Respect user/pass flags to bin/storage for direct DatabaseRef-based queries

Summary:
Ref T11893. Previously, we excuted all `bin/storage` queries through `StorageManagementAPI` objects.

After D16848, we execute some queries through `PhabricatorDatabaseRef`. However, the refs we use weren't getting passed the `-u` / `-p` flags correctly, for specifying alternate administrative credentials.

Test Plan:
  - Created a second account (`trunk`).
  - Ran `bin/storage -u trunk`.
  - Made libphutil throw when not connecting as that user.
  - Before patch: some connections incorrectly used the default user, "root".
  - After patch: all connections correctly used the configured user, "trunk".

Reviewers: chad

Reviewed By: chad

Maniphest Tasks: T11893

Differential Revision: https://secure.phabricator.com/D16901

scripts/sql/manage_storage.php

@@ -206,6 +206,9 @@ foreach ($refs as $ref) {
     ->setDisableUTF8MB4($args->getArg('disable-utf8mb4'));
   PhabricatorEnv::overrideConfig('mysql.user', $api->getUser());
 
+  $ref->setUser($selected_user);
+  $ref->setPass($password);
+
   try {
     queryfx(
       $api->getConn(null),