The directory structure for modules should mimic that of the application/ directory in the recommended project structure:

<modulename>
    configs/
        application.ini
    controllers/
        helpers/
    forms/
    layouts/
        filters/
        helpers/
        scripts/
    models/
    services/
    views/
        filters/
        helpers/
        scripts/
    Bootstrap.php

The purpose of these directories remains exactly the same as for the recommended project directory structure.