Use --packages rather than --package-root

The .packages file is replacing the packages directory of symlinks.
diff --git a/packages/flutter_tools/lib/src/runner/flutter_command.dart b/packages/flutter_tools/lib/src/runner/flutter_command.dart
index 522563c..9aa4d3a 100644
--- a/packages/flutter_tools/lib/src/runner/flutter_command.dart
+++ b/packages/flutter_tools/lib/src/runner/flutter_command.dart
@@ -7,12 +7,13 @@
 
 import 'package:args/command_runner.dart';
 
-import '../dart/pub.dart';
 import '../application_package.dart';
 import '../build_configuration.dart';
+import '../dart/pub.dart';
 import '../device.dart';
 import '../flx.dart' as flx;
 import '../globals.dart';
+import '../package_map.dart';
 import '../toolchain.dart';
 import 'flutter_command_runner.dart';
 
@@ -147,6 +148,12 @@
       }
     }
 
+    String error = PackageMap.instance.checkValid();
+    if (error != null) {
+      printError(error);
+      return false;
+    }
+
     return true;
   }