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Directories Structure

Directory Description
/pimcore/ Core files of Pimcore, do not change anything here.
/plugins/ Directory for plugins / extensions.
/vendor/ All third-party libraries are there. It's the default location for packages installed by Composer / Packagist.
/website/ Everything regarding your individual project/application (templates, controllers, settings, objects, ...). All your code goes there (see below).

Contents of /website

Directory Description
/website/controllers Controllers of your application.
/website/config Configuration files for cache, workflow modules, DI configuration, extensions additional configuration, ... Examples
/website/lib Custom libraries (if needed, use Composer to install dependencies whenever possible)
/website/models Your custom models (if needed).
/website/var This directory contains files created by Pimcore during runtime like assets, classes, thumbnails, ... (Pimcore needs write access on this directory)
/website/views Your templates/views.