Refactor SD update

The former use of multiple boolean control variables made the logic
hard to follow. Without constraints, the two parts of the integrator
are fused, which is now expressed explicitly.

This means it is now clear that the second half of the sd update does
not compute anything from the foreces.

Removed some of the vestiges of the way we once had two SD
integrators.

Refs #2423, #1793

Change-Id: I39d4cd0b8568859220b3a592b138f3f4405f8991