refactor: decouple vars stores from machine instances

Stores now get machine context from generator objects instead of storing
it internally. This enables future machine-independent generators and
reduces coupling.

- StoreBase.__init__ only takes flake parameter
- Store methods receive machine as explicit parameter
- Fixed all callers to pass machine context

pkgs/clan-cli/clan_cli/vars/check.py

@@ -65,6 +65,7 @@ def vars_status(
                     missing_secret_vars.append(file)
                 else:
                     msg = machine.secret_vars_store.health_check(
+                        machine=machine.name,
                         generator=generator,
                         file_name=file.name,
                     )