Remove unnecessary functionality from do_rerun

Remove unnecessary functionality from do_rerun

As discussed in task #1868, the rerun functionality gets reduced to essentially
"take a configuration and calculate forces and energies". If the trajectory contains
velocities, they are ignored. This allows to remove a lot of functionality from
do_rerun, which is done in this commit.

Functionality removed includes

    * Reading of velocities in reruns (reruns won't contain kinetic energy)
    * Constraints
    * Temperature / pressure coupling
    * Essential dynamics
    * Interactive MD
    * Simulated annealing
    * Multisimulations
    * AWH
    * Expanded ensemble
    * Replica exchange
    * Checkpointing
    * Counter resetting (no benchmarking)
    * PME tuning
    * FAHCORE
    * EnergyHistory

The following quantities are not reported:

    * Kinetic energy
    * Total energy
    * Conserved energy
    * Temperature(s)
    * Pressure, pressure tensor, and pressure dispersion correction
    * Virial tensor(s)

This change also changes the rerun tests not to test for correct
reproduction of the velocities (since they are intentionally set
to zero), and adds some information to the documentation.

Refs #1868

Change-Id: I522d56a610f2a6ff189484c9311b6f53c775ed47