diff --git a/interlocks/hook_setup.py b/interlocks/hook_setup.py
index 3e0aa3e..4b5f6c0 100644
--- a/interlocks/hook_setup.py
+++ b/interlocks/hook_setup.py
@@ -9,7 +9,7 @@
 from typing import TypeVar
 
 from interlocks.runner import ok
-from interlocks.setup_state import is_post_edit_command
+from interlocks.setup_state import _git_hooks_dir, is_post_edit_command
 
 _Container = TypeVar("_Container", dict[str, object], list[object])
 
@@ -54,7 +54,7 @@ def install_hooks(project_root: Path | None = None) -> None:
     root = project_root or Path.cwd()
     python = shlex.quote(sys.executable)
 
-    hook = root / ".git" / "hooks" / "pre-commit"
+    hook = _git_hooks_dir(root) / "pre-commit"
     hook.parent.mkdir(parents=True, exist_ok=True)
     script = f"#!/bin/sh\nexec {python} -m interlocks.cli pre-commit\n"
     hook.write_text(script, encoding="utf-8")
diff --git a/interlocks/setup_state.py b/interlocks/setup_state.py
index 66c7ae0..b9b74a6 100644
--- a/interlocks/setup_state.py
+++ b/interlocks/setup_state.py
@@ -75,9 +75,31 @@ def is_post_edit_command(command: object) -> bool:
     )
 
 
+def _git_hooks_dir(project_root: Path) -> Path:
+    """Return the git hooks directory for *project_root*.
+
+    In a linked worktree ``.git`` is a file with content
+    ``gitdir: <path>/.git/worktrees/<name>``.  The actual hooks directory
+    lives two levels up in the common git dir, not inside the per-worktree
+    pseudo-repo.
+    """
+    git_path = project_root / ".git"
+    if not git_path.is_file():
+        return git_path / "hooks"
+    text = git_path.read_text(encoding="utf-8").strip()
+    if not text.startswith("gitdir:"):
+        return git_path / "hooks"
+    gitdir = Path(text.split(":", 1)[1].strip())
+    if not gitdir.is_absolute():
+        gitdir = (project_root / gitdir).resolve()
+    if gitdir.parent.name == "worktrees":
+        return gitdir.parent.parent / "hooks"
+    return gitdir / "hooks"
+
+
 def pre_commit_hook_installed(project_root: Path) -> bool:
     """True when ``.git/hooks/pre-commit`` exists and invokes ``interlocks pre-commit``."""
-    hook = project_root / ".git" / "hooks" / "pre-commit"
+    hook = _git_hooks_dir(project_root) / "pre-commit"
     try:
         body = hook.read_text(encoding="utf-8")
     except OSError:
diff --git a/tests/stages/test_setup_hooks.py b/tests/stages/test_setup_hooks.py
index a72c840..be6aaeb 100644
--- a/tests/stages/test_setup_hooks.py
+++ b/tests/stages/test_setup_hooks.py
@@ -148,6 +148,44 @@ def test_ensure_stop_hook_normalizes_duplicate_post_edit_hooks(self) -> None:
             ],
         )
 
+    def test_keep_existing_hook_preserves_non_command_hook(self) -> None:
+        """Matcher and other non-command hook objects are always kept."""
+        from interlocks.hook_setup import _keep_existing_hook
+
+        matcher = {"type": "matcher", "pattern": ".*error.*"}
+        assert _keep_existing_hook(matcher, "python -m interlocks.cli post-edit") is True
+
+    def test_keep_existing_hook_preserves_non_dict_hook(self) -> None:
+        """Non-dict hook values are treated as unknown and kept unchanged."""
+        from interlocks.hook_setup import _keep_existing_hook
+
+        result = _keep_existing_hook("run-some-script.sh", "python -m interlocks.cli post-edit")
+        assert result is True
+
+    def test_ensure_stop_hook_three_calls_produces_single_entry(self) -> None:
+        """Calling _ensure_stop_hook three times results in exactly one managed entry."""
+        command = "python -m interlocks.cli post-edit"
+        settings: dict[str, object] = {}
+        _ensure_stop_hook(settings, command)
+        _ensure_stop_hook(settings, command)
+        _ensure_stop_hook(settings, command)
+
+        hooks = settings["hooks"]["Stop"][0]["hooks"]  # pyright: ignore[reportIndexIssue]
+        managed = [h for h in hooks if isinstance(h, dict) and h.get("command") == command]
+        assert len(managed) == 1
+
+    def test_ensure_stop_hook_preserves_unmanaged_command_alongside_managed(self) -> None:
+        """An unrecognised command hook coexists with the managed post-edit entry."""
+        settings: dict[str, object] = {
+            "hooks": {"Stop": [{"hooks": [{"type": "command", "command": "my-linter --fix"}]}]}
+        }
+        _ensure_stop_hook(settings, "python -m interlocks.cli post-edit")
+
+        hooks = settings["hooks"]["Stop"][0]["hooks"]  # pyright: ignore[reportIndexIssue]
+        commands = [h["command"] for h in hooks if isinstance(h, dict)]
+        assert "my-linter --fix" in commands
+        assert "python -m interlocks.cli post-edit" in commands
+
     def test_cmd_hooks_writes_hook_file_and_settings(self) -> None:
         from interlocks.stages.setup_hooks import cmd_hooks
 
