Several changes and cleanup

- introducing an overlap remover that can be switched on and off and removes overlapps instead of crashing, while keeping track of the error
- general fixes to overlap checking
- fixes to StructureContainer and connections between planes
- fixes to apply_boundary()
- fixes to fire_single_reaction()
- new domain types for transfers between rod and plane
- revised parent-structure concept
- better ignore lists for searching and overlap checking
- fixes to coordinate transform for the MixedPair2D3D
- etc.