We are having consistent issues with your
"patches"
 
Numerous changes happen on websites to just have your patches do nothing more than "over write" pages already on the web installs.
 
Please start issuing small . programs that will install the correct script lines inside the pages needed as a true patch and not this just copy over the page in your directory this is a nightmare for time consumption because the pages already may have changes already done on them, and your just over right it over write it all!!

Please see http://www.viart.com/php_modification.html which may help a little for blocks. There is also an idea for a global solution on the page but at least we have a start

watching this with interest

Please read our v.4.0.7 release article, the section "New 'blocks_custom' folder", it is at the very bottom of the page:
http://www.viart.com/viart_shop_v.4.0.7_released.html
 
Regards,
ViArt Team

Gizar, understand your frustration here. Yes, your solution would be ideal. Another option would be to provide the new files, and also a changelog that lists the changes in each file, so that those with a lot of customizations can just add the new code into their files.
 
This is what another cart I used did, and it worked just fine for us. Upgrades went smoothly, and I rarely had to contact support.

Customized local versions of php and html files are never going to be easy to update or patch unless the 'customizer' is willing to use something like a change log, and that in itself can be a chore if many lines change.
 
I've tried to avoid modifying scripts and templates for that reason, and it's been a reasonably good approach. I'm going to try out the new blocks_custom folder, which seems like a good idea. Of course you would not want to modify the 'custom_blocks' scripts themselves directly...