Slight improvement to logging message.
Took out problmatic spaces in header for the routes.txt file.
Improved a comment.
Changed to double space logs.
Fixed typo. No functional changes.
Improved warning message. No functional changes.
Made arrival and departure optional instead of required since while the
fields are required as per the GTFS spec the values can and often will
be null.
Generating Mission Bay GTFS now appears to work well.

Moved all agency specific custom software to
org.transitime.custom.AGENCY packages so that it is all grouped into one
place and much easier to maintain.