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Has anyone been able to successfully tinker with quests in FO4 edit?


seekingthesun

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Spoilers for "human error" quest below, though it really sucks

One thing I want to do is try to fix how horrible the quest "Human Error" is(well also the end of the main quest, for the same reasons). 
 There's a lot wrong with it, people are able to know things that they shouldn't. But my main beef is the fact that there's no good ending.
 I'm okay with choosing between competing shades of grey but in the whole quest is contrived to make the decision between two different crimes against humanity. 
Either you let them continue torturing people, OR you have to kill everyone in HQ and Covenant.

So, I've been trying to tinker with the files and first I've been trying to stay away from scripts
 because they are really esoteric and vague, the way they're written.  
I want to make Covenant NPCs not turn hostile after you kill Chambers and free Amelia. 

Things I've tried
1. Successfully was able to remove some NPCs from "Covenant Faction"
 I figured that maybe that faction was set to hostile. Now, it's possible that there's remaining faction code somewhere in fallout.esm but I can't find it.
2. I've tried to change values like their aggression and confidence to as low as possible. They still attack.
3. I've gone through MS17 and removed entries for the hostile quest ending. (though maybe I'd have to start the whole quest over, i'll try that next) and also added the flag for completing the quest to right after you speak with Chambers. 
4. I've tried swapping entries for the two endings, which strangely did work in some ways like pip-boy entries but covenant was still hostile. 

The key piece must be either in some other archive or the relevant triggers are super obscure, or are labeled "unknown"

Can anyone help me identify the anatomy of a quest?
Edited by seekingthesun
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