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/hydroponics/grown.dm

@@ -5,7 +5,7 @@
 	icon = 'icons/obj/hydroponics_products.dmi'
 	icon_state = "blank"
 	desc = "Nutritious! Probably."
-	flags = NOCONDUCT
+	atom_flags = NOCONDUCT
 	slot_flags = SLOT_HOLSTER
 	drop_sound = 'sound/items/drop/herb.ogg'
 	pickup_sound = 'sound/items/pickup/herb.ogg'

code/modules/hydroponics/grown_inedible.dm

@@ -35,7 +35,7 @@
 	desc = "A reminder of meals gone by."
 	icon = 'icons/obj/trash.dmi'
 	icon_state = "corncob"
-	flags = NOCONDUCT
+	atom_flags = NOCONDUCT
 	w_class = ITEMSIZE_SMALL
 	throwforce = 0
 	throw_speed = 4
@@ -54,7 +54,7 @@
 	desc = "A peel from a banana."
 	icon = 'icons/obj/items.dmi'
 	icon_state = "banana_peel"
-	flags = NOCONDUCT
+	atom_flags = NOCONDUCT
 	w_class = ITEMSIZE_SMALL
 	throwforce = 0
 	throw_speed = 4

code/modules/hydroponics/trays/tray.dm

@@ -5,7 +5,7 @@
 	icon_state = "hydrotray3"
 	density = 1
 	anchored = 1
-	flags = OPENCONTAINER
+	atom_flags = OPENCONTAINER
 	volume = 100
 
 	var/mechanical = 1         // Set to 0 to stop it from drawing the alert lights.

code/modules/hydroponics/trays/tray_reagents.dm

@@ -1,7 +1,7 @@
 /obj/item/plantspray
 	icon = 'icons/obj/hydroponics_machines.dmi'
 	item_state = "spraycan"
-	flags = NOBLUDGEON
+	item_flags = NOBLUDGEON
 	slot_flags = SLOT_BELT
 	throwforce = 4
 	w_class = ITEMSIZE_SMALL