Delete the packages/ directory before installing new packages to it.

utils/tests/pub/pub_install_test.dart

Index: utils/tests/pub/pub_install_test.dart
diff --git a/utils/tests/pub/pub_install_test.dart b/utils/tests/pub/pub_install_test.dart
index 01f192ae57e385bec93173a67bc618d84e25c1c8..d9e803daae37f5a77b38c84ac0b065f699f7b78c 100644
--- a/utils/tests/pub/pub_install_test.dart
+++ b/utils/tests/pub/pub_install_test.dart
@@ -93,6 +93,27 @@ main() {
     run();
   });
 
+  test('overwrites the existing packages directory', () {
+    dir(appPath, [
+      appPubspec([]),
+      dir('packages', [
+        dir('foo'),
+        dir('myapp'),
+      ]),
+      libDir('myapp')
+    ]).scheduleCreate();
+
+    schedulePub(args: ['install'],
+        output: const RegExp(@"Dependencies installed!$"));
+
+    dir(packagesPath, [
+      nothing('foo'),
+      dir('myapp', [file('myapp.dart', 'main() => "myapp";')])
+    ]).scheduleValidate();
+
+    run();
+  });
+
   group('creates a packages directory in', () {
     test('"test/" and its subdirectories', () {
       dir(appPath, [