@girish Oh, absolutely with a custom app, I mentioned in the original post that I'm going to build my own Wordpress Stack to simply and only add this. But I saw benefit to other user's being able to script something post-update as that's literally the only thing my stack will do differently than the default Wordpress app (I'll have to integrate your updates into my stack manually each time so I still wish there was a way to run an external custom sh script post-installation).
As you can see my custom script simply uses the CLI to upgrade all databases with any new required formatting if and only if any updated Wordpress core or updated plugin require it. When you update from the Cloudron interface, it simply updates all the files and Wordpress has this really annoying tendency to not upgrade the databases post-upgrade invisibly. The script above is the only way to make sure file versions and database versions stay in sync 100% of the time every update.
This becomes nearly unavoidable if you want to support multisite in the future since the problem becomes more convoluted in that installation type so my script detects multisite installations and runs database upgrades accordingly with WP CLI commands or single site only commands if it's a single site.
I actually think the script below should be an optional "automatic upgrade plugin and themes checkbox when updating Wordpress core" option for Wordpress installations as well, here's the WP CLI code for it:
# Plugin updates
wp plugin update --all
wp plugin update --all --skip-plugins --skip-themes
# Theme updates
wp theme update --all
wp theme update --all --skip-plugins --skip-themes