diff --git a/tests/stages/test_setup_hooks_integration.py b/tests/stages/test_setup_hooks_integration.py
index d4402a6..5741df5 100644
--- a/tests/stages/test_setup_hooks_integration.py
+++ b/tests/stages/test_setup_hooks_integration.py
@@ -66,6 +66,65 @@ def test_setup_hooks_installs_pre_commit_and_stop_hook(tmp_project: Path) -> Non
     assert any(h["type"] == "command" and h["command"].endswith(suffix) for h in hooks)
 
 
+def _init_repo_for_worktree(root: Path) -> None:
+    """Initialise a git repo with an initial commit (required before adding worktrees)."""
+    _git(root, "init", "-q", "-b", "main")
+    _git(root, "config", "user.email", "t@e.co")
+    _git(root, "config", "user.name", "t")
+    _git(root, "config", "commit.gpgsign", "false")
+    (root / "placeholder.txt").write_text("init\n", encoding="utf-8")
+    subprocess.run(["git", "add", "-A"], cwd=root, check=True, capture_output=True)
+    subprocess.run(
+        ["git", "commit", "-q", "-m", "init"],
+        cwd=root,
+        check=True,
+        capture_output=True,
+    )
+
+
+def _make_worktree_pair(tmp_path: Path, branch: str) -> tuple[Path, Path]:
+    """Return (main, linked) after creating a repo and adding a linked worktree."""
+    main = tmp_path / "main"
+    main.mkdir()
+    _init_repo_for_worktree(main)
+    linked = tmp_path / "linked"
+    subprocess.run(
+        ["git", "worktree", "add", "-b", branch, str(linked), "HEAD"],
+        cwd=main,
+        check=True,
+        capture_output=True,
+    )
+    return main, linked
+
+
+def test_install_hooks_in_linked_worktree(tmp_path: Path) -> None:
+    """install_hooks writes the pre-commit hook to the main repo from a linked worktree."""
+    from interlocks.hook_setup import install_hooks
+
+    main, linked = _make_worktree_pair(tmp_path, "feature")
+    assert (linked / ".git").is_file(), "linked worktree .git must be a file"
+
+    install_hooks(linked)
+
+    hook = main / ".git" / "hooks" / "pre-commit"
+    assert hook.exists()
+    assert os.access(hook, os.X_OK)
+    assert "-m interlocks.cli pre-commit" in hook.read_text(encoding="utf-8")
+
+
+def test_pre_commit_hook_installed_detects_linked_worktree(tmp_path: Path) -> None:
+    """pre_commit_hook_installed returns True for a hook in the common git dir."""
+    from interlocks.hook_setup import install_hooks
+    from interlocks.setup_state import pre_commit_hook_installed
+
+    main, linked = _make_worktree_pair(tmp_path, "detect-test")
+
+    install_hooks(linked)
+
+    assert pre_commit_hook_installed(linked)
+    assert pre_commit_hook_installed(main)
+
+
 def test_setup_hooks_is_idempotent(tmp_project: Path) -> None:
     assert _run_setup_hooks(tmp_project).returncode == 0
     assert _run_setup_hooks(tmp_project).returncode == 0
diff --git a/tests/tasks/test_setup.py b/tests/tasks/test_setup.py
index 9f9bd28..28231b1 100644
--- a/tests/tasks/test_setup.py
+++ b/tests/tasks/test_setup.py
@@ -163,6 +163,46 @@ def test_setup_check_succeeds_after_setup(
     assert "Local integrations are installed and current." in out
 
