clan-lib: Move nix_options from Machine class to Flake class

pkgs/clan-cli/clan_cli/tests/helpers/cli.py

@@ -2,7 +2,7 @@ import argparse
 import logging
 import shlex
 
-from clan_cli import create_parser
+from clan_cli import create_flake_from_args, create_parser
 from clan_lib.custom_logger import print_trace
 
 log = logging.getLogger(__name__)
@@ -13,6 +13,10 @@ def run(args: list[str]) -> argparse.Namespace:
     parsed = parser.parse_args(args)
     cmd = shlex.join(["clan", *args])
 
+    # Convert flake path to Flake object with nix_options if flake argument exists
+    if hasattr(parsed, "flake") and parsed.flake is not None:
+        parsed.flake = create_flake_from_args(parsed)
+
     print_trace(f"$ {cmd}", log, "localhost")
     if hasattr(parsed, "func"):
         parsed.func(parsed)