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#!/usr/bin/env perl

...
    $new_string =~ s/\[i\]/\[$i\]/g;
    print "$new_string\n";
}

0 : first_string ref[0] second_string parent_ref.ref[0] third_string
1 : first_string ref[1] second_string parent_ref.ref[1] third_string
2 : first_string ref[2] second_string parent_ref.ref[2] third_string
3 : first_string ref[3] second_string parent_ref.ref[3] third_string
4 : first_string ref[4] second_string parent_ref.ref[4] third_string