microsoft-apm-566-609

total 416
drwxr-xr-x 1 root root   4096 Nov  6 18:58 .
drwxr-xr-x 1 root root   4096 Nov  6 18:58 ..
drwxr-xr-x 1 root root   4096 Nov  6 18:57 .apm
drwxr-xr-x 1 root root   4096 Nov  6 18:58 .git
-rw-r--r-- 1 root root     63 Nov  6 18:57 .gitattributes
drwxr-xr-x 1 root root   4096 Nov  6 18:57 .github
-rw-r--r-- 1 root root    784 Nov  6 18:57 .gitignore
drwxr-xr-x 1 root root   4096 Nov  6 18:57 .vscode
-rw-r--r-- 1 root root    295 Nov  6 18:57 AUTHORS
-rw-r--r-- 1 root root  33688 Nov  6 18:57 CHANGELOG.md
-rw-r--r-- 1 root root    558 Nov  6 18:57 CODE_OF_CONDUCT.md

-rw-r--r-- 1 root root   4086 Nov  6 18:57 CONTRIBUTING.md
-rw-r--r-- 1 root root   1074 Nov  6 18:57 LICENSE
-rw-r--r-- 1 root root   1577 Nov  6 18:57 MANIFESTO.md
-rw-r--r-- 1 root root   5474 Nov  6 18:57 README.md
-rw-r--r-- 1 root root    542 Nov  6 18:57 SECURITY.md
-rw-r--r-- 1 root root    548 Nov  6 18:57 
…[1972 chars omitted]…
st_distributed_compilation.py
./tests/test_empty_string_and_defaults.py
./tests/test_enhanced_discovery.py
./tests/test_github_downloader.py
./tests/test_github_downloader_token_precedence.py
./tests/test_lockfile.py
./tests/test_runnable_prompts.py
./tests/test_runtime_manager_token_precedence.py
./tests/test_token_manager.py
./tests/test_virtual_package_multi_install.py
./tests/__init__.py
./uv.lock

src/apm_cli.egg-info/PKG-INFO
src/apm_cli.egg-info/SOURCES.txt
src/apm_cli.egg-info/dependency_links.txt
src/apm_cli.egg-info/entry_points.txt
src/apm_cli.egg-info/requires.txt
src/apm_cli.egg-info/top_level.txt
src/apm_cli/__init__.py
src/apm_cli/adapters/__init__.py
src/apm_cli/adapters/client/__init__.py
src/apm_cli/adapters/client/base.py
src/apm_cli/adapters/client/codex.py
src/apm_cli/adapters/client/copilot.py

src/apm_cli/adapters/client/cursor.py
src/apm_cli/adapters/client/opencode.py
src/apm_cli/adapters/client/vscode.py
src/apm_cli/adapters/package_manager/__init__.py
src/apm_cli/adapters/package_manager/base.py
src/apm_cli/adapters/package_manager/default_manager.py
src/apm_cli/bundle/__init__.py
src/apm_cli/bundle/lockfile_enrichment.py
src/apm_cli/bundle/packer.py
src/apm_cli/bundle/plugin_exporter.py
src/apm_cli/bundle/unpacker.py
src/apm_cli/cli.py
src/apm_cli/commands
…[8629 chars omitted]…
/unit/integration/test_hook_integrator.py:1020:        integrator = HookIntegrator()
tests/unit/integration/test_hook_integrator.py:1021:        cmd, scripts = integrator._rewrite_command_for_target(
tests/unit/integration/test_hook_integrator.py:1037:        integrator = HookIntegrator()
tests/unit/integration/test_hook_integrator.py:1038:        cmd, scripts = integrator._rewrite_command_for_target(

757 src/apm_cli/integration/hook_integrator.py
"""Hook integration functionality for APM packages.

Integrates hook JSON files and their referenced scripts during package
installation. Supports VSCode Copilot (.github/hooks/), Claude Code
(.claude/settings.json), and Cursor (.cursor/hooks.json) targets.

Hook JSON format (Claude Code  -- nested matcher groups):
    {
        "hooks": {
            "PreToolUse": [
                {

                    "hooks": [
                        {"type": "command", "command": "./scripts/validate.sh", "timeout": 10}
                    ]
                }
            ]
        }
    }

Hook JSON format (GitHub Copilot  -- flat arrays with bash/powershell keys):
    {
        "version": 1,
        "hooks": {
            "preToolUse": [
                {"type": "command", "bash": "./scripts/validate.sh", "timeoutSec": 10}
            ]
        }
  
…[8396 chars omitted]…
tive_to(package_path.resolve()):
                continue
            if source_file.exists() and source_file.is_file():
                target_rel = f"{scripts_base}/{rel_path}"
                scripts_to_copy.append((source_file, target_rel))
                new_command = new_command.replace(rel_ref, target_rel)

        return new_command, scripts_to_copy

    def _rewrite_hooks_data(
        self,

self,
        data: Dict,
        package_path: Path,
        package_name: str,
        target: str,
        hook_file_dir: Optional[Path] = None,
    ) -> Tuple[Dict, List[Tuple[Path, str]]]:
        """Rewrite all command paths in a hooks JSON structure.

        Creates a deep copy and rewrites command paths for the target platform.

        Args:

            data: Parsed hook JSON data
            package_path: Root path of the source package
            package_name: Name for scripts subdirectory
            target: "vscode" or "claude"
            hook_file_dir: Directory containing the hook JSON file (for ./path resolution)

        Returns:
            Tuple of (rewritten_data_copy, list of (source_file, target_rel_path))
        """
        import copy
        rewritten = copy.deepcopy(data)
        all_scripts: List[Tuple[Path, str]] = []

        hooks = rewritten.
…[8629 chars omitted]…
t(target.name)
        if config is not None:
            return self._integrate_merged_hooks(
                config, package_info, project_root,
                force=force, managed_files=managed_files,
                diagnostics=diagnostics,
            )

        return HookIntegrationResult(
            files_integrated=0, files_updated=0,
            files_skipped=0, target_paths=[],
        )

Args:
            package_info: PackageInfo object

        Returns:
            str: Package name derived from install path
        """
        return package_info.install_path.name

    def integrate_package_hooks(self, package_info, project_root: Path,
                                 force: bool = False,
                                 managed_files: set = None,
                                 diagnostics=None) -> HookIntegrationResult:

        """Integrate hooks from a package into .github/hooks/ (VSCode target).

        Deploys hook JSON files with clean filenames and copies referenced
        script files. Skips user-authored files unless force=True.

        Args:
            package_info: PackageInfo with package metadata and install path
            project_root: Root directory of the project
            force: If True, overwrite user-authored files on collision
 
…[7485 chars omitted]…
ge_hooks_cursor(self, package_info, project_root: Path,
                                        force: bool = False,
                                        managed_files: set = None,
                                        diagnostics=None) -> HookIntegrationResult:
        """Integrate hooks into .cursor/hooks.json.

        .. deprecated:: Use :meth:`integrate_hooks_for_target` instead.
        """

def sync_integration(self, apm_package, project_root: Path,
                          managed_files: set = None) -> Dict:
        """Remove APM-managed hook files.

        Uses *managed_files* (relative paths) to surgically remove only
        APM-tracked files.  Falls back to legacy ``*-apm.json`` glob when
        *managed_files* is ``None``.

