You could of course rebuild the document using HTML::Parser...

Or...

sub do_file($$){
  my ($file, $indent) = @_;
  local *FOO;
  open(FOO, $file);
  while (<FOO>) {
    /^(\t+)#&#(.+)/ && $indent = do_file($2, $indent + length $1);
    print;
  }
  close FOO;
  return $indent;
}
[download]

I've not tested it, and I'm not really sure what you want, but if this is what you were thinking of, you should recognize it :)