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/game/objects/items/devices/geiger.dm

@@ -105,7 +105,7 @@
 	plane = TURF_PLANE
 	layer = ABOVE_TURF_LAYER
 	w_class = ITEMSIZE_LARGE
-	flags = NOBLOODY
+	item_flags = NOBLOODY
 	var/circuit = /obj/item/circuitboard/geiger
 	var/number = 0
 	var/last_tick //used to delay the powercheck
@@ -170,4 +170,4 @@
 
 /obj/item/geiger/wall/west
 	pixel_x = -28
-	dir = WEST
+	dir = WEST

code/game/objects/items/devices/radio/intercom.dm

@@ -6,7 +6,7 @@
 	anchored = 1
 	w_class = ITEMSIZE_LARGE
 	canhear_range = 2
-	flags = NOBLOODY
+	item_flags = NOBLOODY
 	var/circuit = /obj/item/circuitboard/intercom
 	var/number = 0
 	var/wiresexposed = 0
@@ -195,4 +195,4 @@
 
 /obj/item/radio/intercom/locked/confessional
 	name = "confessional intercom"
-	frequency = 1480
+	frequency = 1480

code/game/objects/items/devices/scanners.dm

@@ -381,7 +381,7 @@ HALOGEN COUNTER	- Radcount on mobs
 	drop_sound = 'sound/items/drop/device.ogg'
 	icon_state = "spectrometer"
 	w_class = ITEMSIZE_SMALL
-	flags = OPENCONTAINER
+	atom_flags = OPENCONTAINER
 	slot_flags = SLOT_BELT
 	throwforce = 5
 	throw_speed = 4
@@ -463,7 +463,7 @@ HALOGEN COUNTER	- Radcount on mobs
 		return
 
 	if(!isnull(O.reagents))
-		if(!(O.flags & OPENCONTAINER)) // The idea is that the scanner has to touch the reagents somehow. This is done to prevent cheesing unidentified autoinjectors.
+		if(!(O.atom_flags & OPENCONTAINER)) // The idea is that the scanner has to touch the reagents somehow. This is done to prevent cheesing unidentified autoinjectors.
 			to_chat(user, span("warning", "\The [O] is sealed, and cannot be scanned by \the [src] until unsealed."))
 			return