feat(cli): add warnings when gemini-cli is called in the root directory (#4542)

Co-authored-by: gemini-code-assist[bot] <176961590+gemini-code-assist[bot]@users.noreply.github.com>
Co-authored-by: N. Taylor Mullen <ntaylormullen@google.com>

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,