Magento

It would be nice to have an option
to upgrade in the future with migration the new files to the old.

Ive now copyed the new files inside the the same directory as the old files,
so deleted files will stay, or i have to clean everything and start all over. this would be a shame

A more handy upgrade solution would be nice, to not undo any file changes that have been made.

Thanks

Upgrading will be possible in the future regardless of the customizations. This is an important part of Magento.