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In my truffle project I have around 10 contracts. I have created a deployment script, but I also need to initialize the contracts further. EG. Transfer some funds into certain contracts and setup my registry contract with the addresses of the other contracts.

What is the best practice for this? Should I include this setup code in my deployment script in the migration folder? I'm assuming there's a better option I'm just not aware of.

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I think nothing stops you from doing this in the deploy contracts script. As for best practice, I don't know if there is even a better option, so maybe best practice is not an issue

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