from-git: Check out the whole tree instead of just the manifest

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 checkout the whole tree, otherwise we can't parse
the manifest.

Closes: #260
Approved by: alexlarsson

src/builder-main.c

@@ -643,12 +643,11 @@ main (int    argc,
           return 1;
         }
 
-      if (!builder_git_checkout_dir (opt_from_git,
-                                     git_branch,
-                                     manifest_dirname,
-                                     build_subdir,
-                                     build_context,
-                                     &error))
+      if (!builder_git_checkout (opt_from_git,
+                                 git_branch,
+                                 build_subdir,
+                                 build_context,
+                                 &error))
         {
           g_printerr ("Can't check out manifest repo: %s\n", error->message);
           return 1;