I've found a solution : migrate to Angular CLI.
This link help me a lot : 
http://www.codingpedia.org/ama/fast-faster-angular-cli-how-i-converted-my-angular-project-to-use-angular-cli
I add some lines in my .angular.cli.json for styles and scripts. I put my app parameters : 
"apps": [
    {
      "root": "src",
      "outDir": "dist",
      "assets": [
        "assets",
        "app/api",
        "favicon.ico"
      ],
      "index": "index.html",
      "main": "main.ts",
      "polyfills": "polyfills.ts",
      "test": "test.ts",
      "tsconfig": "tsconfig.app.json",
      "testTsconfig": "tsconfig.spec.json",
      "prefix": "app",
      "styles": [
        "styles.scss",
        "../src/assets/vendors/bootstrap/dist/css/bootstrap.min.css",
        "../node_modules/font-awesome/css/font-awesome.css",
        "../src/assets/vendors/iCheck/skins/flat/green.css",
        "../src/assets/build/css/custom.min.css"
      ],
      "scripts": [
          "../src/assets/vendors/jquery/dist/jquery.min.js",
          "../src/assets/vendors/bootstrap/dist/js/bootstrap.min.js",
          "../src/assets/vendors/datatables.net/js/jquery.dataTables.min.js",
          "../src/assets/vendors/datatables.net-bs/js/dataTables.bootstrap.min.js",
          "../src/assets/vendors/datatables.net-buttons/js/dataTables.buttons.min.js",
          "../src/assets/vendors/datatables.net-buttons-bs/js/buttons.bootstrap.min.js",
          "../src/assets/vendors/datatables.net-buttons/js/buttons.flash.min.js",
          "../src/assets/vendors/datatables.net-buttons/js/buttons.html5.min.js",
          "../src/assets/vendors/datatables.net-buttons/js/buttons.print.min.js",
          "../src/assets/vendors/jszip/dist/jszip.min.js",
          "../src/assets/vendors/pdfmake/build/pdfmake.min.js",
          "../src/assets/vendors/pdfmake/build/vfs_fonts.js"
        ],
      "environmentSource": "environments/environment.ts",
      "environments": {
        "dev": "environments/environment.ts",
        "prod": "environments/environment.prod.ts"
      }
    }
  ]
I have to optimise this but it's working now.