GtfsTable now take a directory as argument in order to directly pick the right
file instead of the list of files.

At the moment, we still get the file from the directory's fileList because
there is no other way to get the file from a directory with a DirectoryStub.

A bug in DirectoryStub has also been fixed: the method containsFileByName did
not work.
Remove a XXX comment: orElse was not handled in firstWith(). The commented
code can now replace the longer one above.