Start using Eloquent
In order to have a proper, changeable idea of the database we should start implementing an ORM. After some research I think Laravel and its tools is what we should settle for. Laravel utilizes an ORM called Eloquent, which seems to be usable without using Laravel itself, which makes a great opportunity to migrate slowly: https://www.cloudways.com/blog/eloquent-illuminate-in-php-without-laravel/