Better names for functions

This closes #143.

I have also updated the names of the functions in runner.c to stop linguistic problems between "dog host" and do ghost" for instance. 

See merge request !165

Time-step synchronisation

Ok, this is the final fix to #93. Particles are not allowed to move to a longer time-step unless we are currently doing a time-step of that size. That will prevent particles from being completely all over the place in the time-step hierarchy.

It wasn't physically wrong until now, just not efficient and very confusing.

With this fix in place, there will always be a time-step every so often where all particles are updated. 

See merge request !164