Index: modules/system/system.install
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/system.install,v
retrieving revision 1.105
diff -u -r1.105 system.install
--- modules/system/system.install	11 May 2007 07:33:46 -0000	1.105
+++ modules/system/system.install	12 May 2007 10:03:56 -0000
@@ -3885,6 +3885,16 @@
   return array();
 }
 
+/**
+ * Files directory  now defaults to conf_path()/files
+ */
+function system_update_6015() {
+  if (empty(variable_get('file_directory_path', '')) && is_dir('files') && db_fetch_object(db_query("SELECT COUNT(*) FROM {files} f WHERE f.filepath LIKE 'files/%'", 'f')) >= 1) {
+    variable_set('file_directory_path', 'files');
+  }
+
+  return array();
+}
 
 /**
  * @} End of "defgroup updates-5.x-to-6.x"
Index: includes/file.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/file.inc,v
retrieving revision 1.97
diff -u -r1.97 file.inc
--- includes/file.inc	24 Apr 2007 13:53:10 -0000	1.97
+++ includes/file.inc	12 May 2007 10:03:53 -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');
 }
 
 /**
Index: modules/color/color.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/color/color.module,v
retrieving revision 1.19
diff -u -r1.19 color.module
--- modules/color/color.module	6 May 2007 05:47:51 -0000	1.19
+++ modules/color/color.module	12 May 2007 10:03:53 -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)) {