        **Never** calls ``shutil.rmtree``.

        Also cleans APM entries from ``.claude/settings.json`` and
        ``.cursor/hooks.json`` via the ``_apm_source`` marker.

        """
        stats: Dict[str, int] = {'files_removed': 0, 'errors': 0}

        if managed_files is not None:
            # Manifest-based removal  -- only remove tracked files
            deleted: list = []
            for rel_path in managed_files:
                # Normalize path separators for cross-platform compatibility
                normalized = rel_p
…[4430 chars omitted]…
     del data["hooks"][event_name]

            if not data["hooks"]:
                del data["hooks"]

            if modified:
                with open(json_path, 'w', encoding='utf-8') as f:
                    json.dump(data, f, indent=2)
                    f.write('\n')
                stats['files_removed'] += 1
        except (json.JSONDecodeError, OSError):
            stats['errors'] += 1

"""Target profiles for multi-tool integration.

Each target tool (Copilot, Claude, Cursor, ...) describes where APM
primitives should land.  Adding a new target means adding an entry to
``KNOWN_TARGETS`` -- no new classes required.
"""

from __future__ import annotations

from dataclasses import dataclass, field
from typing import Dict, Optional, Tuple, Union

@dataclass(frozen=True)
class PrimitiveMapping:
    """Where a single primitive type is deployed in a target tool."""

    subdir: str
    """Subdirectory under the target root (e.g. ``"rules"``, ``"agents"``)."""

    extension: str
    """File extension or suffix for deployed files
    (e.g. ``".mdc"``, ``".agent.md"``)."""

    format_id: str
    """Opaque tag used by integrators to select the right
    content transformer (e.g. ``"cursor_rules"``)."""

    deploy_root: Optional[str] = None
    """Override *root_dir* for thi
…[8629 chars omitted]…
package_skill",            "sync_integration",  "skills", multi_target=True),
    }


# Lazily initialized on first access
_DISPATCH: dict[str, PrimitiveDispatch] | None = None


def get_dispatch_table() -> dict[str, PrimitiveDispatch]:
    """Return the primitive dispatch table (lazily built)."""
    global _DISPATCH
    if _DISPATCH is None:
        _DISPATCH = _build_dispatch()
    return _DISPATCH

30:    """Override *root_dir* for this primitive only.
33:    ``target.root_dir`` to compute the deploy directory.
45:    """Short unique identifier (``"copilot"``, ``"claude"``, ``"cursor"``)."""
47:    root_dir: str
57:    """Create *root_dir* if it does not exist (used during fallback or
61:    """If ``True``, only deploy when *root_dir* already exists."""
73:    user_root_dir: Optional[str] = None
74:    """Override for *root_dir* at user scope.
76:    When ``None`` the normal *root_dir* is used at both project and user
78:    user level (e.g. Copilot CLI uses ``~/.copilot/`` instead of
93:        return f"{self.root_dir}/"
102:        At user scope, returns *user_root_dir* when set, otherwise

103:        falls back to the standard *root_dir*.
105:        if user_scope and self.user_root_dir:
106:            return self.user_root_dir
107:        return self.root_dir
124:        - 
…[2794 chars omitted]…
integration/hook_integrator.py:559:        .. deprecated:: Use :meth:`integrate_hooks_for_target` instead.
src/apm_cli/integration/hook_integrator.py:573:        .. deprecated:: Use :meth:`integrate_hooks_for_target` instead.
src/apm_cli/integration/hook_integrator.py:585:    def integrate_hooks_for_target(
src/apm_cli/integration/hook_integrator.py:602:            return self.integrate_package_hooks(

"""Unit tests for HookIntegrator.

Tests cover:
- Hook file discovery (.apm/hooks/ and hooks/ directories)
- VSCode integration (JSON copy + script copy + path rewriting)
- Claude integration (settings.json merge + script copy)
- Sync/cleanup integration (nuke-and-regenerate)
- Official plugin formats (hookify, learning-output-style, ralph-loop)
- Script path rewriting for ${CLAUDE_PLUGIN_ROOT} references
"""

import json

import tempfile
import shutil
from pathlib import Path
from unittest.mock import MagicMock

import pytest

from apm_cli.integration.hook_integrator import HookIntegrator, HookIntegrationResult
from apm_cli.models.apm_package import APMPackage, PackageInfo


def _make_package_info(install_path: Path, name: str = "test-pkg") -> PackageInfo:
    """Create a minimal PackageInfo for testing."""
    package = APMPackage(name=name, version="1.0.0")
    return PackageInfo(pa
…[7485 chars omitted]…
st_integrate_hookify_vscode(self, temp_project):
        """Test VSCode integration of hookify plugin (multiple events + Python scripts)."""
        pkg_info = self._setup_hookify_package(temp_project)
        integrator = HookIntegrator()

        result = integrator.integrate_package_hooks(pkg_info, temp_project)

        assert result.files_integrated == 1
        assert result.scripts_copied == 4

# Check hook JSON was created
        target_json = temp_project / ".github" / "hooks" / "hookify-hooks.json"
        assert target_json.exists()

        # Verify rewritten paths
        data = json.loads(target_json.read_text())
        cmd = data["hooks"]["PreToolUse"][0]["hooks"][0]["command"]
        assert "${CLAUDE_PLUGIN_ROOT}" not in cmd
        assert ".github/hooks/scripts/hookify/hooks/pretooluse.py" in cmd
        assert cmd.startswith("python3 ")

        # Check scripts were copied

        scripts_dir = temp_project / ".github" / "hooks" / "scripts" / "hookify" / "hooks"
        assert (scripts_dir / "pretooluse.py").exists()
        assert (scripts_dir / "posttooluse.py").exists()
        assert (scripts_dir / "stop.py").exists()
        assert (scripts_dir / "userpromptsubmit.py").exists()

    def test_integrate_learning_output_style_vscode(self, temp_projec
…[8629 chars omitted]…
emove existing .claude dir
        shutil.rmtree(temp_project / ".claude")

        pkg_dir = temp_project / "pkg"
        hooks_dir = pkg_dir / "hooks"
        hooks_dir.mkdir(parents=True)
        (hooks_dir / "hooks.json").write_text(json.dumps(RALPH_LOOP_HOOKS_JSON))
        (hooks_dir / "stop-hook.sh").write_text("#!/bin/bash\nexit 0")

        pkg_info = _make_package_info(pkg_dir, "ralph-loop")

"""Test that scripts are copied to .cursor/hooks/<pkg>/."""
        pkg_info = self._setup_hookify_package(temp_project)
        integrator = HookIntegrator()

        result = integrator.integrate_package_hooks_cursor(pkg_info, temp_project)

        # Verify scripts exist under .cursor/hooks/hookify/
        scripts_dir = temp_project / ".cursor" / "hooks" / "hookify" / "hooks"
        assert scripts_dir.exists()
        assert (scripts_dir / "pretooluse.py").exists()
        assert (scripts_dir / "posttooluse.py").exists()
        assert (scripts_dir / "stop.py").exists()

        assert (scripts_dir / "userpromptsubmit.py").exists()

    def test_sync_removes_cursor_hook_entries(self, temp_project):
        """Test that sync removes APM-managed entries from .cursor/hooks.json."""
        hooks_path = temp_project / ".cursor" / "hooks.json"
        hooks_path.write_text(json
…[8629 chars omitted]…
ite_command_for_target(
            "python3 ${CLAUDE_PLUGIN_ROOT}/hooks/check.py",
            pkg_dir,
            "my-pkg",
            "vscode",
        )

        assert cmd.startswith("python3 ")
        assert cmd.endswith("hooks/check.py")

    def test_rewrite_relative_path_with_hook_file_dir(self, temp_project):
        """Test that ./path is resolved from hook_file_dir, not package root."""

