Using CodeIgniter as git submodule . . .

You didn't understood what I want.

It is not about modifying system classes. Let's explain once again.

Now I have application/ folder with all subdirectories.
Let's show an example. In library, helper, ... folder, I have these like classes:
../application/library/Cond.php
../application/library/Form.php
../application/helpers/Debug.php
All classes are reusable in more projects and have almost nothing to do with system classes. Typical way is to copy those classes to another application/ folder in another project. But ... If I make even a little change in those classes, I will have to copy them to all projects which uses them.

As you can see, it wil not help me to untrack CI except application in git or extending system classes. I need to keep my "advanced" codeigniter in one "repository" and use it in all webs as described (sorry about "advanced". I'm not arrogant. I just didn't find better word. :-D)