Assorted fixes to get Chicago GTFS to load.

*  Increase various timeouts
*  Bump memory (scala needed 7GB to calculate Chicago's indicators)
*  Add println statements to indicator calculations, for debugging

@echeipesh is looking into scala logging frameworks.

To get the Chicago GTFS to load, I modified it to add `agency_id` entries, as a temporary workaround for azavea/gtfs-parser#2 .
Maybe @hectcastro knows how to do that, he's pretty knowledgeable about vagrant