"""Test that ./path is resolved from hook_file_dir, not package root."""
        pkg_dir = temp_project / "pkg"
        hooks_dir = pkg_dir / "hooks"
        scripts_dir = hooks_dir / "scripts"
        scripts_dir.mkdir(parents=True)
        (scripts_dir / "lint.sh").write_text("#!/bin/bash")

        integrator = HookIntegrator()
        # Script lives at hooks/scripts/lint.sh — only resolvable from hooks/ dir
        cmd, scripts = integrator._rewrite_command_for_target(
            "./scripts/lint.sh",
            pkg_dir,

            "my-pkg",
            "vscode",
            hook_file_dir=hooks_dir,
        )

        assert "./" not in cmd
        assert ".github/hooks/scripts/my-pkg/scripts/lint.sh" in cmd
        assert len(scripts) == 1
        assert scripts[0][0] == (scripts_dir / "lint.sh").resolve()

    def test_rewrite_relative_path_fails_without_hook_file_dir(
…[8629 chars omitted]…
tor._rewrite_hooks_data(
            data, pkg_dir, "my-pkg", "vscode",
        )

        hook = rewritten["hooks"]["PreToolUse"][0]["hooks"][0]
        assert ".github/hooks/scripts/my-pkg/scripts/validate.sh" in hook["command"]
        assert ".github/hooks/scripts/my-pkg/scripts/validate-linux.sh" in hook["linux"]
        assert len(scripts) == 2
1831 tests/unit/integration/test_hook_integrator.py

118:class TestHookDiscovery:
127:    def test_find_no_hooks(self, temp_project):
134:    def test_find_hooks_in_apm_hooks(self, temp_project):
148:    def test_find_hooks_in_hooks_dir(self, temp_project):
160:    def test_find_hooks_deduplicates(self, temp_project):
176:    def test_should_integrate_always_true(self, temp_project):
185:class TestHookParsing:
194:    def test_parse_valid_hook_json(self, temp_project):
204:    def test_parse_invalid_json(self, temp_project):
211:    def test_parse_non_dict_json(self, temp_project):
218:    def test_parse_missing_file(self, temp_project):
226:class TestVSCodeIntegration:

251:    def test_integrate_hookify_vscode(self, temp_project):
279:    def test_integrate_learning_output_style_vscode(self, temp_project):
317:    def test_integrate_ralph_loop_vscode(self, temp_project):
340:    def test_integrate_no_hooks(self, temp_project):
352:    
…[3776 chars omitted]…
emp_project):
1670:    def test_multiple_packages_lifecycle(self, temp_project):
1714:class TestDeepCopySafety:
1723:    def test_rewrite_does_not_mutate_original(self, temp_project):
1748:class TestCodexHookIntegration:
1784:    def test_codex_hooks_merge_into_hooks_json(self):
1798:    def test_codex_hooks_preserve_user_hooks(self):
1823:    def test_codex_hooks_not_deployed_without_codex_dir(self):

991:        "hooks": 0,
1011:        "hooks": hook_integrator,
1038:                elif _prim_name == "hooks":
1042:                        _deploy_dir = ".cursor/hooks.json"
1044:                        _deploy_dir = ".codex/hooks.json"
1473:        total_hooks_integrated = 0
1814:                        total_hooks_integrated += int_result["hooks"]
2078:                        total_hooks_integrated += int_result["hooks"]
2273:                            total_hooks_integrated += int_result["hooks"]
2438:        if total_hooks_integrated > 0:
2440:                logger.verbose_detail(f"Integrated {total_hooks_integrated} hook(s)")
227:def _sync_integrations_after_uninstall(apm_package, project_root, all_deployed_files, logger, user_scope=False):

230:    When *user_scope* is ``True``, targets are resolved for user-level
236:    from ...integration.targets import resolve_targets
241
…[425 chars omitted]…
94:    for t in _resolved_targets:
302:        result = _integrators["skills"].sync_integration(
305:            targets=_resolved_targets,
309:    # Hooks (multi-target sync_integration handles all targets)
310:    result = _integrators["hooks"].sync_integration(
318:    _targets = _resolved_targets
339:            for _target in _targets:
348:                pkg_info, project_root, targets=_targets,

command_integrator,
    hook_integrator,
    force,
    managed_files,
    diagnostics,
    package_name="",
    logger=None,
    scope=None,
):
    """Run the full integration pipeline for a single package.

    Iterates over *targets* (``TargetProfile`` list) and dispatches each

    primitive to the appropriate integrator via the target-driven API.
    Skills are handled separately because ``SkillIntegrator`` already
    routes across all targets internally.

    When *scope* is ``InstallScope.USER``, targets and primitives that
    do not support user-scope deployment are silently skipped.

    Returns a dict with integration counters and the list of deployed file paths.
    """
    from apm_cli.integration.dispatch import get_dispatch_table

    _dispatch = get_dispatch_table()
    result = {
        "prompts": 0,
        "agents": 0,
        "skills": 0,
        "sub_skills":
…[7263 chars omitted]…
oun = "error" if _err_count == 1 else "errors"
                            logger.package_inline_warning(f"    [!] {_err_count} integration {noun}")
                    continue

                # npm-like behavior: Branches always fetch latest, only tags/commits use cache
                # Resolve git reference to determine type
                from apm_cli.models.apm_package import GitReferenceType

logger.error(f"Failed to remove transitive dep {orphan_key}: {e}")

    from ...integration.base_integrator import BaseIntegrator as _BI
    _BI.cleanup_empty_parents(deleted_orphan_paths, stop_at=apm_modules_dir)
    return removed, actual_orphans


def _sync_integrations_after_uninstall(apm_package, project_root, all_deployed_files, logger, user_scope=False):
    """Remove deployed files and re-integrate from remaining packages.

    When *user_scope* is ``True``, targets are resolved for user-level
    deployment so cleanup and re-integration use the correct paths.

    """
    from ...integration.base_integrator import BaseIntegrator
    from ...models.apm_package import PackageInfo, validate_apm_package
    from ...integration.dispatch import get_dispatch_table
    from ...integration.targets import resolve_targets

    _dispatch = get_dispatch_table()
    _integra
…[8674 chars omitted]…
cs/en/memory#organize-rules-with-claude%2Frules%2F
    "claude": TargetProfile(
        name="claude",
        root_dir=".claude",
        primitives={
            "instructions": PrimitiveMapping(
                "rules", ".md", "claude_rules"
            ),
            "agents": PrimitiveMapping(
                "agents", ".md", "claude_agent"
            ),
            "commands": PrimitiveMapping(

"""Base integrator with shared collision detection and sync logic."""

import re
from pathlib import Path
from typing import Dict, List, Optional, Set

from dataclasses import dataclass, field

from apm_cli.compilation.link_resolver import UnifiedLinkResolver
from apm_cli.primitives.discovery import discover_primitives
from apm_cli.utils.console import _rich_warning

@dataclass
class IntegrationResult:
    """Result of any file-level integration operation.

