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 .
The fact that we were setting these at all is likely a reflection of something not being quite right.

These may well not need to be increased; I just bumped them while increasing other timeouts that I had hit.