Plutonium

I'm confused about this as well. The only mods I can get working are the ones that go in the mods folder and are activated from the in-game menu. Only the alpha versions of Reimagined work for me so I can't load another mod with it. Did plutonium change how mods are read and they have to be from the mods folder now? Anything I put in scripts doesn't seem to do what it's supposed to. I feel like I'm missing key information that I can't find anywhere