I upgraded from 1.2.4 -> 1.2.5 manually and it looks ok, the include option above (not in the docs) seems to do the database delete/update stuff for people who are wondering.
All that said, similar to the other manual process in the docs of just copying files, should we just copy over the version.php over from the latest Abantecart zip file so it doesn't alert us that we still need to upgrade? None of the docs show how to update that file (and one reason I was hesitant to do it manually in case I miss some stuff that's going on behind the scenes).
Lastly, if someone can answer, is it safe to assume that if I unzip the full install (abantecart_1.2.5.zip) and compare my live files to the files in this zip, as long as they are the same, I am good to go?
The auto package update thing hasn't worked well for me probably due to my changes and my hosting provider, but if this is pretty much key (matching the files up and just copying over version.php), then I will probably just do it this way moving forward...
Thanks for any clarification.