At this point, you should have a very basic, barebones bot up and running, and the first time you started your bot, you should have noticed something that was console logged that said something along the lines of
[Success] .vscode/settings.json has been initialized, you can now use intellisense with your message.json file!. All this message is saying is that now that your project has been run, the handler has had a chance to initialize your ability to use intellisense with any message.json file that you create in your project directory.
Your message.json file is completely optional, as one is used by default in the module folder, but it allows you to create your own responses for commands that can be fetched throughout your code. These responses can be whatever you wish, and if you don't want to make your own responses, you can either exclude the "MessageJSONPath" property from the CDCommands class, or get the default message.json file from here. This file will include all of the default command responses and any permission check responses that are triggered in the message event.