Add preferred and unpreferred agencies and fix other issues

Sorry for the mixed bag pull request. I made multiple fix on the same branch and waited before sending a pull request. 

Add preferred and unpreferred agencies (self explanatory). Extract the banned and preferencesPenality logic in RoutingRequest since it was repeated 3 times (in FrequencyAlight, FrequencyBoard and TransitBoardAlight).

It was not possible to set numItineraries in the application-context.xml since the getter was of the wrong type (Integer instead of int).