operation left to cancel.
 	svc.Stop()
 
 	got, err := store.GetTaskPRByRepoAndNumber(ctx, "task-1", "repo-1", 1293)

apps/web/e2e/tests/command-panel.spec.ts

@@ -2,6 +2,7 @@ import { test, expect } from "../fixtures/test-base";
 import { KanbanPage } from "../pages/kanban-page";
 import { SessionPage } from "../pages/session-page";
 import { waitForSessionDone } from "../helpers/session";
+import { createSubmoduleReviewFixture } from "./review/submodule-review-helpers";
 
 type CommandAliasExpectation = {
   query: string;
@@ -231,6 +232,50 @@ test.describe("Command Panel", () => {
     await expect(dialog.getByText("Type to search files...")).toBeVisible();
   });
 
+  test("Cmd+Shift+K finds root and submodule files", async ({
+    testPage,
+    apiClient,
+    seedData,
+    backend,
+  }) => {
+    test.setTimeout(180_000);
+    const fixture = await createSubmoduleReviewFixture(
+      apiClient,
+      seedData,
+      backend.tmpDir,
+      "Submodule file search E2E",
+    );
+
+    try {
+      await testPage.goto(`/t/${fixture.taskId}`);
+      const session = new SessionPage(testPage);
+      await session.waitForLoad();
+      await session.waitForChatIdle({ timeout: 45_000 });
+      await fixture.waitForWorktree(apiClient);
+
+      await openFileSearch(testPage);
+      const dialog = commandDialog(testPage);
+      await expect(dialog).toBeVisible({ timeout: 5_000 });
+      await dialog.getByRole("combobox").fill("README.md");
+
+      const groups = dialog.getByTestId("file-search-repo-group");
+      await expect(groups).toHaveCount(3, { timeout: 45_000 });
+      await expect(
+        dialog.locator('[data-testid="file-search-repo-group"][data-repository=""]'),
+      ).toBeVisible();
+      await expect(
+        dialog.locator('[data-testid="file-search-repo-group"][data-repository="vendor/outer"]'),
+      ).toBeVisible();
+      await expect(
+        dialog.locator(
+          '[data-testid="file-search-repo-group"][data-repository="vendor/outer/vendor/inner"]',
+        ),
+      ).toBeVisible();
+    } finally {
+      fixture.cleanup();
+    }
+  });
+
   test("Cmd+K inline task search shows matching tasks", async ({
     testPage,
     apiClient,

apps/web/e2e/tests/layout/workspace-picker-shortcut.spec.ts

@@ -1,5 +1,7 @@
 import { test, expect } from "../../fixtures/test-base";
 import type { Page } from "@playwright/test";
+import type { ApiClient } from "../../helpers/api-client";
+import type { Workspace } from "../../../lib/types/http";
 
 // WORKSPACE_PICKER (Cmd/Ctrl+E by default) opens the sidebar-header
 // workspace switcher with focus already inside the menu, so a workspace can be
@@ -24,108 +26,121 @@ async function listedWorkspaceIds(page: Page): Promise<string[]> {
   return testIds.map((testId) => testId.replace("sidebar-workspace-item-", ""));
 }
 
+async function withDisposableWorkspace(
+  apiClient: ApiClient,
+  name: string,
+  run: (workspace: Workspace) => Promise<void>,
+): Promise<void> {
+  const workspace = await apiClient.createWorkspace(name);
+  try {
+    await run(workspace);
+  } finally {
+    await apiClient.deleteWorkspace(workspace.id, workspace.name);
+  }
+}
+
 test.describe("Workspace picker shortcut (global)", () => {
   test("opens the picker and switches workspace with arrows and Enter", async ({
     testPage,
     apiClient,
   }) => {
-    const second = await apiClient.createWorkspace("Picker Shortcut Workspace");
+    await withDisposableWorkspace(apiClient, "Picker Shortcut Workspace", async (second) => {
+      await testPage.goto("/");
+      await expect(testPage.getByTestId("sidebar-workspace-trigger")).toBeVisible({
+        timeout: 10_000,
+      });
 