    The core fields (files_integrated, files_skipped, target_paths,
    links_resolved) are used by all integrators.  Hook- and skill-specific
    fields default to zero/False and are ignored by integrators that do
    not produce them.
    """

    files_integrated: int
    files_updated: int  # Kept for CLI compat, always 0 today
    files_skipped: int
    target_paths: List[Path]
    links_resolved: int = 0

    # Hook-specific
…[8629 chars omitted]…
e and register the link resolver for a package."""
        self.link_resolver = UnifiedLinkResolver(project_root)
        try:
            primitives = discover_primitives(package_info.install_path)
            self.link_resolver.register_contexts(primitives)
        except Exception:
            self.link_resolver = None

    def resolve_links(self, content: str, source: Path, target: Path) -> tuple:

assert data["hooks"]["Stop"][0]["hooks"][0]["command"] == original_cmd
        # Rewritten should be different
        assert rewritten["hooks"]["Stop"][0]["hooks"][0]["command"] != original_cmd


# --- Codex hook integration tests ---------------------------------------------


class TestCodexHookIntegration:
    """Tests for Codex hooks.json merge with _apm_source markers."""

    def setup_method(self):

        self.temp_dir = tempfile.mkdtemp()
        self.root = Path(self.temp_dir)
        (self.root / ".codex").mkdir()

    def teardown_method(self):
        shutil.rmtree(self.temp_dir, ignore_errors=True)

    def _make_package_info(self, name="test-pkg", hook_data=None):
        """Create a mock package info with hook files."""
        pkg_dir = self.root / "apm_modules" / name
        hooks_dir = pkg_dir / ".apm" / "hooks"
        hooks_dir.mkdir(parents=True, exist_
…[8629 chars omitted]…
py:401:        result = self.integrator.sync_integration(apm_package, self.project_root, managed_files=managed)
tests/unit/integration/test_instruction_integrator.py:715:    """Test sync_integration_cursor (manifest-based removal)."""
tests/unit/integration/test_instruction_integrator.py:736:        result = self.integrator.sync_integration_cursor(apm_package, self.project_root, managed_files=managed)

result = HookIntegrator().integrate_package_hooks(
            info, tmp_path, force=False, managed_files=managed
        )
        assert result.files_integrated >= 1

    def test_force_overrides_collision(self, tmp_path: Path):
        """force=True overwrites even unmanaged hook files."""
        hooks_dir = tmp_path / ".github" / "hooks"
        hooks_dir.mkdir(parents=True)
        (hooks_dir / "test-pkg-hooks.json").write_text('{"user": true}')

        info = _make_package_info(

            tmp_path, hook_files={"hooks.json": SAMPLE_HOOK_JSON}
        )
        result = HookIntegrator().integrate_package_hooks(
            info, tmp_path, force=True, managed_files=set()
        )
        assert result.files_integrated >= 1
        # Verify user content was overwritten
        assert json.loads((hooks_dir / "test-pkg-hooks.json").read_text()) != {"user": True}


# -----
…[8628 chars omitted]…
 "SKILL.md").exists()
tests/unit/test_copilot_runtime.py:5:from apm_cli.runtime.copilot_runtime import CopilotRuntime
tests/unit/test_copilot_runtime.py:74:            assert config_path.as_posix().endswith(".copilot/mcp-config.json")
tests/unit/test_mcp_lifecycle_e2e.py:616:        copilot_dir = tmp_path / ".copilot"
tests/unit/test_mcp_lifecycle_e2e.py:651:        copilot_dir = tmp_path / ".copilot"

tests/unit/integration/test_scope_integration.py:275:                    assert "hooks" not in t.primitives
tests/unit/integration/test_data_driven_dispatch.py:35:def _make_hook_result(n=0):
tests/unit/integration/test_data_driven_dispatch.py:66:    hook = MagicMock()
tests/unit/integration/test_data_driven_dispatch.py:67:    hook.integrate_hooks_for_target = MagicMock(return_value=_make_hook_result())
tests/unit/integration/test_data_driven_dispatch.py:77:        "hook_integrator": hook,
tests/unit/integration/test_data_driven_dispatch.py:123:        # opencode has no hooks -- hook integrator should NOT be called for .github
tests/unit/integration/test_data_driven_dispatch.py:124:        for call_args in mocks["hook_integrator"].integrate_hooks_for_target.call_args_list:
tests/unit/integration/test_data_driven_dispatch.py:136:                      "hook_integrator"):
tests/unit/integ
…[2928 chars omitted]…
 = HookIntegrationResult(hooks_integrated=0, scripts_copied=0)
tests/unit/integration/test_data_driven_dispatch.py:902:        assert r.hooks_integrated == 0

tests/unit/integration/test_data_driven_dispatch.py:907:        from apm_cli.integration.hook_integrator import HookIntegrationResult
tests/unit/integration/test_data_driven_dispatch.py:913:        assert r.hooks_integrated == 3  # property alias

src/apm_cli/integration/hook_integrator.py:602:            return self.integrate_package_hooks(
tests/unit/integration/test_deployed_files_manifest.py:668:        result = HookIntegrator().integrate_package_hooks(
tests/unit/integration/test_deployed_files_manifest.py:682:        result = HookIntegrator().integrate_package_hooks(
tests/unit/integration/test_deployed_files_manifest.py:700:        result = HookIntegrator().integrate_package_hooks(
tests/unit/integration/test_deployed_files_manifest.py:714:        result = HookIntegrator().integrate_package_hooks(
tests/unit/integration/test_deployed_files_manifest.py:885:        HookIntegrator().integrate_package_hooks(
tests/unit/integration/test_deployed_files_manifest.py:1072:        result = HookIntegrator().integrate_package_hooks(
tests/unit/integration/test_hook_integrator.py:256:        result = integrator.integrate_package_hook
…[3895 chars omitted]…
laude(pkg_info, temp_project)
tests/unit/integration/test_hook_integrator.py:1788:        result = integrator.integrate_package_hooks_codex(pi, self.root)
tests/unit/integration/test_hook_integrator.py:1812:        result = integrator.integrate_package_hooks_codex(pi, self.root)

tests/unit/integration/test_hook_integrator.py:1829:        result = integrator.integrate_package_hooks_codex(pi, self.root)

rewrite: pwsh -File .\scripts\scan.ps1 []
Traceback (most recent call last):
  File "/tmp/repro_hooks.py", line 33, in <module>
    res = integrator.integrate_package_hooks(info, tmp, target=target)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: HookIntegrator.integrate_package_hooks() got an unexpected keyword argument 'target'

[build-system]
requires = ["setuptools>=42", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "apm-cli"
version = "0.8.10"
description = "MCP configuration tool"
readme = "README.md"
requires-python = ">=3.10"
license = {file = "LICENSE"}
authors = [

    {name = "Daniel Meppiel", email = "user@example.com"}
]
classifiers = [
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
]
dependencies = [
    "click>=8.0.0",
    "colorama>=0.4.6",
    "pyyaml>=6.0.0",
    "requests>=2.28.0",
    "python-frontmatter>=1.0.0",
    "llm>=0.17.0",
    "llm-github-models>=0.1.0",
    "tomli>=1.2.0; python_version<'3.11'",
    
…[556 chars omitted]…
ne_length = 88

[tool.mypy]
python_version = "3.12"
warn_return_any = true
warn_unused_configs = true

