mdsim.particle: remove dependency on mdsim.box, use dimension instead

The C++ module did not depend on the box. The dependency was solely
introduced to extract box.dimension ... To keep things simple, the user
will specify the dimension of space explicitly. We let it default to 3,
and add a default value of 1 for species.

Adjust all examples, docs, tests ...
benchmarks: remove config files from version 0.2.x