Should be explained by the question. System-Plugins (like toc, code macro and so on) suddenly show up as "User-Installed" after upgrading them via UPM. Is this behaviour wanted? If that's so, it's very annoying (you'll get a VERY long list of plugins and really have to be careful, which (true user installed) plugins can be removed without danger. See Screenshots for further details...
This is an artifact of how the underlying plugins system treats upgrades to system plugins. It's a bit unfortunate, but there's not much we can do about it.
On the other hand, there are very few system plugins that are updatable via the UPM. Many of these plugins are upgraded with the underlying application.
We are splitting our big plugin into modules and we have created an OBR with the main plugin plus two bundled "system plugins". The bundled "system plugins" are correctly identified as "system plugins" when I run locally on my development machine (atlas-debug) but they are shown as user-installed when I upgrade/install with the UPM.
Can I somehow mark my bundled plugins as "system plugins" or is this something that we have to live with?
I totally agree with Dominic that this is not very user friendly.
Well ... we now have 10 "User Installed" plugins showing up, which are actually system plugins - including the UPM. This reduces the good UPM overview, you should consider changing this behavior or at least add a note to the system plugins name (so they don't get deactivated or removed by accident) - like an Atlassian logo or something (see the screenshot).
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