mkosi: Move all mkosi configuration into mkosi/ subdirectory

Now that mkosi can automatically pick up its main configuration from
a mkosi/ subdirectory if it exists and there is no configuration in the
top level directory, let's make use of it  to reduce the amount of clutter
in the top level directory of the repository.

This will also make it easier to install the mkosi configuration files as
part of the testing packages later on.

tools/fetch-distro.py

@@ -126,7 +126,7 @@ def update_distro(args, distro: str, config: dict):
     print(f"+ {shlex.join(cmd)}")
     changes = subprocess.check_output(cmd, text=True).strip()
 
-    conf_dir = Path('mkosi.conf.d')
+    conf_dir = Path('mkosi/mkosi.conf.d')
     files = conf_dir.glob('**/pkgenv.conf')
     for file in files:
         s = file.read_text()