Made some improvements, using proper JavaScript objects now.
Rewrote flocking neighborhood calculation to fix some issues, result is a much nicer and more flexible flocking algorithm.  Still some areas to improve on.
Increase abstraction, made canvas take up window and dynamically resize with the window.
Added BoidController to manage boids
First iteration of MVC pattern working.
Obstacles added and functioning.  By default 6 obstacles are added at initialization.