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/events/ion_storm.dm

@@ -37,7 +37,7 @@
 		if(!(S.z in affecting_z))
 			continue
 		var/area/A = get_area(S)
-		if(!A || A.flags & RAD_SHIELDED) // Rad shielding will protect from ions too
+		if(!A || A.area_flags & RAD_SHIELDED) // Rad shielding will protect from ions too
 			continue
 		to_chat(S, "<span class='warning'>Your integrated sensors detect an ionospheric anomaly. Your systems will be impacted as you begin a partial restart.</span>")
 		var/ionbug = rand(3, 9)

code/modules/events/radiation_storm.dm

@@ -37,7 +37,7 @@
 		var/area/A = get_area(C)
 		if(!A)
 			continue
-		if(A.flags & RAD_SHIELDED)
+		if(A.area_flags & RAD_SHIELDED)
 			continue
 		if(istype(C,/mob/living/carbon/human))
 			var/mob/living/carbon/human/H = C