Emulator

What's the problem? Describe what went wrong in few words.
Dolphin places "Wii" folder outside of the "User" folder

What did you expect to happen instead?
Dolphin should properly place every folder into the "User" folder

What steps will reproduce the problem?

1. add portable.txt beside Dolphin.exe
2. run and exit Dolphin
3. look wherever you have Dolphin installed, every folder will be inside "User" except for "Wii"

Dolphin 3.5 and 3.5-367 are old versions of Dolphin that have
known issues and bugs, so don't report issues about them and test the
latest Dolphin version first.
Which versions of Dolphin did you test on?
4.0-7320

Is there any other relevant information? (e.g. logs, screenshots,
configuration files)
the Wii folder appears to be an entirely new folder that is created every time you start Dolphin. if you place your existing Wii folder inside "User", and repeat the steps above, a new Wii folder is made every time.