Warning: Do not wipe out the Brotherhood too early.
I ran into a game breaking bug https://steamcommunity.com/app/377160/discussions/0/496881136908929369/ forcing me to either kill Desdemona or Father to be able to move forward, abandoning underground undercover. Luckily I had a save just before wiping out the Brotherhood. I killed them just before going to the Mass Fusion building on the quest that forces you to side with either the Brotherhood or the Institute.
The problem is, that if the Brotherhood is already gone the railroad quest line breaks. 'Fixing' it by wiping out the railroad to continue somehow revives the Brotherhood for the final Institute mission.
Anyway, I finished the game in 1 path, siding with the institute, definitely not in the way I wanted. So now I'm following the other paths by keeping the saves apart. I hope there is still a satisfactory ending in there somewhere after this much time invested.
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