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 .
Ok. A big boost to stability would be go figure out the root cause of why we need these so high in the first place. Bumping them only delays the problem, whereas fixing the root cause would allow us to remove these settings, or at least bring them back down to sensible values.