I just have installed the newest version of angular (5.2.0) and CLI 1.6.6. I did eject command and get webpack.config.js with full scripts path:
"plugins": [
    new NoEmitOnErrorsPlugin(),
    new ScriptsWebpackPlugin({
      "name": "scripts",
      "sourceMap": true,
      "filename": "scripts.bundle.js",
      "scripts": [
        "D:\\GitProjects\\Product\\ProjectName\\node_modules\\jquery\\dist\\jquery.min.js",
        "D:\\GitProjects\\Product\\ProjectName\\node_modules\\tv4\\tv4.js"
      ],
      "basePath": "D:\\GitProjects\\Product\\ProjectName"
    }),
Why does paths are absolute, should not be relative as it was until now ?