fix(hooks): run pre-commit pytest without git's repo-locating env

git exports GIT_DIR and GIT_INDEX_FILE to hooks. The pre-commit pytest
step inherited them, and tests/dev/test_gen_config_deploy.py's scratch
repos (git init --bare / clone / commit / push in tmp dirs) therefore
ran against the repository being committed to: on 2026-10-27 a commit
that staged infra files left its branch on nine "base / docs only / mc
config" commits by author `t`, swapped the index for the fixture's
tree, and wrote uploadpack.allowAnySHA1InWant into the .git/config that
every worktree shares. It only stopped there because `git push origin`
found no `origin` remote.

- sem.hooks: the pytest step gets the hook env minus GIT_DIR,
  GIT_INDEX_FILE, GIT_WORK_TREE, GIT_PREFIX, GIT_COMMON_DIR and the
  object-dir variables.
- test_gen_config_deploy: its git helper and detector runner drop all
  GIT_* from os.environ, so any wrapper that exports them is safe too.
- Regression test: a nested `git init` under a hook-style GIT_DIR lands
  in its own directory.

Refs #1365

src/sem/hooks.py

@@ -233,6 +233,27 @@ def compute_test_targets(
     return deduped, ", ".join(reasons) if reasons else "changed files"
 
 
+# Variables git exports to hooks that pin every nested git call to *this*
+# repository. Tests that build scratch repos in tmp dirs inherited them and
+# committed into the repo being committed to (and wrote its shared config).
+_HOOK_GIT_VARS = (
+    "GIT_DIR",
+    "GIT_INDEX_FILE",
+    "GIT_WORK_TREE",
+    "GIT_PREFIX",
+    "GIT_COMMON_DIR",
+    "GIT_OBJECT_DIRECTORY",
+    "GIT_ALTERNATE_OBJECT_DIRECTORIES",
+)
+
+
+def _test_env() -> dict[str, str]:
+    """The hook's environment minus git's repo-locating variables."""
+    import os
+
+    return {k: v for k, v in os.environ.items() if k not in _HOOK_GIT_VARS}
+
+
 def run_step(label: str, cmd: list[str], **kwargs) -> int:
     """Run a subprocess step, printing the label."""
     print(f"==> pre-commit: {label}")
@@ -318,6 +339,7 @@ def main() -> int:
             ["uv", "run", "python", "-m", "pytest"]
             + targets
             + ["--no-cov", "--tb=short", "-q", "-n", "auto"],
+            env=_test_env(),
         )
         if rc != 0:
             return rc

tests/dev/test_gen_config_deploy.py

@@ -104,9 +104,16 @@ def test_image_jobs_gate_on_changes_outputs_not_head_commit():
 # ── Behavioural: run the detector script against real git history ──────
 
 
+def _clean_env() -> dict[str, str]:
+    """os.environ without GIT_* — under a pre-commit hook GIT_DIR and
+    GIT_INDEX_FILE point at the real repo, and every scratch-repo command
+    here would commit into it instead."""
+    return {k: v for k, v in os.environ.items() if not k.startswith("GIT_")}
+
+
 def _git(*args: str, cwd: Path) -> str:
     env = {
-        **os.environ,
+        **_clean_env(),
         "GIT_AUTHOR_NAME": "t",
         "GIT_AUTHOR_EMAIL": "t@example.invalid",
         "GIT_COMMITTER_NAME": "t",
@@ -170,7 +177,7 @@ def _run_detector(checkout: Path, before: str, sha: str, tmp_path: Path) -> dict
         ["bash", "-e", "-c", step["run"]],
         cwd=checkout,
         env={
-            **os.environ,
+            **_clean_env(),
             "BEFORE": before,
             "GITHUB_SHA": sha,
             "GITHUB_OUTPUT": str(out_file),

tests/sem/test_hooks.py

@@ -9,6 +9,7 @@ from sem.hooks import (
     _changed_test_dirs,
     _classify,
     _staged_files,
+    _test_env,
     _top_level_tests,
     check_syntax,
     compute_test_targets,
@@ -195,6 +196,28 @@ class TestRunStep:
         assert rc == 1
 
 
+class TestTestEnv:
+    def test_strips_repo_locating_git_vars(self, monkeypatch):
+        monkeypatch.setenv("GIT_DIR", "/repo/.git")
+        monkeypatch.setenv("GIT_INDEX_FILE", "/repo/.git/index")
+        monkeypatch.setenv("GIT_AUTHOR_NAME", "kept")
+        env = _test_env()
+        assert "GIT_DIR" not in env
+        assert "GIT_INDEX_FILE" not in env
+        assert env["GIT_AUTHOR_NAME"] == "kept"
+
+    def test_nested_git_sees_its_own_repo(self, tmp_path, monkeypatch):
+        """Under a hook, `git init` in a tmp dir must not land in GIT_DIR."""
+        import subprocess
+
+        monkeypatch.setenv("GIT_DIR", str(tmp_path / "hooked.git"))
+        scratch = tmp_path / "scratch"
+        scratch.mkdir()
+        subprocess.run(["git", "init", "-q"], cwd=scratch, env=_test_env(), check=True)
+        assert (scratch / ".git").is_dir()
+        assert not (tmp_path / "hooked.git").exists()
+
+
 class TestMain:
     @patch("sem.hooks._staged_files", return_value=[])
     def test_no_staged_files_returns_zero(self, mock_staged):

tests/test_final_coverage_gaps.py

@@ -1470,7 +1470,7 @@ class TestSemHooksMainEntry:
         ):
             call_count = [0]
 
-            def step_side_effect(label, cmd):
+            def step_side_effect(label, cmd, **_kw):
                 call_count[0] += 1
                 if "notebook run" in label:
                     return 1  # line 348

tests/test_remaining_gaps.py

@@ -100,7 +100,7 @@ class TestSemHooksFormatCheckFails:
 
         call_count = [0]
 
-        def step_side_effect(label, cmd):
+        def step_side_effect(label, cmd, **_kw):
             call_count[0] += 1
             if "format" in label:
                 return 1
@@ -144,7 +144,7 @@ class TestSemHooksPytestFails:
 
         call_count = [0]
 
-        def step_side_effect(label, cmd):
+        def step_side_effect(label, cmd, **_kw):
             call_count[0] += 1
             if "pytest" in label:
                 return 1
@@ -170,7 +170,7 @@ class TestSemHooksNotebookFail:
 
         call_count = [0]
 
-        def step_side_effect(label, cmd):
+        def step_side_effect(label, cmd, **_kw):
             call_count[0] += 1
             if "marimo" in label:
                 return 1