Important note about KB3081699
Good news! Microsoft has just released KB3081699 to fix the issue that Windows Phone Apps cannot be deployed or added to Allowed Apps or Blocked Apps lists via ConfigMgr. This hotfix applies to ConfigMgr 2012 R2 SP1 and ConfigMgr SP2. However, it’s important to note that, even though this hotfix was released after CU1, the current version of this hotfix should be installed before CU1. Update August 7, 2015: As expected this update is now available in two flavors. In the hotfix request form it’s now possible to select the one of the following: pre-CU1: ConfigMgr_2012_SP2_R2SP1_CU0_QFE_KB3081699_ENU post-CU1: ConfigMgr_2012_SP2_R2SP1_CU1_QFE_KB3081699_ENU