How to better organize files in non-framework PHP projects. Como organizar melhor arquivos em projetos PHP que não usam frameworks

structure-1.md

/public/
    /js/
        /jquery.js
        /app.js
    /css/
        app.css
        some-optional-css-framework.css
    /index.php
    /config.php
    /config_dev.php
    /config_prod.php
/src/
    Source1.php
    Source2.php
    Source3.php
    SourceN.php

structure-2.md

/index.php
/routes.php
/assets/
    /css/
        app.css
    /js/
        app.js
    /img/
        logo.png
    /media/
        song-1.mp4
/models/
    User.php
/helpers/
    /date.php
    /string.php
    /time.php
/controllers/
    UserController.php
/views/
    /partials/
        /app-header.php
    user.php
```