Getting Started

When you got your first bot up and running with Discord.js, you should've installed Discord.js using npm, Node.js' Package Manager. The same applies to Commando, which must be separately installed. You can do this in one of two ways:

Stable: npm i -S discordjs/Commando#11.2
Master: npm i -S discordjs/Commando

If you're using Discord.js master, you'll need Commando master, and vice-versa.

Also note that you are going to need at least Node.js version 7.6.0. Download Node here. If on master, you'll need at least Node 8.

Creating Your index.js File

While it doesn't have to be called index.js, the index file is your main file for your bot, which handles everything from registering new commands to logging in your client. It's quite similar to standard Discord.js in many ways, but there are a few extra steps that need to be done to get your bot up and running.

First thing is to require Commando. Contrary to what you may think, you do not need to require Discord.js to use Commando. That is, unless you are going to use a MessageEmbed, but more on that later.

For now, simply require Commando. We'll also be requiring path for use later on. Don't worry, you don't have to install path.

const { CommandoClient } = require('discord.js-commando');
const path = require('path');

Look familiar? That's just about the same way you required Discord.js in your first bot. The next step is to create a new Commando Client. There's also a few options we are going to set. Some of these are optional, but recommended.

const client = new CommandoClient({
    commandPrefix: '<Insert Your Prefix Here>',
    owner: '<Insert Your User ID Here>',
    disableEveryone: true
});

Looks quite similar to your Discord.js Client doesn't it? Well, aside from all the options and stuff.

In commandPrefix, you should insert the prefix you intend to have for your bot. As of writing, you can only have one, so choose wisely! However, note that a mention will always be allowed alongside your prefix you set here. In other words, this prefix and mentions are how you will use your bot. No, there is no way to disable mentions being a prefix!

After that is the owner field, which should contain the User ID for the owner of the bot. The user you set here has complete control over the bot, can use eval and other Owner-Only Commands, and ignores command throttling and user permissions! So, be sure to only give this to yourself.
Also, if you installed master earlier, this can also be an array of IDs instead of a single one.

owner: ['ID', 'ID']

The final option, disableEveryone, simply prevents the bot from mentioning @everyone. This is simply to prevent things from getting annoying. After all, do you want someone mentioning everyone with the bot? Didn't think so.

Next we're going to register the command groups, args types, and default commands, and register the commands in a folder called commands. You can name the folder whatever you want, but I personally recommend commands , as it... Well, it makes the most sense.

client.registry
    .registerDefaultTypes()
    .registerGroups([
        ['group1', 'Our First Command Group']
    ])
    .registerDefaultGroups()
    .registerDefaultCommands()
    .registerCommandsIn(path.join(__dirname, 'commands'));

Remember how I said we'd need path? There you go.

Doing this we've also created our first command group, in the folder group1 in our commands folder. It will be displayed in the help command as 'Our First Command Group'. You can name both of these whatever you like.

Should you want to disable a default command, say, the help command, you can pass that in registerDefaultCommands.

.registerDefaultCommands({
    help: false
})

Next, we're going to create a ready event, which is about the same as the one in your first Discord.js Bot.

client.on('ready', () => {
    console.log('Logged in!');
    client.user.setActivity('game');
});

This will send Logged in! to your console when the bot is ready, and set the Bot's Game to 'Game'. Set that to whatever you wish.

Last but certainly not least, let's log the bot in.

client.login('Your Secret Token');

You can also use environment variables or a config.json for your token instead of passing it directly.

And there you have it! You've set up your index.js file! You should now create the commands and group1 folders, in the end your file structure should look like this, along with whatever .gitignore or config.json you may have:

commands
- group1
index.js
package.json

And your index.js file should look something like this:

const { CommandoClient } = require('discord.js-commando');
const path = require('path');

const client = new CommandoClient({
    commandPrefix: '<Insert Your Prefix Here>',
    unknownCommandResponse: false,
    owner: '<Insert Your User ID Here>',
    disableEveryone: true
});

client.registry
    .registerDefaultTypes()
    .registerGroups([
        ['group1', 'Our First Command Group']
    ])
    .registerDefaultGroups()
    .registerDefaultCommands()
    .registerCommandsIn(path.join(__dirname, 'commands'));

client.on('ready', () => {
    console.log('Logged in!');
    client.user.setActivity('game');
});

client.login('Your Secret Token');

In the next section, we'll create our first command! How exciting! See you then!