If enabled, the greedy extension only checks chains which have at least 3
contacts in trg/mdl towards the already mapped chains where contact is defined
as CB distance < 8A.

This should prevent any further "substructure has residue [...] which is not
in self.target" errors. Add test and doc to clarify what we ignore.

This fixes a problem where ties aren't being resolved correctly

This improves error messages when the counts line is invalid and the
calls to substr() return raw C++ errors.

comes at limited additional runtime costs

trust me, its a bit better that way...

Apply crude collision detection to avoid pairwise distance computations
between chains that are far apart.