Many fixes for block forest case

CMakeLists.txt

examples/md.py

runtime/boundary_weights.hpp

runtime/domain/block_forest.cpp

runtime/domain/block_forest.hpp

runtime/domain/domain_partitioning.hpp

runtime/domain/regular_6d_stencil.cpp

runtime/domain/regular_6d_stencil.hpp

runtime/pairs.hpp

src/pairs/analysis/__init__.py

src/pairs/sim/domain.py

src/pairs/sim/domain_partitioning.py

src/pairs/sim/simulation.py