You should see in config/initializers/refinery/core.rb that there is a setting `config.plugin_priority`. Here, you can specify which plugins you would like to see appear first in the menu and all the other ones simply appear after it.
This is a change from version 2.x where we had an authentication system built in and could save this config against the user. In 3.x we extracted the authentication system and therefore there is no way for us to store this so we moved it to the initializer.
Here is the relevant change:
https://github.com/refinery/refinerycms/pull/3053