[tool.pytest.ini_options]
addopts = "-m 'not benchmark'"
markers = [
    "integration: marks tests as integration tests that may require network access",
    "slow: marks tests as slow running tests",
    "benchmark: marks performance benchmark tests (deselected by default, run with -m benchmark)",
]

"hooks": [{"type": "command", "command": "echo lint", "timeout": 5}]
        }]
    }
})


class TestHookCollisionDetection:
    """Collision detection in HookIntegrator.integrate_package_hooks."""

    def test_managed_files_none_no_collision_check(self, tmp_path: Path):
        """Legacy mode: managed_files=None → always overwrite."""
        hooks_dir = tmp_path / ".github" / "hooks"

        hooks_dir.mkdir(parents=True)
        (hooks_dir / "test-pkg-hooks.json").write_text('{"user": true}')

        info = _make_package_info(
            tmp_path, hook_files={"hooks.json": SAMPLE_HOOK_JSON}
        )
        result = HookIntegrator().integrate_package_hooks(
            info, tmp_path, force=False, managed_files=None
        )
        assert result.files_integrated >= 1

    def test_empty_managed_set_all_collisions(self, tmp_path: Path):
        """managed_files=set(
…[3558 chars omitted]…
h, hook_files={"hooks.json": SAMPLE_HOOK_JSON}
        )
        result = HookIntegrator().integrate_package_hooks(
            info, tmp_path, force=False, managed_files=set()
        )
        assert result.files_integrated >= 1
        hooks_dir = tmp_path / ".github" / "hooks"
        assert hooks_dir.exists()
        json_files = list(hooks_dir.glob("*.json"))
        assert len(json_files) >= 1

replaced 3160 chars with 6160
    #   VS Code:          https://code.visualstudio.com/docs/copilot/customization/hooks
    #   Claude Code:      https://code.claude.com/docs/en/hooks
    HOOK_COMMAND_KEYS: Tuple[str, ...] = ("command", "bash", "powershell", "windows", "linux", "osx")

    def find_hook_files(self, package_path: Path) -> List[Path]:
        """Find all hook JSON files in a package.

        Searches in:
        - .apm/hooks/ subdirectory (APM convention)
        - hooks/ subdirectory (Claude-native convention)

        Args:
            package_path: Path to the package directory

        Returns:
            List[Path]: List of absolute paths to hook JSON files
        """
        hook_files = []
        seen = set()

        # Search in .apm/hooks/ (APM convention)
        apm_hooks = package_path / ".apm" / "hooks"
        if apm_hooks.exists():
            for f in
…[7265 chars omitted]…
ew_command, unique_scripts

    def _rewrite_hooks_data(
        self,
        data: Dict,
        package_path: Path,
        package_name: str,
        target: str,
        hook_file_dir: Optional[Path] = None,
    ) -> Tuple[Dict, List[Tuple[Path, str]]]:
        """Rewrite all command paths in a hooks JSON structure.

        Creates a deep copy and rewrites command paths for the target platform.

replaced 3212 chars with 4488
        """
        return package_info.install_path.name

    @staticmethod
    def _target_root_dir(target) -> str:
        """Return the scope-resolved root directory for *target*."""
        if target is None:
            return ".github"
        root_dir = getattr(target, "root_dir", None)
        if root_dir:
            return str(root_dir).replace("\\", "/").strip("/")

        if isinstance(target, str):
            from apm_cli.integration.targets import KNOWN_TARGETS

            canonical = "copilot" if target in ("vscode", "agents") else target
            profile = KNOWN_TARGETS.get(canonical)
            if profile is not None:
                return profile.root_dir
        return ".github"

    def integrate_package_hooks(self, package_info, project_root: Path,
                                 force: bool = False,
                         
…[4133 chars omitted]…
 -> HookIntegrationResult:
        """Integrate hooks by merging into a target-specific JSON config.

        This is the shared implementation for Claude, Cursor, and Codex
        targets that merge hook entries into a single JSON file (as
        opposed to Copilot which uses individual JSON files).
        """
        _empty = HookIntegrationResult(
            files_integrated=0, files_updated=0,

patched integrate_hooks_for_target
674-            _MERGE_HOOK_TARGETS["codex"], package_info, project_root,
675-            force=force, managed_files=managed_files,
676-            diagnostics=diagnostics,
677-        )
678-
679-    # ------------------------------------------------------------------
680-    # Target-driven API
681-    # ------------------------------------------------------------------
682-
683:    def integrate_hooks_for_target(
684-        self,

685-        target,
686-        package_info,
687-        project_root: Path,
688-        *,
689-        force: bool = False,
690-        managed_files: set = None,
691-        diagnostics=None,
692-    ) -> "HookIntegrationResult":
693-        """Integrate hooks for a single *target*.
694-
695-        Copilot uses individual JSON files (genuinely different pattern).
696-        All other merge-based targets are dispatche
…[286 chars omitted]…
          diagnostics=diagnostics, target=target,
704-            )
705-
706-        config = _MERGE_HOOK_TARGETS.get(target.name)
707-        if config is not None:
708-            return self._integrate_merged_hooks(
709-                config, package_info, project_root,
710-                force=force, managed_files=managed_files,
711-                diagnostics=diagnostics,
712-            )
713-

replaced 4228 chars with 5943
        ``.cursor/hooks.json`` via the ``_apm_source`` marker.
        """
        stats: Dict[str, int] = {'files_removed': 0, 'errors': 0}

        hook_prefixes = [
            ".github/hooks/",
            ".claude/hooks/",
            ".cursor/hooks/",
            ".codex/hooks/",
        ]
        hook_dirs = [project_root / ".github" / "hooks"]

        if targets:
            from apm_cli.integration.targets import KNOWN_TARGETS

            for target in targets:
                profile = target
                if isinstance(target, str):
                    canonical = "copilot" if target in ("vscode", "agents") else target
                    profile = KNOWN_TARGETS.get(canonical)
                    if profile is None:
                        continue
                primitives = getattr(profile, "primitives", {}) or {}
                mapping
…[5474 chars omitted]…
     del data["hooks"][event_name]

            if not data["hooks"]:
                del data["hooks"]

            if modified:
                with open(json_path, 'w', encoding='utf-8') as f:
                    json.dump(data, f, indent=2)
                    f.write('\n')
                stats['files_removed'] += 1
        except (json.JSONDecodeError, OSError):
            stats['errors'] += 1

force=force, managed_files=managed_files,
                diagnostics=diagnostics,
            )

        return HookIntegrationResult(
            files_integrated=0, files_updated=0,
            files_skipped=0, target_paths=[],
        )

    def sync_integration(self, apm_package, project_root: Path,
                          managed_files: set = None,
                          targets=None) -> Dict:

        """Remove APM-managed hook files.

        Uses *managed_files* (relative paths) to surgically remove only
        APM-tracked files.  Falls back to legacy ``*-apm.json`` glob when
        *managed_files* is ``None``.

        When *targets* is provided, hook prefixes and legacy hook
        directories are derived from those (possibly scope-resolved)
        target profiles as well (e.g. ``.copilot/hooks/``).

