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/paperwork/paperplane.dm

@@ -17,7 +17,7 @@
 	pixel_x = rand(-9, 9)
 	if(newPaper)
 		internalPaper = newPaper
-		flags = newPaper.flags
+		atom_flags = newPaper.atom_flags
 		color = newPaper.color
 		newPaper.forceMove(src)
 	else

code/modules/paperwork/pen.dm

@@ -116,7 +116,7 @@
  */
 
 /obj/item/pen/reagent
-	flags = OPENCONTAINER
+	atom_flags = OPENCONTAINER
 	origin_tech = list(TECH_MATERIAL = 2, TECH_ILLEGAL = 5)
 
 /obj/item/pen/reagent/Initialize()