Increase single shell factor to 3.5 so that it is >= 2* multi shell factor
Another revision of the rootfinding in EDGE_HITS_EDGE cylinder scaling

- Introducing an adaptive enlargement factor; just using TOLERANCE
  sometimes caused the steps to be too large in the first iteration
  and produced rootfinder search intervals with inverted bounds.
Cleanup
Tolerate a certain overlap with overlap_tolerance = TOLERANCE*shell_size
Warn when continuing with overlap within overlap_tolerance
Fix transition pair shell construction problem

The shells have to be constructed at the "real" position of the CoM,
i.e. the one with applied boundaries and projections.

In contrast, the calculations have all to be performed using the
CoM as calculated in one of the two structures (structure1).

That was not the case and is fixed by this commit.

Yet to be cleaned up after testing.
One more warn statement
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