My Webird project has a build system that can optionally pass the code through Ion Cube.
Webird is tightly integrated with Webpack but if you don't want it then you could gut that part out. Additionally bower and npm (nodejs) can be used to install devDependencies and normal dependencies. By default for bower and npm there are no normal dependencies that will survive the build process but you can add them and then they will be available on the other side. The current dependencies are put into the devDependency section because that code is processed by Webpack and emitted as "bundles".
To sum up I think that Webird offers both a nice production/distribution build system while also offering some debugging options like an improved Phalcon Debug Widget.