So I've been busy making lots of modifications to my views/models/controllers - came to test the app and got a blank screen. Nothing in the application.log file so must be a syntax error somewhere... But which file?
The article Fixing extensions without modifying their code reminded me of another patching technique that I used. My conviction and a hard look on the web had led me to an article Redefine PHP class methods or class giving me a head start to do what I wanted: patching third party code without touching the original to allow easy upgrades.
I found a standard Yii app's protected folder structure nearly perfect. With a few simple moves and a little bit change to the code, I managed to bring it to the level, which I found as fully perfect. I want to share my point of view, in case someone would like to use this structure as well.