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/research/circuitprinter.dm

@@ -7,7 +7,7 @@ using metal and glass, it uses glass and reagents (usually sulphuric acid).
 /obj/machinery/r_n_d/circuit_imprinter
 	name = "Circuit Imprinter"
 	icon_state = "circuit_imprinter"
-	flags = OPENCONTAINER
+	atom_flags = OPENCONTAINER
 	circuit = /obj/item/circuitboard/circuit_imprinter
 	var/list/datum/design/queue = list()
 	var/progress = 0

code/modules/research/protolathe.dm

@@ -1,7 +1,7 @@
 /obj/machinery/r_n_d/protolathe
 	name = "Protolathe"
 	icon_state = "protolathe"
-	flags = OPENCONTAINER
+	atom_flags = OPENCONTAINER
 	circuit = /obj/item/circuitboard/protolathe
 	use_power = USE_POWER_IDLE
 	idle_power_usage = 30
@@ -237,4 +237,4 @@
 		return
 	materials[material] -= ejected * S.perunit
 	if(recursive && materials[material] >= S.perunit)
-		eject_materials(material, -1)
+		eject_materials(material, -1)