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 .
So late to the party, but +1 to the prefixed environmental variables technique. There is also a fancier syntax for common attributes (don't think `pae` is one of them, but you should be good without it because the box is 64bit):

```ruby
config.vm.provider "virtualbox" do |v|
  v.memory = MEMORY_MB.to_i
  v.cpus = 3
end
```

Also, that's a healthy shell script!