Fix update of standalone bundle

We regressed on being able to install a bundle twice to update it.

This fixes https://github.com/flatpak/flatpak/issues/462

app/flatpak-transaction.c

@@ -467,7 +467,7 @@ flatpak_transaction_add_ref (FlatpakTransaction *self,
         }
       remote = origin;
     }
-  else
+  else if (kind == FLATPAK_TRANSACTION_OP_KIND_INSTALL)
     {
       g_assert (remote != NULL);
       if (dir_ref_is_installed (self->dir, ref, NULL))

tests/test-bundle.sh

@@ -24,7 +24,7 @@ set -euo pipefail
 skip_without_bwrap
 skip_without_user_xattrs
 
-echo "1..6"
+echo "1..7"
 
 mkdir bundles
 
@@ -147,3 +147,19 @@ run org.test.Hello > hello_out
 assert_file_has_content hello_out '^Hello world, from a sandboxUPDATED$'
 
 echo "ok update"
+
+make_updated_app UPDATED2
+
+${FLATPAK} build-bundle repos/test --repo-url=file://`pwd`/repos/test --gpg-keys=${FL_GPG_HOMEDIR}/pubring.gpg bundles/hello2.flatpak org.test.Hello
+assert_has_file bundles/hello2.flatpak
+
+${FLATPAK} install ${U} -y --bundle bundles/hello2.flatpak
+
+NEW2_COMMIT=`${FLATPAK} ${U} info --show-commit org.test.Hello`
+
+assert_not_streq "$NEW_COMMIT" "$NEW2_COMMIT"
+
+run org.test.Hello > hello_out
+assert_file_has_content hello_out '^Hello world, from a sandboxUPDATED2$'
+
+echo "ok update as bundle"