        **Never** calls ``shutil.rmtree``.

      
…[144 chars omitted]…
stats: Dict[str, int] = {'files_removed': 0, 'errors': 0}

        hook_prefixes = [
            ".github/hooks/",
            ".claude/hooks/",
            ".cursor/hooks/",
            ".codex/hooks/",
        ]
        hook_dirs = [project_root / ".github" / "hooks"]

        if targets:
            from apm_cli.integration.targets import KNOWN_TARGETS

            for target in targets:
COMPILE_OK

patched uninstall engine
 src/apm_cli/commands/uninstall/engine.py   |   1 +
 src/apm_cli/integration/hook_integrator.py | 255 ++++++++++++++++++++++-------
 2 files changed, 199 insertions(+), 57 deletions(-)
diff --git a/src/apm_cli/commands/uninstall/engine.py b/src/apm_cli/commands/uninstall/engine.py
index c2e7165..55cd0bb 100644
--- a/src/apm_cli/commands/uninstall/engine.py
+++ b/src/apm_cli/commands/uninstall/engine.py
@@ -310,6 +310,7 @@ def _sync_integrations_after_uninstall(apm_package, project_root, all_deployed_f
     result = _integrators["hooks"].sync_integration(
         apm_package, project_root,
         managed_files=_buckets["hooks"] if _buckets else None,

+        targets=_resolved_targets,
     )
     counts["hooks"] = result.get("files_removed", 0)

rewrite: pwsh -File .github/hooks/scripts/my-pkg/scripts/scan.ps1 [(PosixPath('/tmp/tmpeci64eq3/apm_modules/my-pkg/scripts/scan.ps1'), '.github/hooks/scripts/my-pkg/scripts/scan.ps1')]
integrated: 1 0 ['.copilot/hooks/my-pkg-hooks.json']
copilot hooks exists True
github hooks exists False
{
  "hooks": {
    "preToolUse": [
      {
        "type": "command",
        "bash": "./scripts/scan.sh",
        "windows": ".\\scripts\\scan.ps1"
      }

    ],
    "PreToolUse": [
      {
        "matcher": "Bash",
        "hooks": [
          {
            "type": "command",
            "command": "pwsh -File .\\scripts\\scan.ps1",
            "windows": "pwsh .\\scripts\\scan.ps1"
          }
        ]
      }
    ]
  }
}

sync: {'files_removed': 1, 'errors': 0}
remaining copilot: []

def test_integrate_hooks_from_apm_convention(self, temp_project):
        """Test VSCode integration using .apm/hooks/ convention."""
        pkg_dir = temp_project / "apm_modules" / "myorg" / "security-hooks"
        hooks_dir = pkg_dir / ".apm" / "hooks"
        scripts_dir = pkg_dir / "scripts"
        hooks_dir.mkdir(parents=True)
        scripts_dir.mkdir(parents=True)

        hook_data = {
            "hooks": {
                "PreToolUse": [
                    {

                        "hooks": [
                            {"type": "command", "command": "./scripts/validate.sh"}
                        ]
                    }
                ]
            }
        }
        (hooks_dir / "security.json").write_text(json.dumps(hook_data))
        (scripts_dir / "validate.sh").write_text("#!/bin/bash\necho 'validate'")

        pkg_info = _make_package_info(pkg_dir, "secur
…[1140 chars omitted]…
pkg_info, temp_project)

        assert result.files_integrated == 1
        assert result.scripts_copied == 0  # No scripts to copy for system commands

        target_json = temp_project / ".github" / "hooks" / "format-pkg-format.json"
        data = json.loads(target_json.read_text())
        cmd = data["hooks"]["PreToolUse"][0]["hooks"][0]["command"]
        assert cmd == "npx prettier --check ."

'.\\scripts\\scan.ps1' => '.github/hooks/scripts/my-pkg/scripts/scan.ps1' [(PosixPath('/tmp/tmpjckut9ir/pkg/scripts/scan.ps1'), '.github/hooks/scripts/my-pkg/scripts/scan.ps1')]
'pwsh -File .\\scripts\\scan.ps1' => 'pwsh -File .github/hooks/scripts/my-pkg/scripts/scan.ps1' [(PosixPath('/tmp/tmpjckut9ir/pkg/scripts/scan.ps1'), '.github/hooks/scripts/my-pkg/scripts/scan.ps1')]
'pwsh .\\scripts\\scan.ps1' => 'pwsh .github/hooks/scripts/my-pkg/scripts/scan.ps1' [(PosixPath('/tmp/tmpjckut9ir/pkg/scripts/scan.ps1'), '.github/hooks/scripts/my-pkg/scripts/scan.ps1')]
'${CLAUDE_PLUGIN_ROOT}\\hooks\\validate.ps1' => '.github/hooks/scripts/my-pkg/hooks/validate.ps1' [(PosixPath('/tmp/tmpjckut9ir/pkg/hooks/validate.ps1'), '.github/hooks/scripts/my-pkg/hooks/validate.ps1')]
'${CLAUDE_PLUGIN_ROOT}/hooks/validate.ps1' => '.github/hooks/scripts/my-pkg/hooks/validate.ps1' [(PosixPath('/tmp/tmpjckut9ir
…[90 chars omitted]…
scan.ps1' => '.github/hooks/scripts/my-pkg/scripts/scan.ps1' [(PosixPath('/tmp/tmpjckut9ir/pkg/scripts/scan.ps1'), '.github/hooks/scripts/my-pkg/scripts/scan.ps1')]
'pwsh -File .\\scripts\\scan.ps1' => 'pwsh -File .claude/hooks/my-pkg/scripts/scan.ps1' [(PosixPath('/tmp/tmpjckut9ir/pkg/scripts/scan.ps1'), '.claude/hooks/my-pkg/scripts/scan.ps1')]
'.\\..\\..\\secrets.txt' => '.\\..\\..\\secrets.txt' []

copilot ('pwsh -File .copilot/hooks/scripts/my-pkg/scripts/scan.ps1', [(PosixPath('/tmp/tmp96jtu9ax/pkg/scripts/scan.ps1'), '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1')])
copilot ('pwsh -File .github/hooks/scripts/my-pkg/scripts/scan.ps1', [(PosixPath('/tmp/tmp96jtu9ax/pkg/scripts/scan.ps1'), '.github/hooks/scripts/my-pkg/scripts/scan.ps1')])
vscode ('pwsh -File .github/hooks/scripts/my-pkg/scripts/scan.ps1', [(PosixPath('/tmp/tmp96jtu9ax/pkg/scripts/scan.ps1'), '.github/hooks/scripts/my-pkg/scripts/scan.ps1')])
claude ('pwsh -File .claude/hooks/my-pkg/scripts/scan.ps1', [(PosixPath('/tmp/tmp96jtu9ax/pkg/scripts/scan.ps1'), '.claude/hooks/my-pkg/scripts/scan.ps1')])
cursor ('pwsh -File .cursor/hooks/my-pkg/scripts/scan.ps1', [(PosixPath('/tmp/tmp96jtu9ax/pkg/scripts/scan.ps1'), '.cursor/hooks/my-pkg/scripts/scan.ps1')])
codex ('pwsh -File .codex/hooks/my-pkg/scripts/scan.ps1', [(PosixPath('/tmp/tmp96jtu9ax/pkg/scripts/scan.ps1'), '.codex/hooks/my-pkg/scripts/scan.ps1')])
weird ('pwsh -File .claude/hooks/my-pkg/scripts/scan.ps1', [(PosixPath('/tmp/tmp96jtu9ax/pkg/scripts/scan.ps1'), '.claude/hooks/my-pkg/scripts/scan.ps1')])

......................................................................   [100%]
70 passed in 1.46s

