SQL Query Tuner is targeted at finding problem SQL in a running load with the profiler and then tuning that (or those) specific queries with the tuner.
It's not efficient just to dump a bunch of procedure code into the tuner and then try and see if any of the SQL in the package or procedure is tunable. Most queries should, by default, run optimally on a database, so the goal of DBO is to tune those queries that for one reason or another are not optimally tuned by the database by default. The easiest way to find those queries is to identify them on a running system. They can be identified on a running system because they take up a lot of resources. If we find a resource intensive query, then it's worth the time to generate cases and analyze it for missing indexes to see if there is a way to tune it.