Index: modules/system/system.install
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/system.install,v
retrieving revision 1.75
diff -u -r1.75 system.install
--- modules/system/system.install	31 Jan 2007 15:49:25 -0000	1.75
+++ modules/system/system.install	31 Jan 2007 17:52:05 -0000
@@ -3536,6 +3536,16 @@
 }
 
 /**
+ * file_directory_path now defaults to conf_path().'/files'
+ *  instead of just 'files'', something more clever is needed here
+ */
+function system_update_2001() {
+  if (empty(variable_get('file_directory_path', '')) && is_dir('files')) {
+    variable_set('file_directory_path', 'files');
+  }
+}
+
+/**
  * @} End of "defgroup updates-5.0-to-x.x"
  * The next series of updates should start at 3000.
  */
Index: modules/color/color.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/color/color.module,v
retrieving revision 1.15
diff -u -r1.15 color.module
--- modules/color/color.module	20 Jan 2007 08:12:20 -0000	1.15
+++ modules/color/color.module	31 Jan 2007 17:51:39 -0000
@@ -228,7 +228,7 @@
 
   // Prepare target locations for generated files
   $id = $theme .'-'. substr(md5(serialize($palette) . microtime()), 0, 8);
-  $paths['color'] = variable_get('file_directory_path', 'files') .'/color';
+  $paths['color'] = file_directory_path() . '/color';
   $paths['target'] = $paths['color'] .'/'. $id;
   foreach ($paths as $path) {
     if (!is_dir($path)) {
Index: includes/file.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/file.inc,v
retrieving revision 1.93
diff -u -r1.93 file.inc
--- includes/file.inc	31 Jan 2007 15:49:22 -0000	1.93
+++ includes/file.inc	31 Jan 2007 17:51:36 -0000
@@ -712,7 +712,7 @@
  * @return A string containing the path to Drupal's 'files' directory.
  */
 function file_directory_path() {
-  return variable_get('file_directory_path', 'files');
+  return variable_get('file_directory_path', conf_path().'/files');
 }
 
 /**