checkout: Fix file descriptor leak for copying checkouts

Hardlink checkouts didn't hit this, but we need to close the input
stream.

src/libostree/ostree-repo-checkout.c

@@ -502,6 +502,9 @@ checkout_one_file_at (OstreeRepo                        *repo,
               goto out;
             }
         }
+
+      if (!g_input_stream_close (input, cancellable, error))
+        goto out;
     }
 
   ret = TRUE;