Create upgrade installation

Hello,
Is there any documentation about how to create upgrade installation?
I tried with version numbers but I get a message about ovewriting files in the location.
Upgrade package shoul avoid such messages.
Thanks

You can configure the package to always overwrite files in case of an upgrade.

Now, I am getting a message that files are going to be overwritten. How to setup the package to avoid these messages?

Here:

Great, Thank’s for your help