The reason it only prints out one directory is that you are not pushing the results of your recursive calls to finddir into the @direct array.

       next unless ( -d "$root$file" );
       $dir = "$root$file";
       $dir =~ s/^\Q$config{home}$user{site_id}\E//;
       push(@direct, $dir);
       push(@direct, finddir("$root$file"));
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