Restored from backup with Migration Assistant - now have many folders at root level?

[dnanian]

The problem is that your UID/User ID might be different on the new volume than it was on the old one. For other users who might be reading this -- do not do it this way. Migrate when first prompted to "Copy from another Mac" during the first boot after install.

Anyway, I don't know why these folders would become visible on you, especially since you just migrated, and never ran SuperDuper at all (not that running SuperDuper! would do this).

You can set a 'hidden' attribute for each folder if you have the Developer Tools installed. If so, use

sudo SetFile -a v path-to-the-file

That removes the 'visible' attribute from the file you specify.