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We'll " it depends" (-:
I assume you are talking about the msi package and not .NET core.
We are using native tools like SCCM (Windows) and RedHat Satelite (Linux), to provision a new version twice a year. Sadly though it requires an IIS restart/reset which will mean downtime. So would have to make sure that the package you deploy also does that. Apart from that our windows SME's seems happy abbout the way the msi is packaged. An upgrade *should* not mess with the XML config file.
Unlike other vendors AppD does not have a solid auto upgrade feature built in.
Sure you want to go 4.5.12 and not 4.5.16?
For .NET core (I mean without framework) you have to include the agent in the build process of your application. Ther's no "real" installation task.
As for the upgrade process it's pretty straight forward. Just chose upgrade. all of AppD's agents can be installed as upgrades on pretty most any previous version. If you have really really old agents there might be issues since I remember that they changed the config from web.config to it's own xml config file but that was a long time ago.