Is there a command line tool (preferably on linux) that does the same thing? The reason being, we want to do this work as part of a nightly build when no humans would be around.
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DCW does not correct all of the possible incompatibilities in the Oracle SQL and PL/SQL, except in trivial cases. Even if there were a command-line tool (though there is not), there would always be some manual tweaking so you would not be able to fully automate the process.