Please do not skip my question due to its length and also please read it completely so that you can know why I am stuck.

My problem in short : How/Where I can learn the structure of a real world Java web application with sample code and explanation

My problem in details : I know basics things like inheritance, logging , MVC etc. I have completed programming tutorials on these topics, but only after I started to do
some maintenance work of an application of a real world company, I realised that these basics and other things need to be properly and efficiently organised in an application. That application
have code for automatically loging the values that are send to data base for debugging purpose, code for automatically loading different property files in different environments and
code for other similar non business but essential functionalities that I do not even know exist in the application. All that kind of codes for that application were already done and since it
was a maintenance project I only had to add new pages, so I did not know how these functionalities were implemented and what other similar non business functionalities exists
in the application.

Could you please let me know, Which book/tutorial/git hub/Video I have to learn to understand what non business functionalities needs to be present in a real world web application
and how that should be put together. I would like to see complete code for a small dummy application with all these codes with explanation that I can download and go through
each class by class to understand all these.

Can I call this architecture of the application or should I refer it as architecture of application at micro level ?

PS: I quit the company due to some personal reasons 🙁 so I do not have access to that code anymore. That is why I can not refer the code, Also when the code was handed over to us for maintenance, it was already in a completed state and these functionalities and structure were already coded so not even the senior most person in our team know what kind of functionalities are there in the application and how those are organised and implemented. We just add new pages and fix if something breaks.

Thanks