1. change the HTML code, so all java dependencies are loaded by the HTML code. This approach is time consuming especially when you plan to protect many HTML files;
2. manually add the missing files to the protected folder structure (the output folder), by copying them from their original folder.
If you want to protect the Java applet source code, then the solution is to put the protected files on a web location and to publish the URL for that product to your customers. By doing this, all files are secured, because your customers can’t access the source code from the server, and they can’t view the source code of the protected files.