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if ( ! -f $BASEDIR/nbssoammsg/tdt/src/tdt9999.cxx ) {
    system ( qq(cd $BASEDIR/nbssoammsg/tdt/src));
...
    print "Skipping tdtgen file generation -- if you want to force a r
+egen\n";
    print "of tdt files, delete $BASEDIR/nbssoammsg/tdt/src/tdt9999.cx
+x\n";
}

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chdir("$BASEDIR/nbssoammsg/tdt/src") or error_code_here();