Upgrade OC 2.0.1.1 to 2.1.0.1 by keeping all customization

Hello everyone,
I am currently using OC 2.0.1.1 and want to upgrade to latest version OC 2.1.0.1.
In my current OC 2.0.1.1, I have made changes in core files as well as in template and like to make these in OC 2.1.0.1.

By replacing all respective files is one option. But what if I want to upgrade next time?
This will again need same time. And this is very lengthy process.
Is there any process or script or any other way, to upgrade by keeping all customization?

Even I tried using system/modification folder, but whenever I install new extension, unfortunately I lose all changes from the files present in modification folder.
So, every time I have to keep doing changes whenever new extension is installed.

So, is there any simple & easy way to upgrade OC to latest & stable version?
And How to do customization in OC?

Thanks in advance!!