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/common.sh

@@ -0,0 +1,70 @@
+source ../common.sh
+
+registry=$TEST_ROOT/registry.json
+
+writeSimpleFlake() {
+    local flakeDir="$1"
+    cat > $flakeDir/flake.nix <<EOF
+{
+  description = "Bla bla";
+
+  outputs = inputs: rec {
+    packages.$system = rec {
+      foo = import ./simple.nix;
+      default = foo;
+    };
+    packages.someOtherSystem = rec {
+      foo = import ./simple.nix;
+      default = foo;
+    };
+
+    # To test "nix flake init".
+    legacyPackages.$system.hello = import ./simple.nix;
+  };
+}
+EOF
+
+    cp ../simple.nix ../simple.builder.sh ../config.nix $flakeDir/
+}
+
+createSimpleGitFlake() {
+    local flakeDir="$1"
+    writeSimpleFlake $flakeDir
+    git -C $flakeDir add flake.nix simple.nix simple.builder.sh config.nix
+    git -C $flakeDir commit -m 'Initial'
+}
+
+writeDependentFlake() {
+    local flakeDir="$1"
+    cat > $flakeDir/flake.nix <<EOF
+{
+  outputs = { self, flake1 }: {
+    packages.$system.default = flake1.packages.$system.default;
+    expr = assert builtins.pathExists ./flake.lock; 123;
+  };
+}
+EOF
+}
+
+writeTrivialFlake() {
+    local flakeDir="$1"
+    cat > $flakeDir/flake.nix <<EOF
+{
+  outputs = { self }: {
+    expr = 123;
+  };
+}
+EOF
+}
+
+createGitRepo() {
+    local repo="$1"
+    local extraArgs="${2-}"
+
+    rm -rf "$repo" "$repo".tmp
+    mkdir -p "$repo"
+
+    git -C "$repo" init $extraArgs
+    git -C "$repo" config user.email "foobar@example.com"
+    git -C "$repo" config user.name "Foobar"
+}