Fixed problem with bond constraint dhdl being left out

Fixed problem with bond constraint dhdl being left out

At some point, the dhdl from the holonomic bond constraints got left out,
because the term got zeroed before being added to the bonded energy.

Also, I made some of the variable names involved more descriptive to
clarify the logic.

Removed velocity constraint calls, as don't contribute to dhdl.

Fixes redmine #1255

Change-Id: I2eebf357d1a922b7636dc015b09f286827283dd0