Update Flag module to v3.9 as the 2.x branch is discontinued. The
patch 0004-accomodate-flag-v3.patch merged with local commons
modules under modules/commons directory.
SA-CONTRIB-2016-050
https://www.drupal.org/node/2793115
Change-Id: I335963fa16b66d8914071ee5c08b61849384ae6f