Hi Brian, MoI shouldn't have put any commands at all in the appdata commands folder, all those would have gotten there from you copying them in there.
It's intended that the stock commands are not in appdata, they are intended to be in the old install directory commands folder. That's so that if any of them are updated with some new features you will get them along with the new install.
When you run a command and the same command is present in both the install commands dir and the appdata commands dir, the install one will take precedence.
So it doesn't do any actual harm to have them additionally in the appdata dir though.
Hope that's what you were asking about!
- Michael
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