Unnecessary configuring on (almost?) any file change

I've noticed that almost any time I have a file change in a project, `stack build` will run the Cabal configure step, slowing down compilations. I've traced this down to some issue with `stack-setup-config-mod`, and it appears that the file we're checking for dirtiness does not exist, triggering regular rebuilds.

I did a blame, and I think this comes down to this commit:

https://github.com/commercialhaskell/stack/commit/681ca331609e555d62e9aacbbc18770f81abd8de

It looks to me like `stack-setup-config-mod` is never being created in this commit. If I'm not mistaken, we need to add an equivalent to the `writeCabalMod` call that appears in this module.

CC @qrilka, I can take a stab at a PR, but input on this would be appreciated.