Something like this should work:

#! /usr/bin/perl
use strict;
use warnings;

opendir(DIR, "/full/path/to/sentence/");
my @filesInDirectoryA = readdir(DIR); 
opendir(DIR, "/full/path/to/name/");
my @filesInDirectoryB = readdir(DIR); 

my $count = @filesInDirectoryA;
my $x = 0;

for ($x = 0; $x<$count; $x += 1)
    {
        if ($filesInDirectoryA[$x] ne $filesInDirectoryB[$x])
            {
                die "mismatched files!\n\n";
            }
    }

for ($x = 0; $x<$count; $x += 1)
    {
        unless ($filesInDirectoryA[$x] =~ m/^\./)
            {
                system("perl run.pl /full/path/to/sentence/$filesInDir
+ectoryA[$x] /full/path/to/name/@filesInDirectoryB > /full/path/to/out
+put/$filesInDirectoryA[$x]");
            }
    }
[download]

That should take all the files in the sentence and name directories and feed them to your script. Provided that the files in each of the directories have the same name. You need to replace the path names.