I may miss the point here, but why not simply building a hash as you go over the directory once.

  foreach (readdir(DIR)) {
    if (/^([a-z0-9]*?-[a-z]{2}-[a-z]{2,3})-(\d{8})(-eol)?\.(pdf|html)$
+/) {
      push(@{$files{$1}}, $2);
    }
  }
[download]

This can than be sorted in a second pass by:

  foreach (keys %files) {
    $files{$_} = [sort @{$files{$_}}];
  }
[download]

Hope this helps, -gjb-