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/detectivework/tools/rag.dm

@@ -23,7 +23,8 @@
 	possible_transfer_amounts = list(5)
 	volume = 10
 	can_be_placed_into = null
-	flags = OPENCONTAINER | NOBLUDGEON
+	atom_flags = OPENCONTAINER
+	item_flags = NOBLUDGEON
 	unacidable = 0
 	drop_sound = 'sound/items/drop/cloth.ogg'
 	pickup_sound = 'sound/items/pickup/cloth.ogg'

code/modules/detectivework/tools/scanner.dm

@@ -5,7 +5,7 @@
 	var/list/stored = list()
 	w_class = ITEMSIZE_SMALL
 	item_state = "electronic"
-	flags = NOBLUDGEON
+	item_flags = NOBLUDGEON
 	slot_flags = SLOT_BELT
 
 	var/reveal_fingerprints = TRUE