Yii's by-default directory organization works well enough, but there are several steps one can take that improve the security and serviceability of the system, especially in the context of multiple Yii projects on the same machine (including multiple versions of the same project).
I installed phpseclib because I needed to do some AES encryption in my project. After all the hassle of installing php lib, I found out that Yii already has a security module (securityManager). I finally decided to keep using phpseclib because it has one big advantage over Yii securityManager module, it does not requite mcrypt to be installed in the phpserver!
Relational databases do not support inheritance so if we need to represent it, we have to somehow store meta info while keeping performance by minimizing JOINs. One way to solve this problem is using single table inheritance. All fields for the whole class tree are stored in a single table. Class name is stored in the type field of the same table.