In a couple of my projects, indexWriter was dying on line 102, saying that $package is not an object. I replaced lines 102 and 103 with the following code, and it seemed to have the desired effect.

$package =& $element->containingPackage();
if (!$package)
{
	$defaultPackage = $rootDoc->phpDoctor()->defaultPackage();
	$package = $rootDoc->packageNamed($defaultPackage, true);
}
$in = 'package <a href="'.$package->asPath().'/package-summary.html">'.$package->name().'</a>';