-    await testPage.goto("/");
-    await expect(testPage.getByTestId("sidebar-workspace-trigger")).toBeVisible({
-      timeout: 10_000,
+      await pressWorkspacePickerShortcut(testPage);
+
+      await expect(testPage.getByTestId("sidebar-workspace-trigger")).toHaveAttribute(
+        "data-state",
+        "open",
+      );
+      const workspaceIds = await listedWorkspaceIds(testPage);
+      expect(workspaceIds).toContain(second.id);
+      expect(workspaceIds.length).toBeGreaterThanOrEqual(2);
+
+      // The shortcut opens a controlled menu. Wait for Radix's focus handoff
+      // before sending navigation keys, otherwise the first ArrowDown can land
+      // on the document body on a busy CI runner.
+      await expect(testPage.getByRole("menu")).toBeFocused();
+
+      // Focus lands on the menu itself, so the first ArrowDown moves to item 1
+      // and the second to item 2, with no mouse needed at any point.
+      await testPage.keyboard.press("ArrowDown");
+      await expect(testPage.getByTestId(`sidebar-workspace-item-${workspaceIds[0]}`)).toBeFocused();
+      await testPage.keyboard.press("ArrowDown");
+      await expect(testPage.getByTestId(`sidebar-workspace-item-${workspaceIds[1]}`)).toBeFocused();
+
+      await testPage.keyboard.press("Enter");
+
+      await expect(testPage).toHaveURL(
+        (url) => url.searchParams.get("workspaceId") === workspaceIds[1],
+        { timeout: 10_000 },
+      );
+      await expect(testPage.locator(WORKSPACE_ITEM_SELECTOR).first()).not.toBeVisible();
     });
-
-    await pressWorkspacePickerShortcut(testPage);
-
-    await expect(testPage.getByTestId("sidebar-workspace-trigger")).toHaveAttribute(
-      "data-state",
-      "open",
-    );
-    const workspaceIds = await listedWorkspaceIds(testPage);
-    expect(workspaceIds).toContain(second.id);
-    expect(workspaceIds.length).toBeGreaterThanOrEqual(2);
-
-    // The shortcut opens a controlled menu. Wait for Radix's focus handoff
-    // before sending navigation keys, otherwise the first ArrowDown can land
-    // on the document body on a busy CI runner.
-    await expect(testPage.getByRole("menu")).toBeFocused();
-
-    // Focus lands on the menu itself, so the first ArrowDown moves to item 1
-    // and the second to item 2 — no mouse needed at any point.
-    await testPage.keyboard.press("ArrowDown");
-    await expect(testPage.getByTestId(`sidebar-workspace-item-${workspaceIds[0]}`)).toBeFocused();
-    await testPage.keyboard.press("ArrowDown");
-    await expect(testPage.getByTestId(`sidebar-workspace-item-${workspaceIds[1]}`)).toBeFocused();
-
-    await testPage.keyboard.press("Enter");
-
-    await expect(testPage).toHaveURL(
-      (url) => url.searchParams.get("workspaceId") === workspaceIds[1],
-      { timeout: 10_000 },
-    );
-    await expect(testPage.locator(WORKSPACE_ITEM_SELECTOR).first()).not.toBeVisible();
   });
 
   test("expands a collapsed sidebar before opening the picker", async ({ testPage, apiClient }) => {
-    await apiClient.createWorkspace("Collapsed Picker Workspace");
+    await withDisposableWorkspace(apiClient, "Collapsed Picker Workspace", async () => {
+      await testPage.goto("/");
+      const sidebar = testPage.getByTestId("app-sidebar");
+      await expect(sidebar).toBeVisible({ timeout: 10_000 });
 
-    await testPage.goto("/");
-    const sidebar = testPage.getByTestId("app-sidebar");
-    await expect(sidebar).toBeVisible({ timeout: 10_000 });
+      await testPage.getByRole("button", { name: "Collapse sidebar" }).click();
+      await expect(sidebar).toHaveAttribute("data-collapsed", "true");
 
-    await testPage.getByRole("button", { name: "Collapse sidebar" }).click();
-    await expect(sidebar).toHaveAttribute("data-collapsed", "true");
+      await pressWorkspacePickerShortcut(testPage);
 
-    await pressWorkspacePickerShortcut(testPage);
-
-    await expect(sidebar).toHaveAttribute("data-collapsed", "false");
-    await expect(testPage.getByTestId("sidebar-workspace-trigger")).toHaveAttribute(
-      "data-state",
-      "open",
-    );
-    await expect(testPage.locator(WORKSPACE_ITEM_SELECTOR).first()).toBeVisible();
+      await expect(sidebar).toHaveAttribute("data-collapsed", "false");
+      await expect(testPage.getByTestId("sidebar-workspace-trigger")).toHaveAttribute(
+        "data-state",
+        "open",
+      );
+      await expect(testPage.locator(WORKSPACE_ITEM_SELECTOR).first()).toBeVisible();
+    });
   });
 
   test("Escape closes the picker and leaves the workspace unchanged", async ({
     testPage,
     apiClient,
   }) => {
-    await apiClient.createWorkspace("Escape Picker Workspace");
+    await withDisposableWorkspace(apiClient, "Escape Picker Workspace", async () => {
+      await testPage.goto("/");
+      await expect(testPage.getByTestId("sidebar-workspace-trigger")).toBeVisible({
+        timeout: 10_000,
+      });
+      const urlBefore = testPage.url();
 
-    await testPage.goto("/");
-    await expect(testPage.getByTestId("sidebar-workspace-trigger")).toBeVisible({
-      timeout: 10_000,
+      await pressWorkspacePickerShortcut(testPage);
+      await expect(testPage.locator(WORKSPACE_ITEM_SELECTOR).first()).toBeVisible();
+
+      await testPage.keyboard.press("Escape");
+
+      await expect(testPage.locator(WORKSPACE_ITEM_SELECTOR).first()).not.toBeVisible();
+      expect(testPage.url()).toBe(urlBefore);
+
+      // The store flag must have cleared on dismiss, or a second press would be
+      // a no-op (open -> open).
+      await pressWorkspacePickerShortcut(testPage);
+      await expect(testPage.locator(WORKSPACE_ITEM_SELECTOR).first()).toBeVisible();
     });
-    const urlBefore = testPage.url();
-
-    await pressWorkspacePickerShortcut(testPage);
-    await expect(testPage.locator(WORKSPACE_ITEM_SELECTOR).first()).toBeVisible();
-
-    await testPage.keyboard.press("Escape");
-
-    await expect(testPage.locator(WORKSPACE_ITEM_SELECTOR).first()).not.toBeVisible();
-    expect(testPage.url()).toBe(urlBefore);
-
-    // The store flag must have cleared on dismiss, or a second press would be
-    // a no-op (open -> open).
-    await pressWorkspacePickerShortcut(testPage);
-    await expect(testPage.locator(WORKSPACE_ITEM_SELECTOR).first()).toBeVisible();
   });
 
   test("does nothing below the sidebar's md boundary", async ({ testPage, apiClient }) => {
-    await apiClient.createWorkspace("Narrow Viewport Workspace");
+    await withDisposableWorkspace(apiClient, "Narrow Viewport Workspace", async () => {
+      // 700px sits in the 640-767px band: the sidebar (and picker trigger) is
+      // display:none, but the menu portals to document.body — without the
+      // viewport guard it opened detached at the corner with a scroll lock.
+      await testPage.setViewportSize({ width: 700, height: 800 });
+      await testPage.goto("/");
+      await testPage.waitForLoadState("networkidle");
 
-    // 700px sits in the 640-767px band: the sidebar (and picker trigger) is
-    // display:none, but the menu portals to document.body — without the
-    // viewport guard it opened detached at the corner with a scroll lock.
-    await testPage.setViewportSize({ width: 700, height: 800 });
-    await testPage.goto("/");
-    await testPage.waitForLoadState("networkidle");
+      await pressWorkspacePickerShortcut(testPage);
 
-    await pressWorkspacePickerShortcut(testPage);
-
-    await expect(testPage.locator(WORKSPACE_ITEM_SELECTOR).first()).not.toBeVisible();
-    await expect(testPage.locator("body")).not.toHaveAttribute("data-scroll-locked", /.+/);
+      await expect(testPage.locator(WORKSPACE_ITEM_SELECTOR).first()).not.toBeVisible();
+      await expect(testPage.locator("body")).not.toHaveAttribute("data-scroll-locked", /.+/);
+    });
   });
 });

apps/web/e2e/tests/office/workspace-deletion-fallback.spec.ts

@@ -39,12 +39,16 @@ test.describe("Office workspace deletion fallback navigation", () => {
     await confirmButton.click();
 
     await expect(testPage).toHaveURL(
-      (url) => url.pathname === "/" && url.searchParams.get("workspaceId") === seedData.workspaceId,
+      (url) => url.pathname === "/" && Boolean(url.searchParams.get("workspaceId")),
       { timeout: 10_000 },
     );
     await expect(testPage).not.toHaveURL(/\/office\/setup/);
 
+    const destinationWorkspaceId = new URL(testPage.url()).searchParams.get("workspaceId");
     const { workspaces } = await apiClient.listWorkspaces();
     expect(workspaces.some((item) => item.id === onboarded.workspaceId)).toBe(false);
+    const destinationWorkspace = workspaces.find((item) => item.id === destinationWorkspaceId);
+    expect(destinationWorkspace).toBeDefined();
+    expect(destinationWorkspace?.office_workflow_id).toBeFalsy();
   });
 });

apps/web/e2e/tests/review/submodule-review-helpers.ts

@@ -80,69 +80,73 @@ export async function createSubmoduleReviewFixture(
   const outerPath = path.join(sourceRoot, "outer");
   const innerPath = path.join(sourceRoot, "inner");
   const env = { ...makeGitEnv(tempRoot), GIT_ALLOW_PROTOCOL: "file" };
+  const cleanup = () => fs.rmSync(sourceRoot, { recursive: true, force: true });
 
-  initializeRepository(innerPath, env, "README.md", "inner base\n");
+  try {
+    initializeRepository(innerPath, env, "README.md", "inner base\n");
 
-  initializeRepository(outerPath, env, "README.md", "outer base\n");
-  runGit(outerPath, [...GIT_PROTOCOL_ARGS, "submodule", "add", "../inner", "vendor/inner"], env);
-  commit(outerPath, env, "add nested inner submodule");
+    initializeRepository(outerPath, env, "README.md", "outer base\n");
+    runGit(outerPath, [...GIT_PROTOCOL_ARGS, "submodule", "add", "../inner", "vendor/inner"], env);
+    commit(outerPath, env, "add nested inner submodule");
 
-  initializeRepository(parentPath, env, "README.md", "parent base\n");
-  runGit(parentPath, [...GIT_PROTOCOL_ARGS, "submodule", "add", "../outer", "vendor/outer"], env);
-  runGit(parentPath, [...GIT_PROTOCOL_ARGS, "submodule", "update", "--init", "--recursive"], env);
-  runGit(
-    path.join(parentPath, "vendor/outer"),
-    [...GIT_PROTOCOL_ARGS, "submodule", "update", "--init", "--recursive"],
-    env,
-  );
-  commit(parentPath, env, "add outer submodule");
+    initializeRepository(parentPath, env, "README.md", "parent base\n");
+    runGit(parentPath, [...GIT_PROTOCOL_ARGS, "submodule", "add", "../outer", "vendor/outer"], env);
+    runGit(parentPath, [...GIT_PROTOCOL_ARGS, "submodule", "update", "--init", "--recursive"], env);
+    runGit(
+      path.join(parentPath, "vendor/outer"),
+      [...GIT_PROTOCOL_ARGS, "submodule", "update", "--init", "--recursive"],
+      env,
+    );
+    commit(parentPath, env, "add outer submodule");
 
-  const repository = await apiClient.createRepository(seedData.workspaceId, parentPath, "main", {
-    name: "nested-submodule-parent",
-  });
-  const { executors } = await apiClient.listExecutors();
-  const directProfile = executors.find(
-    (executor) => executor.type === "local" || executor.type === "local_pc",
-  )?.profiles?.[0];
-  if (!directProfile) throw new Error("Nested submodule fixture needs a direct local executor");
-  const task = await apiClient.createTaskWithAgent(
-    seedData.workspaceId,
-    title,
-    seedData.agentProfileId,
-    {
-      description: "/e2e:simple-message",
-      workflow_id: seedData.workflowId,
-      workflow_step_id: seedData.startStepId,
-      repository_ids: [repository.id],
-      executor_profile_id: directProfile.id,
-    },
-  );
-  if (!task.session_id) throw new Error("Nested submodule fixture did not start a session");
+    const repository = await apiClient.createRepository(seedData.workspaceId, parentPath, "main", {
+      name: "nested-submodule-parent",
+    });
+    const { executors } = await apiClient.listExecutors();
+    const directProfile = executors.find(
+      (executor) => executor.type === "local" || executor.type === "local_pc",
+    )?.profiles?.[0];
+    if (!directProfile) throw new Error("Nested submodule fixture needs a direct local executor");
+    const task = await apiClient.createTaskWithAgent(
+      seedData.workspaceId,
+      title,
+      seedData.agentProfileId,
+      {
+        description: "/e2e:simple-message",
+        workflow_id: seedData.workflowId,
+        workflow_step_id: seedData.startStepId,
+        repository_ids: [repository.id],
+        executor_profile_id: directProfile.id,
+      },
+    );
+    if (!task.session_id) throw new Error("Nested submodule fixture did not start a session");
 
