Allow using COM of previous step as PBC reference

Allow using COM of previous step as PBC reference

Add an option, when pulling, to use the COM of the group of
the previous step, to calculate PBC jumps, instead of a reference
atom, which can sometimes move a lot during the simulation. When
there is no previous step (when the COM of the previous step is
not set) use the COM based on the reference atom. The COM of the
previous step is written to the checkpoint.

Fixes #2625

Change-Id: I6120b76a15f92167753463326125428f822848ab