If it's not too much work to do so, I would turn each of your applications into thin wrappers that drive a module that embodies all the "business logic". Then the modules could be used without your application wrappers, as the models for your Mojolicious::Lite application. The Mojolicious::Lite app would drive the two modules based on whatever RESTful API you cook up. This avoids the level of paranoia that has to go in to invoking system commands using arguments passed from a web application.