Manipulating velocities in addition to positions

[GiovanniBussi]

We could consider passing velocities as well. We must make sure there are no effects related to different integrator algorithms used in different codes. Combined with #345, this might allow a standalone implementation of methods such as forward flux or transition path sampling, where multiple trajectories are launched without the need to restart the MD code. Might be beneficial in cases where the trajectory segments are short, since all the overhead due to initialization will disappear.

I think I've seen discussion on the mailing list about this, but nobody contributed this feature yet.