 
+def test_setup_state_no_duplicate_artifacts_in_check_output(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch, capsys: pytest.CaptureFixture[str]
+) -> None:
+    """setup_artifact_statuses returns no duplicate labels after two install runs."""
+    from interlocks.setup_state import setup_artifact_statuses
+
+    _write_pyproject(tmp_path)
+    _run_setup(monkeypatch, tmp_path)
+    _run_setup(monkeypatch, tmp_path)
+    capsys.readouterr()
+
+    statuses = setup_artifact_statuses(tmp_path)
+    labels = [s.label for s in statuses]
+    assert len(labels) == len(set(labels)), f"duplicate artifact labels: {labels}"
+
+
+def test_git_hooks_dir_returns_dot_git_hooks_for_plain_repo(tmp_path: Path) -> None:
+    """_git_hooks_dir returns <root>/.git/hooks for a normal (non-worktree) repo."""
+    from interlocks.setup_state import _git_hooks_dir
+
+    # Plain repo: .git is a directory
+    (tmp_path / ".git").mkdir()
+    assert _git_hooks_dir(tmp_path) == tmp_path / ".git" / "hooks"
+
+
+def test_git_hooks_dir_resolves_linked_worktree(tmp_path: Path) -> None:
+    """_git_hooks_dir follows a gitdir file to the common hooks directory."""
+    from interlocks.setup_state import _git_hooks_dir
+
+    main = tmp_path / "main"
+    (main / ".git" / "worktrees" / "feat").mkdir(parents=True)
+    # Write a .git file as git would in the linked worktree
+    linked = tmp_path / "linked"
+    linked.mkdir()
+    gitdir = main / ".git" / "worktrees" / "feat"
+    (linked / ".git").write_text(f"gitdir: {gitdir}\n", encoding="utf-8")
+
+    assert _git_hooks_dir(linked) == main / ".git" / "hooks"
+
+
 def _write_pyproject_with_preset(project: Path, preset: str | None) -> None:
     body = '[project]\nname = "probe"\nversion = "0.0.0"\nrequires-python = ">=3.11"\n'
     if preset is not None:
diff --git a/tests/test_git.py b/tests/test_git.py
index d2aebc5..6b0e463 100644
--- a/tests/test_git.py
+++ b/tests/test_git.py
@@ -176,3 +176,36 @@ def test_src_test_prefixes_empty_src_with_tests_matches_all(
     """Empty src with a configured test dir still matches everything (no narrowing)."""
     _stub_cfg(monkeypatch, "", "tests")
     assert git_mod._src_test_prefixes() == ("",)
+
+
+def test_changed_py_files_vs_works_in_linked_worktree(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    """changed_py_files_vs works when invoked from a linked git worktree.
+
+    In a linked worktree git commands operate on the checked-out branch normally;
+    ``changed_py_files_vs`` must return files relative to the worktree root.
+    """
+    main = tmp_path / "main"
+    main.mkdir()
+    _init_repo(main)
+    (main / "pyproject.toml").write_text(
+        '[tool.interlocks]\nsrc_dir = "interlocks"\ntest_dir = "tests"\n',
+        encoding="utf-8",
+    )
+    (main / "interlocks").mkdir()
+    (main / "interlocks" / "base.py").write_text("x = 1\n", encoding="utf-8")
+    _commit_all(main, "base")
+
+    linked = tmp_path / "linked"
+    _git("worktree", "add", "-b", "feature", str(linked), "HEAD", cwd=main)
+
+    # .git in a linked worktree is a file, not a directory
+    assert (linked / ".git").is_file()
+
+    # Write an untracked .py file in the linked worktree
+    (linked / "interlocks" / "new_feature.py").write_text("y = 2\n", encoding="utf-8")
+
+    monkeypatch.chdir(linked)
+    result = changed_py_files_vs("HEAD")
+    assert result == {"interlocks/new_feature.py"}