open(my $in_fh,  '<', "input.filename")  or die "ack: $!";
open(my $out_fh, '>', "output.filename") or die "ack: $!";

while(<$in_fh>) {
  m{^/index} and $_ .= "%";
  print {$out_fh} $_;
}

close $in_fh;
close $out_fh;

rename( "output.filename", "input.filename" )
  or die "ack: $!";