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/library/lib_items.dm

@@ -174,7 +174,7 @@ Book Cart End
 	item_state = "book"
 	throw_speed = 1
 	throw_range = 5
-	flags = NOCONDUCT
+	atom_flags = NOCONDUCT
 	w_class = ITEMSIZE_NORMAL		 //upped to three because books are, y'know, pretty big. (and you could hide them inside eachother recursively forever)
 	attack_verb = list("bashed", "whacked", "educated")
 	var/dat			 // Actual page content
@@ -405,4 +405,4 @@ Book Cart End
 		to_chat(user, "<font color=green>Computer has been associated with this unit.</font>")
 	else
 		to_chat(user, "<font color=red>No associated computer found. Only local scans will function properly.</font>")
-	to_chat(user, "\n")
+	to_chat(user, "\n")