assorted bugfixes + improvments

A few minor bug fixes + improvements:

(If need be I can create separate pull request, but this seemed simpler...)

The commits
* update comments in StoptimeUpdater (BlockUpdate -> TripUpdate)
* fix a stopIndex/hopIndex mixup, which I previously missed
* correctly removes expired route patches, which were removed with the wrong key
  * also adds PatchService#getAllPatches()
* keeps track of timestamps for GTFS-rt alerts, to avoid needlessly updating the graph
* in TransitIndexBuilder, warn if the parentStation is missing for a stop
* in TransitIndexService, avoid a needless iteration over all trips in a pattern to get the route
* when destroying the ApiServlet evicts all the graphs, which stops the per-graph updater thread
* in PlanGenerator, for transit legs also returns the serviceDate for the trip.
* use the protobuf "PARSER" for parsing GTFS-rt FeedMessages, which -- according to the documentation -- yields a ~25% speed improvement.