src/Pure/Tools/update.scala

   val update_elements: Markup.Elements =
     Markup.Elements(Markup.UPDATE, Markup.LANGUAGE)
 
   def update_xml(options: Options, xml: XML.Body): XML.Body = {
     val path_cartouches = options.bool("update_path_cartouches")
+    val cite_commands = options.bool("update_cite_commands")
 
     def upd(lang: Markup.Language, ts: XML.Body): XML.Body =
       ts flatMap {
         case XML.Wrapped_Elem(markup, body1, body2) =>
           val body = if (markup.name == Markup.UPDATE) body1 else body2

               case None => upd(lang1, body)
             }
           }
           else upd(lang1, body)
         case XML.Elem(_, body) => upd(lang, body)
+        case XML.Text(s) if lang.is_document && cite_commands =>
+          List(XML.Text(Bibtex.update_cite(s)))
         case t => List(t)
       }
     upd(Markup.Language.outer, xml)
   }