Yii 3 and many Yii 2 package sources are contained within src directory which is convenient since you have less directories to check.

/config
/runtime
/src
  /assets
  /commands
  /controllers
  /mail
  /models
  /views
  /widgets
/tests
/vendor
/web
yii

Let's start with the basic applicaiton template.

1. Create src directory.
2. Move source directories there.
3. Adjust config/web.php:

$config = [
    // ...
    'basePath' => dirname(__DIR__) . '/src',
    // ...
    'aliases' => [
        '@vendor' => dirname(__DIR__) . '/vendor',
        '@runtime' => dirname(__DIR__) . '/runtime',
        // ...
    ],
    // ...
];

And config/console.php:

$config = [
    // ...
    'basePath' => dirname(__DIR__) . '/src',
    // ...
    'aliases' => [
        '@vendor' => dirname(__DIR__) . '/vendor',
        '@runtime' => dirname(__DIR__) . '/runtime',
        // ...
    ],
    // ...
];

That's it now you have both console and web application source code in src.