jwickers

The following would work without needing to inject a controller, you simply add a close method to the alert you are building:

.factory('AppAlert', ['$rootScope', ($rootScope) ->
      $rootScope.alerts = []
      alertService = 
        add: (type, msg) ->
          $rootScope.alerts.push { type: type, msg: msg, close: -> alertService.closeAlert(this) } 
        closeAlert: (alert) ->
          @closeAlertIdx $rootScope.alerts.indexOf(alert)
        closeAlertIdx: (index) ->
          $rootScope.alerts.splice index, 1
      ])

and in the alert directive simply replace the close to
close="alert.close()"