From 1c24b4c6cb8ea6b534cd2314bd08dbb6cbd6e5c2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= <joerg@thalheim.io>
Date: Wed, 20 Aug 2025 16:16:17 +0200
Subject: [PATCH] S604: fix

---
 .../clan_cli/tests/fixtures_flakes.py         | 42 ++++++++++++++++---
 pkgs/clan-cli/clan_lib/ssh/remote_test.py     |  8 ++--
 2 files changed, 40 insertions(+), 10 deletions(-)

diff --git a/pkgs/clan-cli/clan_cli/tests/fixtures_flakes.py b/pkgs/clan-cli/clan_cli/tests/fixtures_flakes.py
index 9f15a4b94..c34b01b10 100644
--- a/pkgs/clan-cli/clan_cli/tests/fixtures_flakes.py
+++ b/pkgs/clan-cli/clan_cli/tests/fixtures_flakes.py
@@ -441,14 +441,44 @@ def writable_clan_core(
 
         # Copy all tracked and untracked files (excluding ignored)
         # Using git ls-files with -z for null-terminated output to handle filenames with spaces
-        sp.run(
-            f"(git ls-files -z; git ls-files -z --others --exclude-standard) | "
-            f"xargs -0 cp --parents -t {temp_flake}/",
-            shell=True,
-            cwd=clan_core,
-            check=True,
+
+        # Get tracked files
+        tracked_files = (
+            sp.run(
+                ["git", "ls-files", "-z"],
+                cwd=clan_core,
+                capture_output=True,
+                text=True,
+                check=True,
+            )
+            .stdout.rstrip("\0")
+            .split("\0")
         )
 
+        # Get untracked files (excluding ignored)
+        untracked_files = (
+            sp.run(
+                ["git", "ls-files", "-z", "--others", "--exclude-standard"],
+                cwd=clan_core,
+                capture_output=True,
+                text=True,
+                check=True,
+            )
+            .stdout.rstrip("\0")
+            .split("\0")
+        )
+
+        # Combine and filter out empty strings
+        all_files = [f for f in tracked_files + untracked_files if f]
+
+        # Copy files preserving directory structure
+        if all_files:
+            sp.run(
+                ["cp", "--parents", "-t", str(temp_flake), "--", *all_files],
+                cwd=clan_core,
+                check=True,
+            )
+
         # Copy .git directory to maintain git functionality
         if (clan_core / ".git").is_dir():
             shutil.copytree(
diff --git a/pkgs/clan-cli/clan_lib/ssh/remote_test.py b/pkgs/clan-cli/clan_lib/ssh/remote_test.py
index 40d93205b..9c4ec3f54 100644
--- a/pkgs/clan-cli/clan_lib/ssh/remote_test.py
+++ b/pkgs/clan-cli/clan_lib/ssh/remote_test.py
@@ -157,7 +157,7 @@ def test_run_environment(hosts: list[Remote], runtime: AsyncRuntime) -> None:
             None,
             host.run_local,
             ["echo $env_var"],
-            RunOpts(shell=True, log=Log.STDERR),
+            RunOpts(shell=True, log=Log.STDERR),  # noqa: S604
             extra_env={"env_var": "true"},
         )
     assert proc.wait().result.stdout == "true\n"
@@ -230,13 +230,13 @@ def test_run_exception(hosts: list[Remote], runtime: AsyncRuntime) -> None:
             None,
             host.run_local,
             ["exit 1"],
-            RunOpts(shell=True, check=False),
+            RunOpts(shell=True, check=False),  # noqa: S604
         )
     assert proc.wait().result.returncode == 1
 
     try:
         for host in hosts:
-            runtime.async_run(None, host.run_local, ["exit 1"], RunOpts(shell=True))
+            runtime.async_run(None, host.run_local, ["exit 1"], RunOpts(shell=True))  # noqa: S604
         runtime.join_all()
         runtime.check_all()
     except Exception:
@@ -248,7 +248,7 @@ def test_run_exception(hosts: list[Remote], runtime: AsyncRuntime) -> None:
 
 def test_run_function_exception(hosts: list[Remote], runtime: AsyncRuntime) -> None:
     def some_func(h: Remote) -> CmdOut:
-        return h.run_local(["exit 1"], RunOpts(shell=True))
+        return h.run_local(["exit 1"], RunOpts(shell=True))  # noqa: S604
 
     try:
         for host in hosts: