2 files changed, 82 insertions, 1 deletions
diff --git a/packages/cli/src/utils/userStartupWarnings.test.ts b/packages/cli/src/utils/userStartupWarnings.test.ts
index 61053029..7c0e1264 100644
--- a/packages/cli/src/utils/userStartupWarnings.test.ts
+++ b/packages/cli/src/utils/userStartupWarnings.test.ts
@@ -8,6 +8,7 @@ import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
 import { getUserStartupWarnings } from './userStartupWarnings.js';
 import * as os from 'os';
 import fs from 'fs/promises';
+import path from 'path';
 
 vi.mock('os', () => ({
   default: { homedir: vi.fn() },
@@ -71,4 +72,60 @@ describe('getUserStartupWarnings', () => {
   //   // Tests for node version check would go here
   //   // This shows how easy it is to add new test sections
   // });
+
+  describe('root directory check', () => {
+    it('should return a warning when running in root directory on Unix', async () => {
+      vi.mocked(fs.realpath)
+        .mockResolvedValueOnce('/')
+        .mockResolvedValueOnce(homeDir);
+
+      const warnings = await getUserStartupWarnings('/');
+
+      expect(warnings).toContainEqual(
+        expect.stringContaining('root directory'),
+      );
+      expect(warnings).toContainEqual(
+        expect.stringContaining('folder structure will be used'),
+      );
+    });
+
+    it('should return a warning when running in root directory on Windows', async () => {
+      vi.mocked(fs.realpath)
+        .mockResolvedValueOnce('C:\\')
+        .mockResolvedValueOnce(homeDir);
+
+      vi.spyOn(path, 'dirname').mockImplementation(path.win32.dirname);
+
+      const warnings = await getUserStartupWarnings('C:\\');
+
+      expect(warnings).toContainEqual(
+        expect.stringContaining('root directory'),
+      );
+      expect(warnings).toContainEqual(
+        expect.stringContaining('folder structure will be used'),
+      );
+    });
+
+    it('should not return a warning when running in a non-root directory', async () => {
+      vi.mocked(fs.realpath)
+        .mockResolvedValueOnce('/some/project/path')
+        .mockResolvedValueOnce(homeDir);
+
+      const warnings = await getUserStartupWarnings('/some/project/path');
+      expect(warnings).not.toContainEqual(
+        expect.stringContaining('root directory'),
+      );
+    });
+
+    it('should handle errors when checking root directory', async () => {
+      vi.mocked(fs.realpath)
+        .mockRejectedValueOnce(new Error('FS error'))
+        .mockResolvedValueOnce(homeDir);
+
+      const warnings = await getUserStartupWarnings('/');
+      expect(warnings).toContainEqual(
+        expect.stringContaining('Could not verify'),
+      );
+    });
+  });
 });
diff --git a/packages/cli/src/utils/userStartupWarnings.ts b/packages/cli/src/utils/userStartupWarnings.ts
index 3d76a6e1..8a740906 100644
--- a/packages/cli/src/utils/userStartupWarnings.ts
+++ b/packages/cli/src/utils/userStartupWarnings.ts
@@ -6,6 +6,7 @@
 
 import fs from 'fs/promises';
 import * as os from 'os';
+import path from 'path';
 
 type WarningCheck = {
   id: string;
@@ -32,8 +33,31 @@ const homeDirectoryCheck: WarningCheck = {
   },
 };
 
+const rootDirectoryCheck: WarningCheck = {
+  id: 'root-directory',
+  check: async (workspaceRoot: string) => {
+    try {
+      const workspaceRealPath = await fs.realpath(workspaceRoot);
+      const errorMessage =
+        'Warning: You are running Gemini CLI in the root directory. Your entire folder structure will be used for context. It is strongly recommended to run in a project-specific directory.';
+
+      // Check for Unix root directory
+      if (path.dirname(workspaceRealPath) === workspaceRealPath) {
+        return errorMessage;
+      }
+
+      return null;
+    } catch (_err: unknown) {
+      return 'Could not verify the current directory due to a file system error.';
+    }
+  },
+};
+
 // All warning checks
-const WARNING_CHECKS: readonly WarningCheck[] = [homeDirectoryCheck];
+const WARNING_CHECKS: readonly WarningCheck[] = [
+  homeDirectoryCheck,
+  rootDirectoryCheck,
+];
 
 export async function getUserStartupWarnings(
   workspaceRoot: string,