Looks really nice. Just gave you a review on coursera. There is one minor bug which is ignored in the web-ide internal OS representation:
In Boid.draw and Boid.clear you call:
do Screen.drawRectangle(positionX, positionY, positionX + size, positionY + size);
This creates a rectangle with height and width of (size + 1)! As a consequence your screen wrap is off by one and allows coordinates 512 for x or 256 for y. The Java-based emulator or the referene OS.vm files will therefore quickly crash with ERR9 as soon as the first Boid reaches the bottom of the screen.
I would recommend to change the 2 calls in class Boid to
do Screen.drawRectangle(positionX, positionY, positionX + size - 1, positionY + size - 1);
to have a boid with the expected size (of 10).