Index: modules/color/color.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/color/color.module,v
retrieving revision 1.18
diff -u -r1.18 color.module
--- modules/color/color.module	6 Apr 2007 13:27:21 -0000	1.18
+++ modules/color/color.module	14 Apr 2007 20:17:58 -0000
@@ -238,7 +238,7 @@
 
   // 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: modules/system/system.install
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/system.install,v
retrieving revision 1.90
diff -u -r1.90 system.install
--- modules/system/system.install	13 Apr 2007 08:53:24 -0000	1.90
+++ modules/system/system.install	14 Apr 2007 20:18:00 -0000
@@ -3705,6 +3705,17 @@
 }
 
 /**
+ * Default files directory, file_directory_path,
+ *  now defaults to conf_path()/files 
+ */
+function system_update_6008() {
+  if (empty(variable_get('file_directory_path', '')) && is_dir('files') && count(db_fetch_object(db_query("SELECT fid FROM {files} WHERE filepath LIKE 'files/%' LIMIT 1")))) {
+    variable_set('file_directory_path', 'files');
+  }
+
+  return array();
+}
+/**
  * @} End of "defgroup updates-5.x-to-6.x"
  * The next series of updates should start at 7000.
  */
Index: includes/file.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/file.inc,v
retrieving revision 1.96
diff -u -r1.96 file.inc
--- includes/file.inc	13 Apr 2007 08:56:57 -0000	1.96
+++ includes/file.inc	14 Apr 2007 20:17:58 -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');
 }
 
 /**