perl -i.bak -pe's/old text/new text/g' directory/*.ext
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Or if you want to do that inside your Perl program:

@ARGV == 2 or die "usage: $0 directory extention\n";

my ( $dir, $ext ) = splice @ARGV;

( $^I, @ARGV ) = ( '.bak', <$dir*.$ext> );

while ( <> ) {
    s/old text/new text/g;
    print;
    }
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