-  return {
-    taskId: task.id,
-    sessionId: task.session_id,
-    sourceRoot,
-    waitForWorktree: (client) => waitForWorktreePath(client, task.id, task.session_id!),
-    applyNestedChanges(worktreePath: string) {
-      const outerWorktree = path.join(worktreePath, "vendor/outer");
-      const innerWorktree = path.join(outerWorktree, "vendor/inner");
-      if (!fs.existsSync(innerWorktree)) {
-        runGit(
-          worktreePath,
-          [...GIT_PROTOCOL_ARGS, "submodule", "update", "--init", "--recursive"],
-          env,
-        );
-      }
-      fs.appendFileSync(path.join(worktreePath, "README.md"), "parent working-tree change\n");
-      fs.appendFileSync(path.join(outerWorktree, "README.md"), "outer committed change\n");
-      commit(outerWorktree, env, "change outer submodule");
-      fs.appendFileSync(path.join(innerWorktree, "README.md"), "inner committed change\n");
-      commit(innerWorktree, env, "change inner submodule");
-      commit(outerWorktree, env, "record inner submodule change");
-    },
-    cleanup() {
-      fs.rmSync(sourceRoot, { recursive: true, force: true });
-    },
-  };
+    return {
+      taskId: task.id,
+      sessionId: task.session_id,
+      sourceRoot,
+      waitForWorktree: (client) => waitForWorktreePath(client, task.id, task.session_id!),
+      applyNestedChanges(worktreePath: string) {
+        const outerWorktree = path.join(worktreePath, "vendor/outer");
+        const innerWorktree = path.join(outerWorktree, "vendor/inner");
+        if (!fs.existsSync(innerWorktree)) {
+          runGit(
+            worktreePath,
+            [...GIT_PROTOCOL_ARGS, "submodule", "update", "--init", "--recursive"],
+            env,
+          );
+        }
+        fs.appendFileSync(path.join(worktreePath, "README.md"), "parent working-tree change\n");
+        fs.appendFileSync(path.join(outerWorktree, "README.md"), "outer committed change\n");
+        commit(outerWorktree, env, "change outer submodule");
+        fs.appendFileSync(path.join(innerWorktree, "README.md"), "inner committed change\n");
+        commit(innerWorktree, env, "change inner submodule");
+        commit(outerWorktree, env, "record inner submodule change");
+      },
+      cleanup,
+    };
+  } catch (error) {
+    cleanup();
+    throw error;
+  }
 }

apps/web/e2e/tests/review/submodule-review.spec.ts

@@ -1,8 +1,29 @@
+import crypto from "node:crypto";
+import fs from "node:fs";
+import path from "node:path";
 import { test, expect } from "../../fixtures/test-base";
 import { SessionPage } from "../../pages/session-page";
-import path from "node:path";
 import { createSubmoduleReviewFixture, readGitValue } from "./submodule-review-helpers";
 
+test.describe("Submodule review fixture", () => {
+  test("cleans source repositories when setup fails", async ({ apiClient, seedData, backend }) => {
+    const tempRoot = fs.mkdtempSync(path.join(backend.tmpDir, "submodule-review-failure-"));
+    try {
+      await expect(
+        createSubmoduleReviewFixture(
+          apiClient,
+          { ...seedData, workspaceId: crypto.randomUUID() },
+          tempRoot,
+          "Failing submodule fixture E2E",
+        ),
+      ).rejects.toThrow();
+      expect(fs.readdirSync(tempRoot)).toEqual([]);
+    } finally {
+      fs.rmSync(tempRoot, { recursive: true, force: true });
+    }
+  });
+});
+
 test.describe("Nested submodule Review", () => {
   test.describe.configure({ retries: 1, timeout: 180_000 });
 

