replaces atom.initialized with ATOM_INITIALIZED

refactors atom/var/flags to atom_flags and area_flags
moves NOBLOODY, NOBLUDGEON, and PHORONGUARD to item_flags instead of atom_flags
corrects various misapplied flags

code/modules/lighting/lighting_atom.dm

@@ -43,15 +43,6 @@
 		else
 			light = new /datum/light_source(src, .)
 
-/atom/Initialize()
-	. = ..()
-
-	if(light_power && light_range)
-		update_light()
-
-	if(opacity && isturf(loc))
-		var/turf/T = loc
-		T.has_opaque_atom = TRUE // No need to recalculate it in this case, it's guranteed to be on afterwards anyways.
 
 /atom/Destroy()
 	if(light)