Sometimes people can forget or not know the prefix for your bot, so letting them use command with a mention is useful.
This can be enabled with the allowMention option.

this.commandHandler = new CommandHandler(this, {
  directory: "./commands/",
  prefix: "?",
  allowMention: true
});

Now both ?ping and @BOT ping works!

A prefix can change based on the message.
Use a function as the prefix option to do so.
This is most useful with an actual database to back it up, so check out the Using Providers section.

this.commandHandler = new CommandHandler(this, {
  directory: "./commands/",
  prefix: msg => {
    // Get prefix here...
    return prefix;
  },
  allowMention: true
});

Prefix overrides are command-specific prefixes.
To use them, simply add the prefix option.

import { Command } from "discord-akairo";
import { Message } from "discord.js";

export default class SecretCommand extends Command {
  constructor() {
    super("secret", {
      aliases: ["secret"],
      prefix: "???"
    });
  }

  exec(message: Message) {
    return message.reply("Woah! How did you find this!?");
  }
}

Now, if our prefix was ?, ?secret won't work, but ???secret would.
An array works too, so you can do prefix: ['???', '??'] and both would work.

To speed up your development, you can make command aliases automatically.
For example, if you had a command alias that is two words, you might want both command-name and commandname to be valid.
Use the aliasReplacement option, which takes a regular expression to make aliases:

this.commandHandler = new CommandHandler(this, {
  directory: "./commands/",
  prefix: "?",
  aliasReplacement: /-/g,
  allowMention: true
});

The option is passed /-/g which means that all dashes are to be removed to make an alias.
So now, in a command, you can pass aliases: ['command-name'] and both command-name and commandname would be valid.