docs/plans/submodule-workspace-search/plan.md

@@ -0,0 +1,125 @@
+---
+spec: docs/specs/ui/task-workspace-content-search.md
+created: 2026-08-11
+status: implemented
+---
+
+# Implementation Plan: Preserve Root Search With Submodules
+
+## Overview
+
+Fix workspace search tracker selection so a real Git root remains eligible when
+initialized submodules add named trackers. Prove the behavior first at the
+agentctl manager boundary, preserve bare multi-repository task-root behavior,
+then exercise Cmd/Ctrl+Shift+K through the existing command palette.
+
+## Confirmed Root Cause
+
+`SearchWorkspaceFileResults` and `contentSearchTrackers` include the root in a
+mixed tracker graph only when `RepositoryName()` is non-empty. A real workspace
+Git root intentionally uses the empty repository identity, so adding the first
+submodule changes both searches from root-only to child-only. The correct
+distinction is whether the root owns Git metadata, which `RepositoryScopes`
+already represents with `gitIndexPath != ""`.
+
+Retaining the root exposed a second file-enumeration defect: the root's
+`git ls-files --cached --others --exclude-standard` output includes mode-160000
+submodule Gitlinks, but every output line was classified as a file. Searching
+the submodule directory name could therefore return a directory as a root file.
+
+---
+
+## Backend
+
+### Search tracker selection
+
+- Update `apps/backend/internal/agentctl/server/process/workspace_files.go` and
+  `workspace_content_search.go` to include the unnamed root when it owns a real
+  Git repository, even when named submodule trackers coexist.
+- Keep the current single-repository fallback and named sibling-repository
+  aggregation unchanged. Do not search a bare task root or change response
+  paths, repository identities, ordering, limits, or fuzzy scoring.
+- Use the same real-Git-root predicate as `Manager.RepositoryScopes`; do not
+  infer repository ownership from the display/transport name.
+- Preserve tracked Git modes while enumerating files and exclude mode-160000
+  Gitlinks. Continue including untracked, non-ignored files.
+
+## Frontend
+
+No production frontend change is planned. The command palette already renders
+the structured `results` returned by `workspace.files.search` without filtering
+the unnamed root, and content search already groups the same empty root identity.
+
+## Tests
+
+- **What:** File-name search returns matches from a Git root and initialized
+  submodule in one response.
+  **File:** `apps/backend/internal/agentctl/server/process/workspace_search_submodule_test.go`.
+  **How:** Construct real parent/child Git repositories, add the child as an
+  initialized submodule, refresh tracker file lists, and assert both structured
+  repository identities and task-root-relative paths.
+- **What:** Content search returns matches from the same mixed root/submodule
+  graph.
+  **File:** `apps/backend/internal/agentctl/server/process/workspace_search_submodule_test.go`.
+  **How:** Search matching tracked content through `Manager.SearchWorkspaceContent`
+  and assert one result from each scope.
+- **What:** Bare task roots containing named sibling repositories remain
+  excluded.
+  **Files:** Existing `workspace_file_search_test.go` and
+  `workspace_content_search_test.go` coverage.
+  **How:** Rerun the existing multi-repository tests beside the new regressions.
+- **What:** Searching the exact submodule directory name does not return the
+  parent Gitlink as a file, while the child tracker's real files remain eligible.
+  **File:** `apps/backend/internal/agentctl/server/process/workspace_search_submodule_test.go`.
+  **How:** Search the real initialized fixture for `lib`, reject the root
+  `vendor/lib` pseudo-file, and retain the existing child-file assertion.
+
+## E2E Tests
+
+- **Scenario:** Given a task whose Git root and initialized submodules each
+  contain `README.md`, when the user opens Files with Cmd/Ctrl+Shift+K and
+  searches for that name, root and child repository groups all appear.
+- **File:** `apps/web/e2e/tests/command-panel.spec.ts`.
+- **What to verify:** Reuse `createSubmoduleReviewFixture`, wait for the task
+  session/worktree, search through the command palette, and assert the empty
+  root plus direct and nested submodule group identities. Always remove the
+  disposable source tree in `finally`.
+- No mobile-specific E2E is added. This fix changes shared backend result data,
+  not layout, touch behavior, navigation, scrolling, or viewport composition;
+  the existing mobile file-search interaction consumes the same API contract.
+
+## Verification Results
+
+Task 01 passed its focused gate: 3 process tests and 1 API test. Both new
+regressions failed for the expected child-only result before their production
+changes, then passed; the final full run of both touched backend packages also
+passed. Task 02 passed 1 Chromium test after its RED run showed the original
+bug's 2 groups instead of the expected root plus 2 submodules. Review
+remediation added and passed setup-failure cleanup coverage for the shared E2E
+fixture, then revalidated the command-palette happy path with retries disabled.
+PR CI remediation also removed workspace-picker fixture leakage and corrected
+two order-dependent E2E expectations. The two affected specs passed together
+with one worker, and exact Chromium/mobile shard 4/14 passed 137 tests with 7
+intentional skips and retries disabled.
+Independent review then found that retaining the root also exposed its
+mode-160000 Gitlink as a pseudo-file. A focused regression failed on
+`vendor/lib`, passed after mode-aware enumeration excluded Gitlinks, and the
+four-test behavior gate, both touched backend packages, and CI-style
+changed-file lint all passed.
+
+## Implementation Waves And Parallel Candidates
+
+Default execution is sequential in the primary conversation. No task is marked
+parallel-safe because the browser proof depends on the backend behavior.
+
+Wave 1:
+
+- [x] [Task 01: Correct mixed-graph search](task-01-correct-mixed-graph-search.md)
+
+Wave 2:
+
+- [x] [Task 02: Prove command-palette search](task-02-prove-command-palette-search.md)
+
+## Open Questions
+
+None.

