What is the best way to change PHP ini values when provisioning a Homestead box?
E.g. I want to change the value of display_startup_errors to On.
Would you find/replace the value in the php.ini file using sed?
Do I just put the commands in after.sh or is it better to use config.vm.provision "shell"?
Do this with sed via after.sh. That's exactly what that script is for. That way you don't have to worry about changing any files that Homestead may overwrite in a future update.