Updating a hard-coded customized Piwik (no replies)

Hello,
I have a suggestion, or rather a question: how can I update Piwik without losing all the customization i made? For sure I am not the only one in this situation.

For instance, after any update I need to re-do all the files i modified. In my case it is about the live plugin (i have a custom controller.php because i want the visitors of "today" starting with midnight like google analytics, not last 24 hours; i have custom images for my pages; and i have a custom getLastVisitsStart.twig with lots of modifications).

Is there any way to update Piwik without worrying about this? Most of the times i manually compare my custom template with fresh-installed one and add/modify the lines. But I have come to the conclusion that these particularly files i talk about rarely modify in core, if at all. Maybe dont try to upload a new file on server if it was not modified between piwik versions? Is there a way to do that in my end? Same goes for the images.

I tried removing writing permission on the live plugin folder on my server, but it is not working, it resets itself to 777.