Put functional tests in tests/functional

I think it is bad for these reasons when `tests/` contains a mix of
functional and integration tests

 - Concepts is harder to understand, the documentation makes a good
   unit vs functional vs integration distinction, but when the
   integration tests are just two subdirs within `tests/` this is not
   clear.

 - Source filtering in the `flake.nix` is more complex. We need to
   filter out some of the dirs from `tests/`, rather than simply pick
   the dirs we want and take all of them. This is a good sign the
   structure of what we are trying to do is not matching the structure
   of the files.

With this change we have a clean:
```shell-session
$ git show 'HEAD:tests'
tree HEAD:tests

functional/
installer/
nixos/
```

tests/functional/check-refs.nix

@@ -0,0 +1,77 @@
+with import ./config.nix;
+
+rec {
+
+  dep = import ./dependencies.nix {};
+
+  makeTest = nr: args: mkDerivation ({
+    name = "check-refs-" + toString nr;
+  } // args);
+
+  src = builtins.toFile "aux-ref" "bla bla";
+
+  test1 = makeTest 1 {
+    builder = builtins.toFile "builder.sh" "mkdir $out; ln -s $dep $out/link";
+    inherit dep;
+  };
+
+  test2 = makeTest 2 {
+    builder = builtins.toFile "builder.sh" "mkdir $out; ln -s ${src} $out/link";
+    inherit dep;
+  };
+
+  test3 = makeTest 3 {
+    builder = builtins.toFile "builder.sh" "mkdir $out; ln -s $dep $out/link";
+    allowedReferences = [];
+    inherit dep;
+  };
+
+  test4 = makeTest 4 {
+    builder = builtins.toFile "builder.sh" "mkdir $out; ln -s $dep $out/link";
+    allowedReferences = [dep];
+    inherit dep;
+  };
+
+  test5 = makeTest 5 {
+    builder = builtins.toFile "builder.sh" "mkdir $out";
+    allowedReferences = [];
+    inherit dep;
+  };
+
+  test6 = makeTest 6 {
+    builder = builtins.toFile "builder.sh" "mkdir $out; ln -s $out $out/link";
+    allowedReferences = [];
+    inherit dep;
+  };
+
+  test7 = makeTest 7 {
+    builder = builtins.toFile "builder.sh" "mkdir $out; ln -s $out $out/link";
+    allowedReferences = ["out"];
+    inherit dep;
+  };
+
+  test8 = makeTest 8 {
+    builder = builtins.toFile "builder.sh" "mkdir $out; ln -s ${test1} $out/link";
+    inherit dep;
+  };
+
+  test9 = makeTest 9 {
+    builder = builtins.toFile "builder.sh" "mkdir $out; ln -s $dep $out/link";
+    inherit dep;
+    disallowedReferences = [dep];
+  };
+
+  test10 = makeTest 10 {
+    builder = builtins.toFile "builder.sh" "mkdir $out; echo $test5; ln -s $dep $out/link";
+    inherit dep test5;
+    disallowedReferences = [test5];
+  };
+
+  test11 = makeTest 11 {
+    __structuredAttrs = true;
+    unsafeDiscardReferences.out = true;
+    outputChecks.out.allowedReferences = [];
+    buildCommand = ''echo ${dep} > "''${outputs[out]}"'';
+  };
+
+}