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/reagents/holder/distilling.dm

@@ -1,7 +1,7 @@
 /datum/reagents/distilling/handle_reactions()
 	if(QDELETED(my_atom))
 		return FALSE
-	if(my_atom.flags & NOREACT)
+	if(my_atom.atom_flags & NOREACT)
 		return FALSE
 	var/reaction_occurred
 	var/list/eligible_reactions = list()
@@ -23,4 +23,4 @@
 	for(var/i in effect_reactions)
 		var/decl/chemical_reaction/C = i
 		C.post_reaction(src)
-	update_total()
+	update_total()

code/modules/reagents/holder/holder.dm

@@ -78,7 +78,7 @@
 /datum/reagents/proc/handle_reactions()
 	if(QDELETED(my_atom))
 		return FALSE
-	if(my_atom.flags & NOREACT)
+	if(my_atom.atom_flags & NOREACT)
 		return FALSE
 	var/reaction_occurred
 	var/list/eligible_reactions = list()

code/modules/reagents/machinery/chem_master.dm

@@ -19,7 +19,7 @@
 	var/pillsprite = 1
 	var/max_pill_count = 20
 	var/printing = FALSE
-	flags = OPENCONTAINER
+	atom_flags = OPENCONTAINER
 	clicksound = "button"
 
 /obj/machinery/chem_master/Initialize()
@@ -495,4 +495,4 @@
 
 /obj/machinery/chem_master/condimaster
 	name = "CondiMaster 3000"
-	condi = 1
+	condi = 1

code/modules/reagents/machinery/chemalyzer.dm

@@ -53,11 +53,11 @@
 				to_chat(user, span("notice", "Contains [R.volume]u of <b>[R.name]</b>.<br>[R.description]<br>"))
 
 		// Last, unseal it if it's an autoinjector.
-		if(istype(I,/obj/item/reagent_containers/hypospray/autoinjector/biginjector) && !(I.flags & OPENCONTAINER))
-			I.flags |= OPENCONTAINER
+		if(istype(I,/obj/item/reagent_containers/hypospray/autoinjector/biginjector) && !(I.atom_flags & OPENCONTAINER))
+			I.atom_flags |= OPENCONTAINER
 			to_chat(user, span("notice", "Sample container unsealed.<br>"))
 
 		to_chat(user, span("notice", "Scanning of \the [I] complete."))
 		analyzing = FALSE
 		update_icon()
-		return
+		return

code/modules/reagents/machinery/dispenser/cartridge.dm

@@ -55,10 +55,10 @@
 	..()
 	if (is_open_container())
 		to_chat(usr, "<span class = 'notice'>You put the cap on \the [src].</span>")
-		flags ^= OPENCONTAINER
+		atom_flags ^= OPENCONTAINER
 	else
 		to_chat(usr, "<span class = 'notice'>You take the cap off \the [src].</span>")
-		flags |= OPENCONTAINER
+		atom_flags |= OPENCONTAINER
 
 /obj/item/reagent_containers/chem_disp_cartridge/afterattack(obj/target, mob/user , flag)
 	if (!is_open_container() || !flag)

code/modules/reagents/reagent_containers/glass.dm

@@ -14,7 +14,7 @@
 	possible_transfer_amounts = list(5,10,15,25,30,60)
 	volume = 60
 	w_class = ITEMSIZE_SMALL
-	flags = OPENCONTAINER | NOCONDUCT
+	atom_flags = OPENCONTAINER | NOCONDUCT
 	unacidable = 1 //glass doesn't dissolve in acid
 	drop_sound = 'sound/items/drop/bottle.ogg'
 	pickup_sound = 'sound/items/pickup/bottle.ogg'
@@ -74,14 +74,14 @@
 	..()
 	if(is_open_container())
 		to_chat(usr, "<span class = 'notice'>You put the lid on \the [src].</span>")
-		flags ^= OPENCONTAINER
+		atom_flags ^= OPENCONTAINER
 	else
 		to_chat(usr, "<span class = 'notice'>You take the lid off \the [src].</span>")
-		flags |= OPENCONTAINER
+		atom_flags |= OPENCONTAINER
 	update_icon()
 
 /obj/item/reagent_containers/glass/attack(mob/M as mob, mob/user as mob, def_zone)
-	if(force && !(flags & NOBLUDGEON) && user.a_intent == I_HURT)
+	if(force && !(item_flags & NOBLUDGEON) && user.a_intent == I_HURT)
 		return	..()
 
 	if(standard_feed_mob(user, M))
@@ -134,7 +134,7 @@
 			update_name_label()
 	if(istype(W,/obj/item/storage/bag))
 		..()
-	if(W && W.w_class <= w_class && (flags & OPENCONTAINER) && user.a_intent != I_HELP)
+	if(W && W.w_class <= w_class && (atom_flags & OPENCONTAINER) && user.a_intent != I_HELP)
 		to_chat(user, "<span class='notice'>You dip \the [W] into \the [src].</span>")
 		reagents.touch_obj(W, reagents.total_volume)
 
@@ -209,7 +209,7 @@
 	volume = 120
 	amount_per_transfer_from_this = 10
 	possible_transfer_amounts = list(5,10,15,25,30,60,120)
-	flags = OPENCONTAINER
+	atom_flags = OPENCONTAINER
 
 /obj/item/reagent_containers/glass/beaker/noreact
 	name = "cryostasis beaker"
@@ -219,7 +219,7 @@
 	matter = list("glass" = 500)
 	volume = 60
 	amount_per_transfer_from_this = 10
-	flags = OPENCONTAINER | NOREACT
+	atom_flags = OPENCONTAINER | NOREACT
 
 /obj/item/reagent_containers/glass/beaker/bluespace
 	name = "bluespace beaker"
@@ -230,7 +230,7 @@
 	volume = 300
 	amount_per_transfer_from_this = 10
 	possible_transfer_amounts = list(5,10,15,25,30,60,120,300)
-	flags = OPENCONTAINER
+	atom_flags = OPENCONTAINER
 
 /obj/item/reagent_containers/glass/beaker/vial
 	name = "vial"
@@ -242,7 +242,7 @@
 	w_class = ITEMSIZE_TINY
 	amount_per_transfer_from_this = 10
 	possible_transfer_amounts = list(5,10,15,30)
-	flags = OPENCONTAINER
+	atom_flags = OPENCONTAINER
 
 /obj/item/reagent_containers/glass/beaker/cryoxadone
 	name = "beaker (cryoxadone)"
@@ -259,7 +259,7 @@
 	volume = 120
 	amount_per_transfer_from_this = 10
 	possible_transfer_amounts = list(5,10,15,25,30,60,120)
-	flags = OPENCONTAINER
+	atom_flags = OPENCONTAINER
 
 /obj/item/reagent_containers/glass/bucket
 	desc = "It's a bucket."
@@ -273,7 +273,7 @@
 	amount_per_transfer_from_this = 20
 	possible_transfer_amounts = list(10,20,30,60,120)
 	volume = 120
-	flags = OPENCONTAINER
+	atom_flags = OPENCONTAINER
 	unacidable = 0
 	drop_sound = 'sound/items/drop/helm.ogg'
 	pickup_sound = 'sound/items/pickup/helm.ogg'
@@ -331,7 +331,7 @@
 	amount_per_transfer_from_this = 20
 	possible_transfer_amounts = list(10,20,30,60,120)
 	volume = 120
-	flags = OPENCONTAINER
+	atom_flags = OPENCONTAINER
 	unacidable = 0
 	drop_sound = 'sound/items/drop/wooden.ogg'
 	pickup_sound = 'sound/items/pickup/wooden.ogg'

code/modules/reagents/reagent_containers/hypospray.dm

@@ -12,7 +12,7 @@
 	unacidable = 1
 	volume = 30
 	possible_transfer_amounts = null
-	flags = OPENCONTAINER
+	atom_flags = OPENCONTAINER
 	slot_flags = SLOT_BELT
 	drop_sound = 'sound/items/drop/gun.ogg'
 	pickup_sound = 'sound/items/pickup/gun.ogg'
@@ -115,7 +115,7 @@
 			if(!do_after(user,30) || loaded_vial || !(W in user))
 				return 0
 			if(W.is_open_container())
-				W.flags ^= OPENCONTAINER
+				W.atom_flags ^= OPENCONTAINER
 				W.update_icon()
 			user.drop_item()
 			W.loc = src
@@ -152,13 +152,13 @@
 
 /obj/item/reagent_containers/hypospray/autoinjector/used/Initialize()
 	. = ..()
-	flags &= ~OPENCONTAINER
+	atom_flags &= ~OPENCONTAINER
 	icon_state = "[initial(icon_state)]0"
 
 /obj/item/reagent_containers/hypospray/autoinjector/do_injection(mob/living/carbon/human/H, mob/living/user)
 	. = ..()
 	if(.) // Will occur if successfully injected.
-		flags &= ~OPENCONTAINER
+		atom_flags &= ~OPENCONTAINER
 		update_icon()
 
 /obj/item/reagent_containers/hypospray/autoinjector/update_icon()

code/modules/reagents/reagent_containers/spray.dm

@@ -5,7 +5,8 @@
 	icon_state = "cleaner"
 	item_state = "cleaner"
 	center_of_mass = list("x" = 16,"y" = 10)
-	flags = OPENCONTAINER|NOBLUDGEON
+	atom_flags = OPENCONTAINER
+	item_flags = NOBLUDGEON
 	matter = list("glass" = 300, MAT_STEEL = 300)
 	slot_flags = SLOT_BELT
 	throwforce = 3

code/modules/reagents/reagent_containers/unidentified_hypospray.dm

@@ -7,102 +7,102 @@
 // The good.
 /obj/item/reagent_containers/hypospray/autoinjector/bonemed/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/clonemed/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/brute/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/burn/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/toxin/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/oxy/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/purity/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/pain/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/organ/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/clotting/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/combat/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/healing_nanites/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 // The somewhat bad.
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/stimm/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/bliss/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/expired/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/serotrotium/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/cryptobiolin/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/mindbreaker/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/psilocybin/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/soporific/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 // The very bad.
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/cyanide/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/impedrezene/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/mutagen/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/defective_nanites/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0
 
 /obj/item/reagent_containers/hypospray/autoinjector/biginjector/contaminated/unidentified
 	init_hide_identity = TRUE
-	flags = 0
+	atom_flags = 0