I just made an extension that uses a shell tool (a JSON pretty printer). This requires a tool be installed, which is not an app and thus has no bundle identifier (it’s installed with brew).
It would be nice if the “app” action had a way to check for a tool to be present (which could be checked in PopClick either by using the which tool or by letting us specify the full path to it, or PopClip looking for the file in the various %PATH% locations itself.