Index: src/wp-admin/includes/class-wp-upgrader.php
===================================================================
--- src/wp-admin/includes/class-wp-upgrader.php	(revision 25761)
+++ src/wp-admin/includes/class-wp-upgrader.php	(working copy)
@@ -1504,11 +1504,15 @@
 
 		$check_dirs = array_unique( $check_dirs );
 
+		$checkout = false;
 		// Search all directories we've found for evidence of version control.
-		foreach ( $vcs_dirs as $vcs_dir ) {
-			foreach ( $check_dirs as $check_dir ) {
-				if ( $checkout = is_dir( rtrim( $check_dir, '\\/' ) . "/$vcs_dir" ) )
-					break 2;
+		foreach ( $check_dirs as $check_dir ) {
+			$files = @scandir( $check_dir );
+			if ( false === $files )
+				break;
+			if ( array_intersect( $files, $vcs_dirs ) ) {
+				$checkout = true;
+				break;
 			}
 		}
 		return apply_filters( 'auto_upgrade_is_vcs_checkout', $checkout, $context );