itch.io

So this is what Wapper is actually doing:

When you load your html file it gets renamed to index.html (required to make it work) and copies it to the source folder. If you only have a single html file with no other required files, you don't need to copy the html folder. If your project does have assets (including css or js files or other required files for your game), they need to be copied from the html folder.

Wapper creates a webview wrapper to load your project files into. The exe that Wapper outputs is the wrapper. The wrapper looks in the source folder for your html file and assets. The wrapper uses an http server to serve your files to the window.

The _internal folder is the wrapper's internal workings, the files it needs to work. If you build in Onefile mode (single exe), there is no _internal folder because the files are packed into the exe.

So the source folder is required for your project to work. And the _internal folder is required if using Onedir mode.

Wapper does have a custom archive (.efa file) to obfuscate your files that will not open in things like 7zip or other archive software. This is not encryption or DRM. My archive uses custom offsets, header, and file extension. But a person that knows what they are doing could still crack it. But it would not be easy for the average person.