........................................................................ [ 11%]
........................................................................ [ 23%]
........................................................................ [ 34%]
........................................................................ [ 46%]
........................................................................ [ 57%]
........................................................................ [ 69%]
........................................................................ [ 80%]
........................................................................ [ 92%]
...............................................                          [100%]
623 passed in 3.86s

Traceback (most recent call last):
  File "/tmp/repro_hooks2.py", line 46, in <module>
    assert len(sc) == 1 and sc[0][1] == expected, sc
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError: [(PosixPath('/tmp/tmp25_x8jvp/apm_modules/my-pkg/scripts/scan.ps1'), '.github/hooks/scripts/my-pkg/scripts/scan.ps1')]

38	for cmd, expected in [
    39	    (r".\scripts\scan.ps1", ".github/hooks/scripts/my-pkg/scripts/scan.ps1"),
    40	    (r"pwsh -File .\scripts\scan.ps1", "pwsh -File .github/hooks/scripts/my-pkg/scripts/scan.ps1"),
    41	    (r"pwsh .\scripts\scan.ps1", "pwsh .github/hooks/scripts/my-pkg/scripts/scan.ps1"),
    42	    (r"${CLAUDE_PLUGIN_ROOT}\scripts\scan.ps1", ".github/hooks/scripts/my-pkg/scripts/scan.ps1"),
    43	]:
    44	    out, sc = integrator._rewrite_command_for_target(cmd, pkg, "my-pkg", "vscode")
    45	    assert out == expected, (cmd, out)
    46	    assert len(sc) == 1 and sc[0][1] == expected, sc
    47	    assert "\\" not in out
    48	
    49	out, sc = integrator._rewrite_command_for_target(r".\..\..\secrets.txt", pkg, "my-pkg", "vscode")

    50	assert out == r".\..\..\secrets.txt" and not sc

integrated: 1 1 ['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
Traceback (most recent call last):
  File "/tmp/repro_hooks2.py", line 70, in <module>
    assert (tmp/".copilot"/"hooks"/"scripts"/"my-pkg"/"scripts"/"scan.sh").exists()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError

integrated: 1 2 ['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.sh', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
sync: {'files_removed': 3, 'errors': 0}
Traceback (most recent call last):
  File "/tmp/repro_hooks2.py", line 99, in <module>
    assert stats["files_removed"] == 1
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError

patched sync string target roots
integrated: 1 2 ['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.sh', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
sync: {'files_removed': 3, 'errors': 0}
ALL OK
OK

grep: src/apm_cli/integration/__pycache__/hook_integrator.cpython-312.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_hook_integrator.cpython-312-pytest-9.2.0.pyc: binary file matches

1 2 ['.copilot/hooks/pkg-hooks.json', '.copilot/hooks/scripts/pkg/hooks/validate.ps1', '.copilot/hooks/scripts/pkg/scripts/scan.ps1']
Traceback (most recent call last):
  File "<stdin>", line 17, in <module>
  File "/usr/local/lib/python3.12/pathlib.py", line 1027, in read_text
    with self.open(mode='r', encoding=encoding, errors=errors) as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/pathlib.py", line 1013, in open
    return io.open(self, mode, buffering, encoding, errors, newline)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp0yrm7b6a/.copilot/hooks/my-pkg-hooks.json'

1 1 ['.copilot/hooks/pkg-hooks.json', '.copilot/hooks/scripts/pkg/scripts/scan.ps1']
{
  "hooks": {
    "preToolUse": [
      {
        "type": "command",
        "windows": ".copilot/hooks/scripts/pkg/scripts/scan.ps1"
      }
    ]
  }
}

Traceback (most recent call last):
  File "<stdin>", line 19, in <module>
ValueError: substring not found
134:    def find_hook_files(self, package_path: Path) -> List[Path]:
142:            package_path: Path to the package directory
151:        apm_hooks = package_path / ".apm" / "hooks"
160:        hooks_dir = package_path / "hooks"
189:    def _canonical_target_name(target) -> Optional[str]:
196:    def _hooks_scripts_base(self, target, package_name: str) -> str:
205:        target_name = getattr(target, "name", target)
213:            canonical = "copilot" if target_name in ("vscode", "agents") else target_name
216:                target_name = profile.name

219:            elif target_name not in (None, "claude", "cursor", "codex"):
223:        if target_name in ("vscode", "agents"):
224:            target_name = "copilot"
231:        if target_name == "copilot":
237:    def _rew
…[297 chars omitted]…
oup(1)[1:], package_path)
306:        resolve_base = hook_file_dir if hook_file_dir else package_path
329:    def _rewrite_hooks_data(
332:        package_path: Path,
343:            package_path: Root path of the source package
367:                            matcher[key], package_path, package_name, target,
386:                                hook[key], package_path, package_name, target,
COMPILE_OK

def _rewrite_command_for_target($
        self,$
        command: str,$
        package_path: Path,$
        package_name: str,$
        target,$
        hook_file_dir: Optional[Path] = None,$
    ) -> Tuple[str, List[Tuple[Path, str]]]:$
        """Rewrite a hook command to use installed script paths.$
$
        Handles:$
        - ${CLAUDE_PLUGIN_ROOT}/path and ${CLAUDE_PLUGIN_ROOT}\\path$

          references (resolved from package root)$
        - ./path and .\\path relative references (resolved from the hook$
          file's parent directory)$
$
        Rewritten commands and target paths use forward slashes only.$
$
        Args:$
            command: Original command string$
            package_path: Root path of the source package$
            package_name: Name used for the scripts subdirectory$
            target: TargetProfile or target name (e.g. "vscode", "claude")$

…[1035 chars omitted]…
         data: Parsed hook JSON data$
            package_path: Root path of the source package$
            package_name: Name for scripts subdirectory$
            target: "vscode" or "claude"$
            hook_file_dir: Directory containing the hook JSON file (for ./path resolution)$
$
        Returns:$
            Tuple of (rewritten_data_copy, list of (source_file, target_rel_path))$
        """$

Traceback (most recent call last):
  File "<stdin>", line 18, in <module>
ValueError: substring not found
    def _rewrite_command_for_target(
        self,
        command: str,
        package_path: Path,
        package_name: str,
        target,
        hook_file_dir: Optional[Path] = None,
    ) -> Tuple[str, List[Tuple[Path, str]]]:
        """Rewrite a hook command to use installed script paths.

        Handles:
        - ${CLAUDE_PLUGIN_ROOT}/path and ${CLAUDE_PLUGIN_ROOT}\\path
          references (resolved from package root)
        - ./path and .\\path relative references (resolved from the hook
          file's parent directory)

        Rewritten commands and target paths use forward slashes only.