docs/plans/submodule-workspace-search/task-01-correct-mixed-graph-search.md

@@ -0,0 +1,96 @@
+---
+id: "01-correct-mixed-graph-search"
+title: "Correct mixed-graph search"
+status: done
+wave: 1
+depends_on: []
+plan: "plan.md"
+spec: "../../specs/ui/task-workspace-content-search.md"
+---
+
+# Task 01: Correct Mixed-Graph Search
+
+## Acceptance
+
+- File-name and content search each return root and submodule matches from a
+  mixed unnamed-root/named-child tracker graph.
+- Bare task roots with named sibling repositories remain excluded, with no
+  duplicate results or search failure.
+- Parent repository Gitlinks are excluded from file results; real files owned
+  by initialized child trackers remain searchable.
+- Response identities, paths, ranking, limits, and existing single/multi-repo
+  behavior remain unchanged.
+
+## Verification
+
+```bash
+cd apps/backend && go test ./internal/agentctl/server/process ./internal/agentctl/server/api -run '^(TestManagerSearchWorkspaceFileResultsIncludesRootAndSubmodule|TestManagerSearchWorkspaceFileResultsExcludesSubmoduleGitlink|TestManagerSearchWorkspaceContentIncludesRootAndSubmodule|TestManagerSearchWorkspaceContentGroupsResultsByRepository|TestGetFileList_HidesOnlyRootOwnershipMarker|TestHandleFileSearchIncludesEveryTaskRepository)$' -count=1 -v
+```
+
+## Files likely touched
+
+- `apps/backend/internal/agentctl/server/process/workspace_files.go`
+- `apps/backend/internal/agentctl/server/process/workspace_content_search.go`
+- `apps/backend/internal/agentctl/server/process/workspace_search_submodule_test.go` (new)
+
+## Dependencies
+
+None.
+
+## Parallelism
+
+`sequential` — both search paths share the same tracker-graph invariant and
+regression fixture.
+
+## Inputs
+
+- Spec bullets and scenarios for mixed root/submodule and bare multi-repo search.
+- `Manager.RepositoryScopes` as the existing real-Git-root predicate.
+- `manager_submodule_test.go` and `workspace_tracker_test.go` Git fixture helpers.
+- Confirmed failing repro: searching a parent file plus submodule file returned
+  only the submodule path.
+
+## Output contract
+
+Report RED and GREEN commands/results, root-selection change, exact files
+changed, bare-root preservation, cleanup, blockers/risks, and synchronized
+task/plan status.
+
+## Results
+
+Implemented mixed-graph root retention for file-name and content search by
+using the same real-Git-root predicate as `Manager.RepositoryScopes`. The new
+fixture builds real parent/child repositories and an initialized submodule;
+existing bare multi-repository tests preserve the exclusion boundary.
+
+RED:
+
+- `go test ./internal/agentctl/server/process -run '^TestManagerSearchWorkspaceFileResultsIncludesRootAndSubmodule$' -count=1 -v`
+  failed as expected: only `vendor/lib|vendor/lib/child-search-target.txt`
+  was returned.
+- `go test ./internal/agentctl/server/process -run '^TestManagerSearchWorkspaceContentIncludesRootAndSubmodule$' -count=1 -v`
+  failed as expected: only `vendor/lib|child-search-target.txt` was returned.
+
+GREEN:
+
+- Each focused regression passed after its corresponding one-line production
+  change.
+- Final task gate:
+  `go test ./internal/agentctl/server/process ./internal/agentctl/server/api -run '^(TestManagerSearchWorkspaceFileResultsIncludesRootAndSubmodule|TestManagerSearchWorkspaceContentIncludesRootAndSubmodule|TestManagerSearchWorkspaceContentGroupsResultsByRepository|TestHandleFileSearchIncludesEveryTaskRepository)$' -count=1 -v`
+  passed 3 process tests and 1 API test.
+- Final package audit:
+  `go test ./internal/agentctl/server/process ./internal/agentctl/server/api -count=1`
+  passed both touched packages.
+- Independent-review remediation RED:
+  `go test ./internal/agentctl/server/process -run '^TestManagerSearchWorkspaceFileResultsExcludesSubmoduleGitlink$' -count=1 -v`
+  failed because root search returned `{Path:vendor/lib}` as a file.
+- Independent-review remediation GREEN: the same focused regression passed
+  after file enumeration retained tracked modes and excluded mode-160000
+  Gitlinks. The four-test behavior gate passed, including tracked root/child,
+  content-search, and untracked-file coverage. Both touched packages passed
+  again, and the CI-style changed-file lint reported 0 issues against base
+  `66eb87ac307db76b8cb3ba5fcfae73ff6d7d3e6c`.
+
+Production and regression files match **Files likely touched**; the spec and
+plan were synchronized with the remediation. Temporary artifacts: none.
+Blockers/remaining Task 01 risks: none.

