You can try this:

I modified your OP using your description below:

use warnings;
use strict;
use Cwd qw(abs_path);

die "Please give the directory to the file on CLI" unless @ARGV == 2;
my ( $dir, $file_to_reference ) = @ARGV;

my @ds;
open my $fh, '<', $file_to_reference or die "can't open file: $!";
while (<$fh>) {
    chomp;
    push @ds, $_;
}
close $fh or die "can't close file: $!";

$dir = abs_path($dir);
chdir $dir or die "No such directory: $!";

my @result;

opendir my $dh, $dir or die "can't open dir: $!";
while ( my $file = readdir $dh ) {
    for (@ds) {
        push @result, $_ if $_ eq $file;
    }
}
closedir $dh or die "can't close directory: $!";

print $_, $/ for @result;
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