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/datums/elements/_element.dm

@@ -6,7 +6,7 @@
   */
 /datum/element
 	/// Option flags for element behaviour
-	var/element_flags = NONE
+	var/element_flags = EMPTY_BITFIELD
 	/**
 	  * The index of the first attach argument to consider for duplicate elements
 	  *