SIP

If there is a newer version of a plugin available how do I install it?

As far as I can see UPDATE ENABLED only enables/disables plugins by changing the .py file permissions. So the only way is to uninstall the plugin and reinstall it, losing the setting in the process.

In plugin_manager.py should update_plugins() not call install_plugins() one way or another?

Another option might be to have three separate functions Enable/Disable, Update and Uninstall

You can just install the new version over the existing one and not loose settings.

So simple, I'm embarrassed