Index: multidomain.module
===================================================================
RCS file: /cvs/drupal-contrib/contributions/modules/multidomain/multidomain.module,v
retrieving revision 1.1.2.4
diff -u -r1.1.2.4 multidomain.module
--- multidomain.module	7 Mar 2007 23:20:58 -0000	1.1.2.4
+++ multidomain.module	25 Apr 2007 21:53:05 -0000
@@ -324,6 +324,7 @@
     static $default = null;
     static $force_default = null;
     static $domains = null;
+    static $clean_url = null;
 
     $path = ( $alias ) ? $alias : $real_path;
     if (strpos($path, '://') !== FALSE) {
@@ -335,6 +336,7 @@
       $default = variable_get('singlesignon_master_url','');
       $force_default = variable_get('multidomain_force_default_domain', false);
       $domains = variable_get('multidomain_sites', array());
+      $clean_url = (bool)variable_get('clean_url', '0');
       $protocol = $_SERVER['HTTPS'] ? 'https://' : 'http://' ;
     }
     $base = $force_default ? $default : NULL;
@@ -375,7 +377,7 @@
     }
     if ($type == 'alias') {
       if (($protocol . $_SERVER['HTTP_HOST'] != $base) && !is_null($base) && (strpos($path, '://') === FALSE)) {
-        $path = $base .'/'. $path;
+        $path = $base .'/'. (!$clean_url ? '?q=' : '') . $path;
       }
     }
     else {
Index: multidomain_alias.patch
===================================================================
RCS file: /cvs/drupal-contrib/contributions/modules/multidomain/Attic/multidomain_alias.patch,v
retrieving revision 1.1.2.1
diff -u -r1.1.2.1 multidomain_alias.patch
--- multidomain_alias.patch	19 Dec 2006 02:26:22 -0000	1.1.2.1
+++ multidomain_alias.patch	25 Apr 2007 21:47:46 -0000
@@ -1,25 +1,23 @@
 Index: includes/common.inc
 ===================================================================
 RCS file: /cvs/drupal/drupal/includes/common.inc,v
-retrieving revision 1.602
-diff -u -r1.602 common.inc
---- includes/common.inc	15 Dec 2006 07:47:08 -0000	1.602
-+++ includes/common.inc	19 Dec 2006 02:22:41 -0000
-@@ -1174,11 +1174,15 @@
-   }
- 
-   $base = ($absolute ? $base_url . '/' : base_path());
--
+retrieving revision 1.611
+diff -u -r1.611 common.inc
+--- includes/common.inc	10 Jan 2007 23:30:07 -0000	1.611
++++ includes/common.inc	20 Apr 2007 23:56:29 -0000
+@@ -1181,8 +1181,13 @@
    // The special path '<front>' links to the default front page.
    if (!empty($path) && $path != '<front>') {
      $path = drupal_get_path_alias($path);
 -    $path = drupal_urlencode($path);
+-    if (!$clean_url) {
 +    if (strpos($path, '://') !== FALSE) {
 +      $base = '';
 +    }
 +    else {
 +      $path = drupal_urlencode($path);
 +    }
-     if (!$clean_url) {
++    if (!$clean_url && strpos($path, '://') === FALSE) {
        if (isset($query)) {
          return $base . $script .'?q='. $path .'&'. $query . $fragment;
+       }