I tried
stack setup --upgrade-cabal
in a project directory (that has stack.yaml with (default) system-ghc: true). It failed with
/opt/ghc/stable/new-cabal: createDirectory: permission denied (Permission denied)
That was unexpected. I think it should not want to do that.
$ which ghc
/opt/ghc/stable/bin/ghc
$ stack --version
Version 1.0.4.3 x86_64