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perl -pi -e 'm{^/index} and s/$/%/' file

use Tie::File;

...
for(@fl) {
  m{^/index} and s/$/%/;
}

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

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