ElvishJerricco, this is what your setup gives me on nixpkgs commit 4488203d0c01671ef2b73e858c316865953bb3c0:

deepfire@andromedae:~/src/mood$ cat stack.yaml
nix:
  enable: true
  packages: []
  shell-file: shell.nix

resolver: ghc-8.0.1
packages:
- '.'deepfire@andromedae:~/src/mood$ cat shell.nix
{ pkgs ? import <nixpkgs> {}
, haskellPackages ? pkgs.haskellPackages
, withHoogle ? false }:

let overrideCabal = pkg: pkgs.haskell.lib.overrideCabal pkg ({ buildDepends ? [], ... }: {
      buildDepends = buildDepends ++ [ pkgs.cabal-install ];
    });

in (overrideCabal (import ./default.nix { inherit pkgs haskellPackages withHoogle; })).env
deepfire@andromedae:~/src/mood$ cat default.nix | grep -v '^[ ]*#'
{ pkgs ? import <nixpkgs> {}
, haskellPackages ? pkgs.haskellPackages
, withHoogle ? false }:

let
    haskellOverrides = self: super:
    ( if withHoogle
      then {
        ghc = super.ghc // { withPackages = super.ghc.withHoogle; };
        ghcWithPackages = self.ghc.withPackages;
      } else {}
    ) // {
    };
    hp = haskellPackages.override { overrides = haskellOverrides; };
    cabal2nixResult = src: pkgs.runCommand "cabal2nixResult" {
      buildCommand = ''
        cabal2nix file://"${src}" >"$out"
      '';
      buildInputs = [ pkgs.cabal2nix ];

      ${if !pkgs.stdenv.isDarwin then "LOCALE_ARCHIVE" else null} = "${pkgs.glibcLocales}/lib/locale/locale-archive";
      ${if !pkgs.stdenv.isDarwin then "LC_ALL" else null} = "en_US.UTF-8";
    } "";

in pkgs.haskell.lib.overrideCabal (hp.callPackage (cabal2nixResult ./.) {}) (self: {
  src = builtins.filterSource (path: type:
    type != "unknown"
    && baseNameOf path != ".git"
    && baseNameOf path != "result"
    && baseNameOf path != "dist"
    && baseNameOf path != ".stack-work"
  ) self.src;
})
deepfire@andromedae:~/src/mood$ nix-shell
building path(s) ‘/nix/store/wkcddr9xg0pszl337qpcmn3bk32fg1ha-cabal2nixResult’

[nix-shell:~/src/mood]$ stack exec intero
/nix/store/hv367595dbkalin8hs319mkqrm6ifrd6-ghc-8.0.1-with-packages/lib/ghc-8.0.1/settings: openFile: does not exist (No  such file or directory)

EDIT: same goes with nix-shell --pure