from-git: Fetch the submodules as well

Some manifests now make use of the shared-modules Git repo from Flathub.
At least Totem does that, and we might see others do the same.

    https://gitlab.gnome.org/GNOME/totem/blob/master/flatpak/org.gnome.Totem.json
    http://sdkbuilder.gnome.org/logs/build-2019-01-18-141001/build-gnome-apps-nightly-master-org.gnome.Totem-x86_64.txt

That means we have to fetch the Git submodules before we can parse the
manifest.

Closes: #260
Approved by: alexlarsson

src/builder-main.c

@@ -627,9 +627,16 @@ main (int    argc,
 
       cleanup_manifest_dir = g_object_ref (build_subdir);
 
+      int mirror_flags = FLATPAK_GIT_MIRROR_FLAGS_MIRROR_SUBMODULES;
+
+      if (opt_disable_updates)
+        {
+          mirror_flags |= FLATPAK_GIT_MIRROR_FLAGS_UPDATE;
+	}
+
       if (!builder_git_mirror_repo (opt_from_git,
                                     NULL,
-                                    opt_disable_updates?0:FLATPAK_GIT_MIRROR_FLAGS_UPDATE,
+                                    mirror_flags,
                                     git_branch, build_context, &error))
         {
           g_printerr ("Can't clone manifest repo: %s\n", error->message);