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.
I recently had to have a checkbox column in my grid view that supported the 'disabled' attribute. This was easy enough to do by extending the CCheckBoxColumn. However, I also wanted the checkbox to be selected when clicking on the table's row (supported via CGridView's selectableRows option). I discovered I had to tweak yiigridview.js so that it would not select disabled rows when clicking on it or on the 'select all' checkbox.