Replaced public access to RigidBodyTree:bodies by call to body(index)
Replaced public access to RigidBodyTree:bodies by call to body(index)

sheim/drake,sheim/drake,billhoffman/drake,billhoffman/drake,sheim/drake,sheim/drake,sheim/drake,sheim/drake,billhoffman/drake,billhoffman/drake,billhoffman/drake,sheim/drake,billhoffman/drake,billhoffman/drake,sheim/drake,billhoffman/drake