docs/plans/submodule-workspace-search/task-02-prove-command-palette-search.md

@@ -0,0 +1,77 @@
+---
+id: "02-prove-command-palette-search"
+title: "Prove command-palette search"
+status: done
+wave: 2
+depends_on: ["01-correct-mixed-graph-search"]
+plan: "plan.md"
+spec: "../../specs/ui/task-workspace-content-search.md"
+---
+
+# Task 02: Prove Command-Palette Search
+
+## Acceptance
+
+- Cmd/Ctrl+Shift+K shows matching files from the unnamed Git root, direct
+  submodule, and nested submodule in their existing repository groups.
+- The test drives the user-facing palette, reuses the established disposable
+  submodule fixture, and cleans its source tree even after failure.
+- No production UI or mobile composition changes are introduced.
+
+## Verification
+
+```bash
+cd apps && pnpm install --frozen-lockfile
+cd apps/web && pnpm e2e:run tests/command-panel.spec.ts -- --grep 'finds root and submodule files'
+cd apps/web && pnpm e2e:run --no-build tests/review/submodule-review.spec.ts -- --grep 'cleans source repositories when setup fails' --retries=0
+```
+
+## Files likely touched
+
+- `apps/web/e2e/tests/command-panel.spec.ts`
+
+## Dependencies
+
+Task 01.
+
+## Parallelism
+
+`sequential` — browser proof requires the corrected backend aggregation.
+
+## Inputs
+
+- Spec scenario for Files search across a Git root and initialized submodules.
+- `apps/web/e2e/tests/review/submodule-review-helpers.ts` for disposable Git
+  graph creation, task startup, worktree readiness, and cleanup.
+- Existing `openFileSearch` and command-dialog helpers in `command-panel.spec.ts`.
+- Mobile-parity exception for shared data-only changes with no rendered,
+  touch, navigation, scrolling, or breakpoint change.
+
+## Output contract
+
+Report the discovered Playwright project/test count, exact E2E command/result,
+group assertions, disposable fixture cleanup, changed files, blockers/risks,
+and synchronized task/plan status.
+
+## Results
+
+- `pnpm install --frozen-lockfile` completed successfully from `apps/`.
+- RED: with the original file-search predicate restored in the built backend,
+  `pnpm e2e:run --no-build tests/command-panel.spec.ts -- --grep 'finds root and submodule files'`
+  discovered one Chromium test and failed with 2 repository groups instead of
+  3; the unnamed root group was missing.
+- GREEN: after restoring the fix and rebuilding,
+  `pnpm e2e:run tests/command-panel.spec.ts -- --grep 'finds root and submodule files'`
+  passed 1 Chromium test. It asserted the unnamed root, `vendor/outer`, and
+  `vendor/outer/vendor/inner` groups.
+- Review remediation moved setup-failure cleanup into the shared fixture helper
+  while preserving caller cleanup after successful setup. The focused regression
+  failed RED with one leaked directory, then passed GREEN; the command-palette
+  happy path also passed with retries disabled.
+- PR CI remediation made workspace-picker workspaces disposable, aligned its
+  focus assertion with Radix's initial item focus, and made office deletion
+  accept any remaining kanban workspace. Both specs passed together (5 tests),
+  then exact Chromium/mobile shard 4/14 passed 137 tests with 7 intentional
+  skips and retries disabled.
+- No production UI or mobile composition changed; both use the same corrected
+  backend response.

docs/specs/ui/task-workspace-content-search.md

@@ -36,6 +36,11 @@ repositories.
   paths so same-named files remain distinguishable and open in the correct
   repository. The palette groups those matches by repository and shows paths
   relative to each group.
+- For both **Files** and **Contents**, a Git workspace root remains searchable
+  when initialized submodules add named repository scopes. Root matches retain
+  the empty repository identity while child matches retain their task-root-relative
+  scope names. A bare task directory containing sibling repositories is not
+  treated as an additional repository.
 - Search covers every repository materialized for the active task session.
   Tracked files and untracked, non-ignored files are eligible; ignored files,
   directories, and workspace metadata are not.
@@ -135,6 +140,19 @@ repositories without parsing path strings.
 - **GIVEN** a task with two repositories containing matching file names,
   **WHEN** the user searches in **Files** mode, **THEN** matching paths from both
   repositories appear with their repository prefixes.
+- **GIVEN** a Git workspace root and an initialized submodule both contain
+  matching file names, **WHEN** the user searches in **Files** mode, **THEN**
+  matches from the root and submodule appear in separate repository groups.
+- **GIVEN** an initialized submodule path matches a file-search query, **WHEN**
+  the user searches in **Files** mode, **THEN** the parent repository's Gitlink
+  path is not returned as a file and real files inside the child scope remain
+  searchable.
+- **GIVEN** a Git workspace root and an initialized submodule both contain a
+  matching text query, **WHEN** the user searches in **Contents** mode,
+  **THEN** results from both repository scopes appear.
+- **GIVEN** a bare task directory contains multiple sibling repositories,
+  **WHEN** the user searches in **Files** or **Contents** mode, **THEN** only
+  those repositories contribute results and no duplicate task-root group appears.
 - **GIVEN** two repositories with the same relative path, **WHEN** the user
   selects the result from the second repository, **THEN** Kandev opens the
   second repository's file at the returned line and column.