How to group methods by classes?

https://github.com/documentationjs/documentation-theme-light/blob/master/screenshot.png shows the methods in the sidebar grouped by JS classes. I run the default theme or theme-light and all I get in the sidebar is all the methods across the codebase dumped out as one long list (creating, e.g., a long line of `init` entries). How do I group the methods by their associated classes and/or modules? I'm feeding all the JS files in the codebase into the `documentation build` command, if that matters. Also the `--github`, `--format`, and `--output` options are added. Thanks!