Reject single reactions in which a product crosses a plane

This caused problems with particles leaking out of the box structure.
Same thing for the BD mode, slightly more effort required
Rename crossing_comparison_vector -> side_comparison_vector

This just makes more sense.
Remove comment that is not true any more
Merge commit 'upstream/develop' into develop
Merge pull request #106 from YetAnotherTomek/develop

Fixes a problem with particles leaking out of a closed box