What have you got at the moment (just the half dozen lines that deal with iterating over files)? It may be that all you have to do is:

    while (...) {
        open INFILE, '<', ...;
        my $buffer = do {local $/; <INFILE>};
        next if $buffer =~ /CLEAR/;
        ...
   } continue {
        close INFILE;
   }
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