Add native Windows compatibility for config, bootstrap, and CLI.

Support profile-based config resolution with auto-selection of a sole profile,
native IPA.exe -n bootstrap on Windows, platform-aware process cleanup, and
Windows-friendly userdata backup path inference.

Co-authored-by: Cursor <cursoragent@cursor.com>

src/plugin_helper/cli.py

@@ -61,6 +61,8 @@ def print_updates(report: dict[str, Any]) -> None:
 
 def _add_common(parser: argparse.ArgumentParser, *, suppress_default: bool = False) -> None:
     default = argparse.SUPPRESS if suppress_default else None
+    parser.add_argument("--config", default=default, help="plugin-helper config TOML path")
+    parser.add_argument("--profile", default=default, help="Config profile id from [[profiles]]")
     parser.add_argument("--instances-root", default=default, help="BSManager instances root")
     parser.add_argument("--state-dir", default=default, help="plugin-helper state directory")
 
@@ -120,13 +122,14 @@ def build_parser() -> argparse.ArgumentParser:
 
     bootstrap = subcommands.add_parser(
         "bootstrap",
-        help="Install locked BSIPA, run IPA.exe -n through Proton, and record bootstrap files",
+        help="Install locked BSIPA, run IPA.exe -n, and record bootstrap files",
         parents=[_common_parent()],
     )
     bootstrap.add_argument("--instance", required=True)
     bootstrap.add_argument("--registry", default="registry/plugins.toml")
     bootstrap.add_argument("--lockfile")
-    bootstrap.add_argument("--proton", help="Path to Proton executable")
+    bootstrap.add_argument("--proton", help="Path to Proton executable (Linux/Proton installs)")
+    bootstrap.add_argument("--native", action="store_true", help="Run IPA.exe -n natively instead of through Proton")
     bootstrap.add_argument("--json", action="store_true", help="Print full JSON bootstrap output")
 
     bootstrap_check = subcommands.add_parser(
@@ -282,6 +285,8 @@ def run(argv: list[str] | None = None) -> int:
         runtime = resolve_runtime_config(
             instances_root_value=getattr(args, "instances_root", None),
             state_dir_value=getattr(args, "state_dir", None),
+            config_path_value=getattr(args, "config", None),
+            profile_id=getattr(args, "profile", None),
         )
         inst_roots = runtime.instances_roots
         st_root = runtime.state_root
@@ -409,6 +414,7 @@ def run(argv: list[str] | None = None) -> int:
                 state_root=st_root,
                 repo_root=root,
                 proton=Path(args.proton).expanduser() if args.proton else None,
+                native=True if args.native else None,
                 progress=lambda message: print(f"  {message}", flush=True),
             )
             if args.json: