So you're trying to print out all the directories without the path attached onto them? If so, this might work:

use warnings;
use diagnostics;
use strict;

my %config = ( home => '/home/cjf/' );
my %user   = ( site_id => 'code'    );

finddir("$config{home}$user{site_id}");

sub finddir {
   my $root = shift;
   chomp $root;
   $root = $root . '/' unless ( $root =~ m|/$| );
   opendir ( DIR, $root ) or die "Can't open Directory: $!";
   my @userfiles = sort grep !/^\.\.?\z/, readdir DIR;
   foreach my $file (@userfiles) {
       next unless ( -d "$root$file" );
       print $file, "\n";
       finddir("$root$file");
   }
}
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You might want to consider File::Find as well.