В project.json возможность указать абсолютный путь

[ildar-ceo]

Будет подключен assets/script.js

{
    "name": "Project",
    "languages": ["php", "es6"],
    "modules":
    [
        {
            "src": "lib",
            "type": "folder"
        }
    ],
    "assets":
    [
        {
            "type": "js",
            "dest": "assets/app.js",
            "modules":
            [
                "App"
            ]
        },
        {
            "type": "js",
            "dest": "assets/runtime.js",
            "modules":
            [
                "Runtime",
                "Runtime.Web",
                "Runtime.Widget",
                "Runtime.Widget.Crud",
                "@assets/script.js"
            ]
        }
    ],
    "exclude":
    [
        "./vendor"
    ]
}