To include your own files in Hybrid Web Container, copy them into the appropriate place in the Generated Hybrid Apps folder.
To load external JavaScript and CSS files dynamically, copy the relevant third-party JavaScript and CSS files to the Generated Hybrid Apps\<package_name>\html and js or css folders. If the files are JavaScript files, and are in the html\js folder, they are automatically included in the HTML as script.
These files will be included in the Hybrid App manifest.xml and ZIP files automatically when the Hybrid App package is regenerated.