Implement velocity terms for virtual sites

Implement velocity terms for virtual sites

This change
* introduces velocity terms for virtual site reporting replacing the
  displacement hack used prior,
* removes work-arounds used to keep virtual sites frozen during real
  atom propagation,
* allows users of the VirtualSiteHandler object to chose whether to
  calculate positions only (used for non-output steps), positions
  and velocities (used for output-steps except in md-vv), or
  velocities only (used for output-steps in md-vv), which mitigates
  the fact that calculating the velocities requires a few additional
  operations,
* adds tests of the virtual velocity,
* updates the documentation accordingly.

Fixes #3866