use Archive::Zip;
use Archive::Zip::Tree;
use File::Temp;
use File::Basename;

my $zip = Archive::Zip->new();
$zip->read($target) and die "can't read $target\n"
   if -f $target;
$zip->addTree($project_root, $project_root);
if (-f $target) # existing file?
{
  my ($tmpfh, $tmpname) = File::Temp::tempfile( DIR => dirname($target
+));
  $zip->writeToFileHandle( $tmpfh ) and die "Can't write to $tmpname\n
+";
  $tmpfh->close();
  unlink($target) or die "can't remove $target: $!\n";
  rename($tmpname, $target) or die "can't rename $target: $!\n";
}
else
{
    $zip->writeToFileNamed($target) and die "can't write to $target\n"
+;
}
[download]

Hmm... maybe I should add the write back to same file ability to Archive::Zip.