Delete window after editing is complete
Patch from flameeyes

--- a/lib/quilt.el
+++ b/lib/quilt.el
@@ -399,6 +399,7 @@
     (cd quilt-header-directory)
     (shell-command (concat "EDITOR=cat quilt -r header <" tmp))
     (kill-buffer (current-buffer))
+    (delete-window)
     (delete-file tmp)))
 
 (defvar quilt-header-mode-map (make-keymap))
