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That's not a bad thing just the clutter. This makes all leaders addons compatible with each others. Don't worry, when you assign a version of a leader to a settlement, all other versions should be unavailable for other settlements
No, you will still need to build a tool and die shop where you want level 4 farms, the effects are not global. And buildings still need to go through upgrade stages. You just don't need dependencies anymore, like the hazmat for nuclear enrichment
Donation is used if you have a deficit of food or water in your network and can't supply enough food/water for your settlers. Vanilla behavior is they take a happiness loss. When a city produces water/food it deposit any excess in your workbench for you to do whatever with them. If at one point...
The scrap collection is good if you don't want to hit the scrap limit (at which point no scrap is added anymore).
As for local industry, none uses items by default, they only produce. Only advanced industrial can use it but it requires you to place the products back into their stockpile...
Try a quest reset. Search for ID with:
help "medical research" 4
then
ResetQuest id
Make a save in case something goes wrong
Then go refresh a plot and the quest should start again as you enter
If you are in pc just do a help infused 4 in console and player.additem into your inventory. I also got it on a few other recipes but can't remember which.
Update: I've been messing around with stuff and decided to change the leader, I had Blake Abernathy from a mod, Ted's Leaders I think, he had the Lifebringer thing that gives +2 food to farms (basically all my farms gave me 1 less food, eg a level 1 farm gave 3 food when it should be 4, 2+2)
I...
I had the same problem and It just hit me again after I installed Uncapped Settlement Surplus. I don't know why or how, I played a 60 hour save without this ever occurring (without USS), yesterday decided to give USS a try again and today my level 1 farms produce 1 food. It's too big of a...