Running LOOT through MO reactivates deactivated plugins

[swiftfoxmark2]

Whenever I run LOOT, Mod Organizer reactivates the plugins I deactivated.  Those plugins were deactivated because they were merged into my bashed patch.

[tjax323]

That is happening. It is a bug on the MO2 github. I opened it myself, and I received confirmation of it a few days later.