As discussed in the context of T261285, we decided for v1 of WBManifest to create 2 new keys for the action API (api.php) and REST API (rest.php).
Hints: Probably use the rootscripturl and concatenate it.
We do this with subkeys in an API object
{ api: { action: 'foo.com/api.php', rest: 'foo.com/rest.php' } }