Basic code structure for overlap remover routine

Does not work yet, but also does not change anything yet.
Continue
Merge pull request #106 from YetAnotherTomek/develop

Fixes a problem with particles leaking out of a closed box
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
Finish first version of a working overlap remover

Still lacking some features, like checking whether particle is
in the right structure after overlap removal.

Apart from that there seems to be some problem with planar surface
pairs updated close to the edge of the system (with periodic BC)
that shall be fixed separately.
Introduce a function to default-connect one plane in periodic BCs

Otherwise the Bossonic new version of apply_boundary does not work
correctly.
Use do_back_transform correctly

I.e. apply overlap prevention only if particles are to end up
on orthogonal planes.
Include overlap error into print_report
Reconstruct periodic connection correctly upon reloading via the
loadsave system
Fix an object creation loop that caused huge memory leaks
WIP - some debug statements
Merge branch 'overlap_remover_fix' into overlap_remover
This is not the right way to treat it...
further WIP
Only try to establish connections at loading if such
are declared in the input file.
Avoid applying boundary cond. to self-connected planes + warn
+ link logger into StructureContainer.hpp
WIP