update: Update custom installations too

Currently the update command only checks the default system and user
installations (unless overridden by a command line flag). This commit
makes it check custom installations as well, so they are not left out.

Care is taken so that an empty or broken installation doesn't cause the
whole update operation to fail.

Fixes flatpak#2006

app/flatpak-builtins-update.c

@@ -84,7 +84,7 @@ flatpak_builtin_update (int           argc,
   g_option_context_set_translation_domain (context, GETTEXT_PACKAGE);
 
   if (!flatpak_option_context_parse (context, options, &argc, &argv,
-                                     FLATPAK_BUILTIN_FLAG_STANDARD_DIRS,
+                                     FLATPAK_BUILTIN_FLAG_ALL_DIRS | FLATPAK_BUILTIN_FLAG_OPTIONAL_REPO,
                                      &dirs, cancellable, error))
     return FALSE;
 
@@ -108,9 +108,18 @@ flatpak_builtin_update (int           argc,
 
   transactions = g_ptr_array_new_with_free_func ((GDestroyNotify) g_object_unref);
 
-  for (k = 0; k < dirs->len; k++)
+  /* Walk through the array backwards so we can safely remove */
+  for (k = dirs->len; k > 0; k--)
     {
-      FlatpakTransaction *transaction = flatpak_cli_transaction_new (g_ptr_array_index (dirs, k), opt_yes, FALSE, error);
+      FlatpakDir *dir = g_ptr_array_index (dirs, k - 1);
+      OstreeRepo *repo = flatpak_dir_get_repo (dir);
+      if (repo == NULL)
+        {
+          g_ptr_array_remove_index (dirs, k - 1);
+          continue;
+        }
+
+      FlatpakTransaction *transaction = flatpak_cli_transaction_new (dir, opt_yes, FALSE, error);
       if (transaction == NULL)
         return FALSE;
 
@@ -120,7 +129,7 @@ flatpak_builtin_update (int           argc,
       flatpak_transaction_set_disable_dependencies (transaction, opt_no_deps);
       flatpak_transaction_set_disable_related (transaction, opt_no_related);
 
-      g_ptr_array_add (transactions, transaction);
+      g_ptr_array_insert (transactions, 0, transaction);
     }
 
   kinds = flatpak_kinds_from_bools (opt_app, opt_runtime);