I understand that you have a small time tracking app, but that is not going to jibe with Time trex other than they both offer some level of time tracking.
If what you are saying is that you are trying to understand the time tracking app you had built, then we would need to know more about that specific application. There isn't a universal way these things work.
If the app was built with a specific framework, then there are frequently tell tale signs of that, but we can't guess.
Obviously you want to start with an index.php assuming that exists. What does that include/require and where does it go from there. Are there rewrite rules that come with it?
Most well built web apps have some form of MVC pattern, so there's typically a controller, with separate db model classes and views/templates that are loaded as needed by the controller.