add test python script
Remove alerts index mapping and the alerts table from the database
Add gtfs proto file
Add protocol buffer output file to src, library to libs

Conflicts:

	.classpath
Refactoring alerts
Implemented gtfs-realtime alerts parser
'agencyid' in the database will now correspond to GTFS route_type
Rewrite commuterrail_tosql.py to use GTFS stop ids
Merge branch 'gtfs-realtime-alerts' into commuterrail_and_new_alerts
change commuter rail handling
Merge branch 'master' into commuterrail_and_new_alerts

Conflicts:
	src/boston/Bus/Map/parser/CommuterRailPredictionsFeedParser.java
Change commuter rail parser to use json
Change autogenerate.sh to work with new commuterrail_tosql.py
Remove alerts_tosql.py
Fix duplicate stop insertion
Fix last updated time
Fix path creation
Handle errors if route isn't found
more tools to graph and convert shape data
fix plotting bug