The good news is that the Fallout 4 1.2 patch is now in full release on Steam. The bad news, according to this Nexus Mods forum thread, is that intentionally or not, it breaks support for mods.
The patch makes the following changes:
New Features
Number pad keys can now be used for remapping (PC)
Remapping Activate now works on Quick Container (PC)
Fixes
General memory and stability improvements
Performance improvements inside the Corvega Assembly Plant
Optimizations to skinned decal rendering
Fixed issue with player becoming stuck in terminals
Fixed issue where equipped weapons become locked after completing Reunions
Fixed issue with "When Freedom Calls" where the quest would not complete
During "Confidence Man" fixed issue where player's health would continuously regenerate
Fixed crash related to jumping into water and reloading saved games
Fixed issue where Launcher would not save God Rays Quality setting properly (PC)
But the patch also adds a new launcher that disables mods on startup, and the .INI edit that previously got around this limitation no longer works. There is a fix, but it's not the most streamlined process ever: You'll need to launch the Nexus Mod Manager, then launch Fallout 4, then switch back to the NMM and re-enable mods, then go back to Fallout 4 and do your thing.
A patch-compatible version of the Fallout 4 Script Extender has also been released, but it too will require a certain amount of dicking around to get things done, and also relies on the Nexus Mod Manager to operate. Even with support re-enabled, it sounds like some mods aren't working properly, although it's still a bit hazy at this point since the patch is so new. I've reached out to Bethesda to find out what's going on, and I'll let you know when I hear back.