Zero length penetrations

Just some minor cleanup and comments about some NaN's that I noticed and tracked down.  No functional change.

Note: dividing the penetration by TREE_SCALE is not necessary for the updateCollisionSound() call (which just tries to normalized penetration --> more accuracy when the elements of penetration are not too small), but is still necessary for the applyHardCollision() call, so I just moved that divide operation down a line.