Removed restriction of one reference pull group

The pull code now uses separate pull groups and coordinates,
which removes any restriction on group pairing.
The pull geometry "position" has been removed, but the origin
option replaces this functionaliy in case of an absolute reference.
Removed triple use of the init option.
Refs #1346

Change-Id: I90736ac6b6f18e3bf26a344072172a69627566e9