GamingDaemon

I have proven that the solution below works!! https://www.reddit.com/r/fo4/comments/3x62lk/found_a_way_to_fix_supply_lines_for_nonexistant/

Asking for some clarification... I use NMM so I load it up and check and all the mods have a green check. I go to the upper left and Launch Fallout4. NMM goes away and the FO4 Play\Option\Support comes up. I then open NMM again and they are all green still.. i start the game and none of my mods are working. Did I miss something simple? Are you looking at the Mods tab, or the Plugins tab. Make sure you click at the top-left on the Plugins tab, and you will see that they are disabled.