To include your own files in the container application, copy them into the appropriate place in the Generated Workflows folder.
To load external JavaScript and CSS files dynamically, copy the relevant third-party JavaScript and CSS files to the Generated Workflow\<Workflow_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 Mobile Workflow manifest.xml and .zip files automatically when the Mobile Workflow package is re-generated.