Removing an agency in transformer, does not remove fares with derived routes

[barbeau]

Moved here from OneBusAway/onebusaway-application-modules#231, by @skinkie.

I think the issue is clear. I am trying to remove an agency.

{"op":"remove","match":{"file":"agency.txt","agency_id":"63"}}

The result is a GTFS container with the agency removed. But it seems that the fare_rules.txt file is not being processed for the routes the agency might have defined but that have been removed with the above operation.

[skinkie]

@barbeau tnx