Index: wp-admin/includes/class-wp-upgrader.php
===================================================================
--- wp-admin/includes/class-wp-upgrader.php	(revision 20460)
+++ wp-admin/includes/class-wp-upgrader.php	(working copy)
@@ -207,7 +207,7 @@
 			$source_files = array_keys( $wp_filesystem->dirlist($source) );
 
 		//Protection against deleting files in any important base directories.
-		if ( in_array( $destination, array(ABSPATH, WP_CONTENT_DIR, WP_PLUGIN_DIR, WP_CONTENT_DIR . '/themes') ) ) {
+		if ( in_array( $destination, apply_filters( 'upgrader_base_directories', array(ABSPATH, WP_CONTENT_DIR, WP_PLUGIN_DIR, WP_CONTENT_DIR . '/themes') ) ) ) {
 			$remote_destination = trailingslashit($remote_destination) . trailingslashit(basename($source));
 			$destination = trailingslashit($destination) . trailingslashit(basename($source));
 		}