Index: modules/system/system.install
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/system.install,v
retrieving revision 1.103
diff -u -r1.103 system.install
--- modules/system/system.install	9 May 2007 11:39:23 -0000	1.103
+++ modules/system/system.install	10 May 2007 19:07:02 -0000
@@ -3873,6 +3873,19 @@
   system_theme_data();
 }
 
+/**
+ * Default files directory, file_directory_path,
+ * now defaults to conf_path()/files
+ */
+function system_update_6014() {
+  $ret = array();
+
+  if (db_fetch_object(db_query("SELECT COUNT(*) FROM {variable} v WHERE v.name='file_directory_path'")) == 0 && is_dir('files') && db_fetch_object(db_query("SELECT COUNT(*) FROM {files} f WHERE f.filepath LIKE 'files/%'")) >= 1) {
+    $ret[] = update_sql("INSERT INTO {variable} (name, value) VALUES ('file_directory_path', 'files'");
+  }
+
+  return $ret;
+}
 
 /**
  * @} 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	10 May 2007 19:07:00 -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	10 May 2007 19:07:00 -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)) {