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/flakes/flake-in-submodule.sh

@@ -0,0 +1,52 @@
+source common.sh
+
+# Tests that:
+# - flake.nix may reside inside of a git submodule
+# - the flake can access content outside of the submodule
+#
+#   rootRepo
+#   ├── root.nix
+#   └── submodule
+#       ├── flake.nix
+#       └── sub.nix
+
+
+requireGit
+
+clearStore
+
+# Submodules can't be fetched locally by default.
+# See fetchGitSubmodules.sh
+export XDG_CONFIG_HOME=$TEST_HOME/.config
+git config --global protocol.file.allow always
+
+
+rootRepo=$TEST_ROOT/rootRepo
+subRepo=$TEST_ROOT/submodule
+
+
+createGitRepo $subRepo
+cat > $subRepo/flake.nix <<EOF
+{
+    outputs = { self }: {
+        sub = import ./sub.nix;
+        root = import ../root.nix;
+    };
+}
+EOF
+echo '"expression in submodule"' > $subRepo/sub.nix
+git -C $subRepo add flake.nix sub.nix
+git -C $subRepo commit -m Initial
+
+createGitRepo $rootRepo
+
+git -C $rootRepo submodule init
+git -C $rootRepo submodule add $subRepo submodule
+echo '"expression in root repo"' > $rootRepo/root.nix
+git -C $rootRepo add root.nix
+git -C $rootRepo commit -m "Add root.nix"
+
+# Flake can live inside a submodule and can be accessed via ?dir=submodule
+[[ $(nix eval --json git+file://$rootRepo\?submodules=1\&dir=submodule#sub ) = '"expression in submodule"' ]]
+# The flake can access content outside of the submodule
+[[ $(nix eval --json git+file://$rootRepo\?submodules=1\&dir=submodule#root ) = '"expression in root repo"' ]]