Refresh the index before constructing the status buffer.

This should get rid of files that are spuriously listed as modified,
while they in fact aren't.

magit.el

@@ -1957,6 +1957,7 @@ in log buffer."
 	  (if rebase
 	      (insert (apply 'format "Rebasing: %s (%s of %s)\n" rebase))))
 	(insert "\n")
+        (magit-run-git "update-index" "--refresh")
 	(magit-insert-untracked-files)
 	(magit-insert-stashes)
 	(magit-insert-topics)