Update runtime structure

Makefile

runtime/array.hpp

runtime/device_flags.hpp

runtime/devices/cuda.cu

runtime/devices/device.hpp

runtime/devices/dummy.cpp

runtime/domain/domain_partitioning.hpp

runtime/domain/no_partition.hpp

runtime/domain/regular_6d_stencil.hpp

runtime/pairs.cpp

runtime/pairs.hpp

runtime/pairs_common.hpp

runtime/property.hpp

runtime/read_from_file.hpp

runtime/vector3.hpp

runtime/vtk.hpp

src/pairs/code_gen/cgen.py