I hope that i'm not totally Perl-Blind but a good refactoring might be to rewrite your fancy sub like this:

sub index_menu {
  my $dir = shift;
  # my @file_list = file_list('.');
  my @file_list = file_list($dir); # if this is what you meant
  my $files = [
    map  { anchor( textify($_), { href => $_ } ) }
    grep { /^[A-Z].+/ &&  -f $_ }
    sort { article_sort($a, $b) }
    @file_list
  ];
  return $files;
}
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You may also consider to use the more hard-boiled style and omit the explicit return but that's a matter of taste.

And if i where in your shoes i would leave my old working code untouched and use the BLOCK LIST style (which is the natural way IMHO) from today on.

Best regards, Karl