Refactoring still in process.
Merge branch 'refactored_code' of https://github.com/mchandra/grim into refactored_code

Conflicts:
	boundary.h
	boundary/boundary.h
	geometry.h
	geometry/geometry.h
	physics.h
	physics/physics.c
	physics/physics.h
	riemannsolver.c
	riemannsolver/riemannsolver.c
	src/boundary/boundary.h
	src/geometry/geometry.h
	src/physics/physics.h
	src/riemannsolver/riemannsolver.c