Are mu-plugins plugins still deployed via wordpress.org/plugins?

No, mu-plugins cannot be updated from wordpress.org. When you submit a plugin to that repository, it will be available as a regular plugin only. You can ask your users to isntall it as a mu-plugin, but they will not receive updates then.

The “other code” should be written in a way that it doesn’t do anything when your plugin is disabled. This is much better than using the mu-plugins directory.

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