Better "missing region" penalties

[ryan-williams]

The "missing region penalty" (step.rs) should be proportional to the distance each shape is from the required region existing. Among other improvements, this would allow shapes to rotate to get closer to one another.

Currently, I just move their centers closer together, which often just causes them to thrash against added error in other regions, and not converge.

Training examples starting from the "Disjoint" layout is one way to see this in action:

disjoint-variant-callers.mp4