Fixed rotation bug

If a triangle is already rotated exactly north or exactly south,
rounding error can cause arccos to fail and return nan. Added a
workaround to detect this: if the triangle is already pointing north,
the function returns the triangle untouched; if the triangle is
pointing south, theta is set to pi before doing the rotation.
Modifications to run many chains or metrics

Added new code to run all metrics for all chains. Modified code to
handle the measurement of structure in the dynamic and combined sets.
Also, pre-computing the meaning distances for the stable set, so that
the distances aren't repeatedly computed. plotAll now plots both the
positive and negative 95% confidence level.