Essential dynamics: fixed restarts when ED group has > 1 molecule

To ensure proper restarts when the ED group consists of more than a
single molecule, the PBC-correct positions of the ED group are now
stored in the checkpoint file.

Change-Id: Id87bee610ad248f8695927d0027254e7d6d4c677
Fixed a bug that with multiple exchanges

Fixed a very subtle bug with multiple exchanges: with multiple
exchanges, Swapping states and swapping configurations are NOT
equivalent, for the same reason that the cycles 1->2->3->1 and
1->3->2->1 are not equivalent.  Also added a number of comments
to help explain the code more.

Change-Id: I52b4543d5b6e1b035d8d6225df3388d0f07cd76f
Merge "Essential dynamics: fixed restarts when ED group has > 1 molecule" into release-4-6
Merge "Fixed a bug that with multiple exchanges" into release-4-6