Merge pull request #104 from YetAnotherTomek/zero-rate-issue

Zero rate issue
Merge commit 'upstream/develop' into develop
Some cleanup in shells.py
Merge pull request #105 from YetAnotherTomek/develop

Mainly fixes some issue with determining rootfinder boundaries in EDGE_HITS_EDGE cylinder collision and TransitionPair shell construction
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
Basic code structure for overlap remover routine

Does not work yet, but also does not change anything yet.
Continue
Merge commit 'origin/overlap_remover' into overlap_remover
WIP + fix weird merge conflict