Repository file structure is using the following layout:
/setup/: development utilities (e.g. configuration & deployment)/src/: deployable code (that should be copied to your web server)/src/engine/: core file shared (included) with most other components/src/entity/: entity classes persisted in database (a.k.a MVC "models")/src/library/: third-party PHP libraries/src/page/: request handlers holding business logic (a.k.a MVC "controllers")/src/resource/: resource files used by code but not served directly/src/static/: static files served directly by HTTP server/src/storage/: read-write data (e.g. logs, caches, etc.)
/test/: functional tests
When looking at the codebase for the first time, a good idea is probably to
look at /src/route.php file that contains every route (URL path patterns)
accepted by the website and pointers to the request handler associated to it
(within /src/page/ directory). What the /src/index.php entry point does is
basically instantiate and configure core files (from /src/engine/), then look
for a route maching URL from input HTTP request and invoke associated request
handler to process it.
PHP source code is following PSR-2 style guide.
Unless your patch is trivial, please consider opening a GitHub issue to discuss the change you'd like to submit before opening a pull request.