1.4 Folder structure

assets/      javascript, css and images of the application
classes/     php classes, for intern use (no access by URLs)
docs/        documentation, default folder where to put your notes
templates/   layouts for the screen, slideshow and output as vendor/      external libraries, open source ones
html page

In the root folder, you'll find, among others,

.htaccess           Apache configuration file
custom.css          Your own css definition (see below)
custom.js           Your own javascript functions (see below)
index.php           entry point
settings.json.dist  Application's configuration file (see below)