sabayon-apply is run as the user itself, so running sabayon-apply as
sudo would, of course, apply the profile to root.

sabayon-apply doesn't do anything wierd, it just didn't do what you
expected it to do.  I'll look at fleshing out the manpage a bit more
upstream.

** Changed in: sabayon (Ubuntu)
       Status: New => Confirmed

** Changed in: sabayon (Ubuntu)
   Importance: Undecided => Wishlist

** Changed in: sabayon (Ubuntu)
     Assignee: (unassigned) => Scott Balneaves (sbalneav)

-- 
sabayon-apply hosed my system due to inadequate documentation
https://bugs.launchpad.net/bugs/592489
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