I’ve updated to Mv3. I don’t see a packages folder:
But if I do “Meteor list” in the terminal, I see packages:
Where did that packages folder go? 
I think they are here:
~/.meteor/packages
If someone can confirm, I will mark this as solved.
I think you are conflating two things here. First you have the packages files in .meteor, that one lists what Meteor packages are being used and all the stuff related to that.
packages folder in your app root is folder where you put Meteor packages code that are then used over anything else that you might pull from Atmosphere or for you to have local/private packages. I personally often used it to debug issues in packages or develop new ones.
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