        Args:
            command: Original command string
            package_path: Root path of the source package
            package_name: Name used for the scripts subdi
…[464 chars omitted]…
.resolve()
        scripts_base = self._hooks_scripts_base(target, package_name)
        new_command = command

        def _resolve_reference(
            rel_path: str, resolve_base: Path
        ) -> Optional[Tuple[Path, str]]:
39:                            matcher[key], package_path, package_name, target,
58:                                hook[key], package_path, package_name, target,
COMPILE_OK

329:    def _rewrite_hooks_data(
407:    def _get_package_name(self, package_info) -> str:

'    def _rewrite_command_for_target(\n' 8654
'    def _rewrite_hooks_data(\n' 12608
'    def _get_package_name(\n' -1
after first -1 12618
start2 12618
ERR substring not found
'    def _rewrite_hooks_data(\n        self,\n        data: Dict,\n        package_path: Path,\n        package_name: str,\n        target: str,\n        hook_file_dir: Optional[Path] = None,\n    ) -> Tuple[Dict, List[Tuple[Path, str]]]:\n        """Rewrite all command paths in a hooks JSON structure.\n\n        Creates a deep copy and rewrites command paths for the target platform.\n\n        Args:\n            data: Parsed hook JSON data\n            package_path: Root path of the source package\n            package_name: Name for scripts subdirectory\n            target: "vscode" or "claude"\n            ho'

renamed parameters
    def _rewrite_command_for_target(
        self,
        command: str,
        package_dir: Path,
        package_name: str,
        target_name,
        hook_file_dir: Optional[Path] = None,
    ) -> Tuple[str, List[Tuple[Path, str]]]:
        """Rewrite a hook command to use installed script paths.

        Handles:

        - ${CLAUDE_PLUGIN_ROOT}/path and ${CLAUDE_PLUGIN_ROOT}\\path
    def _rewrite_hooks_data(
        self,
        data: Dict,
        package_dir: Path,
        package_name: str,
        target_name,
        hook_file_dir: Optional[Path] = None,
    ) -> Tuple[Dict, List[Tuple[Path, str]]]:
        """Rewrite all command paths in a hooks JSON structure.

        Creates a deep copy and rewrites command paths for the target platform.

        Args:
            data: Parsed hook JSON data
            package_dir: Root path of the source package

…[1352 chars omitted]…
_COMMAND_KEYS:
                        if key in hook:
                            new_cmd, scripts = self._rewrite_command_for_target(
                                hook[key], package_dir, package_name, target_name,
                                hook_file_dir=hook_file_dir,
                            )
                            if scripts:
                                _log.debug(
COMPILE_OK

integrated: 1 2 ['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.sh', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
sync: {'files_removed': 3, 'errors': 0}
ALL OK
........................................................................ [ 38%]
........................................................................ [ 76%]
.............................................                            [100%]
189 passed in 1.80s

15:- Hook merge logic deduplicated: three copy-pasted JSON-merge methods replaced with `_integrate_merged_hooks()` + config dict (#562)
25:- Hook integrator now processes the `windows` property in hook JSON files, copying referenced scripts and rewriting paths during install/compile (#311)
52:- Codex as integration target: skills to `.agents/skills/`, agents to `.codex/agents/*.toml`, hooks to `.codex/hooks.json`, `--target codex` on install/compile/pack (#504)
126:- SSL certificate verification in PyInstaller binary via `certifi` runtime hook (#429)
234:- Native Cursor IDE integration — `apm install` deploys instructions→rules (`.mdc`), agents, skills, hooks (`hooks.json`), and MCP (`mcp.json`) to `.cursor/` (#301)
367:- Support hooks as an agent primitive with install-time integration and dependency display (hooks execute at agent runtime, not during `apm install`) (#97)
src/apm_cli
…[4623 chars omitted]…
argets.py:260:        user_root_dir=".config/opencode",
src/apm_cli/integration/targets.py:329:    2. **Directory detection**: profiles whose ``effective_root(user_scope=True)``
src/apm_cli/integration/targets.py:355:        if p.user_supported and (home / p.effective_root(user_scope=True)).is_dir()
src/apm_cli/integration/targets.py:422:    the requested scope -- no ``effective_root()`` calls needed.

replaced helper
        except (json.JSONDecodeError, OSError):
            return None

    def _hooks_scripts_base(self, target, package_name: str) -> str:
        """Return the target-relative directory for copied hook scripts.

        ``target`` may be a :class:`TargetProfile` (possibly scope-resolved)
        or one of the legacy target-name strings accepted by this integrator.
        The returned path always uses forward slashes.
        """
        from apm_cli.integration.targets import KNOWN_TARGETS

        target_name = getattr(target, "name", target)
        root_dir = getattr(target, "root_dir", None)
        mapping = None

        if target is not None and not isinstance(target, str):
            primitives = getattr(target, "primitives", None)
            if isinstance(primitives, dict):
                mapping = primitives.get("hooks")
            if not isinstance(
…[1530 chars omitted]…
}/{subdir}/scripts/{package_name}"
        return f"{root_dir}/{subdir}/{package_name}"

    def _rewrite_command_for_target(
        self,
        command: str,
        package_dir: Path,
        package_name: str,
        target_name,
        hook_file_dir: Optional[Path] = None,
    ) -> Tuple[str, List[Tuple[Path, str]]]:
        """Rewrite a hook command to use installed script paths.

COMPILE_OK

patched sync fallback
            ".claude/hooks/",
            ".cursor/hooks/",
            ".codex/hooks/",
        ]
        hook_dirs = [project_root / ".github" / "hooks"]

        if targets:
            from apm_cli.integration.targets import KNOWN_TARGETS

            for target in targets:
                profile = target

                if isinstance(target, str):
                    canonical = "copilot" if target in ("vscode", "agents") else target
                    profile = KNOWN_TARGETS.get(canonical)
                    if profile is None:
                        continue
                primitives = getattr(profile, "primitives", None)
                mapping = (
                    primitives.get("hooks")
                    if isinstance(primitives, dict)
                    else None
                )
                deploy_root = (
                    getattr(m
…[1279 chars omitted]…
                  hook_dir = hook_dir / subdir
                    if hook_dir not in hook_dirs:
                        hook_dirs.append(hook_dir)

        if managed_files is not None:
            # Manifest-based removal  -- only remove tracked files
            deleted: list = []
            for rel_path in managed_files:
                # Normalize path separators for cross-platform compatibility

1 1 ['.copilot/hooks/pkg-hooks.json', '.copilot/hooks/scripts/pkg/scripts/scan.ps1']
{'files_removed': 2, 'errors': 0}
SIMPLE OK
integrated: 1 2 ['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.sh', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
sync: {'files_removed': 3, 'errors': 0}
ALL OK
........................................................................ [ 11%]
........................................................................ [ 23%]
........................................................................ [ 34%]
........................................................................ [ 46%]
........................................................................ [ 57%]
........................................................................ [ 69%]

........................................................................ [ 80%]
........................................................................ [ 92%]
...............................................                          [100%]
623 passed in 3.44s

diff --git a/src/apm_cli/integration/hook_integrator.py b/src/apm_cli/integration/hook_integrator.py
index c174edd..2c9c0a3 100644
--- a/src/apm_cli/integration/hook_integrator.py
+++ b/src/apm_cli/integration/hook_integrator.py
@@ -185,83 +185,157 @@ class HookIntegrator(BaseIntegrator):
         except (json.JSONDecodeError, OSError):
             return None
 
+    def _hooks_scripts_base(self, target, package_name: str) -> str:
+        """Return the target-relative directory for copied hook scripts.
+
+        ``target`` may be a :class:`TargetProfile` (possibly scope-resolved)

+        or one of the legacy target-name strings accepted by this integrator.
+        The returned path always uses forward slashes.
+        """
+        from apm_cli.integration.targets import KNOWN_TARGETS
+
+        target_name = getattr(target, "name", target)
+        root_dir = getattr(target, "ro
…[8629 chars omitted]…
ved': 0, 'errors': 0}
 
+        hook_prefixes = [
+            ".github/hooks/",
+            ".claude/hooks/",
+            ".cursor/hooks/",
+            ".codex/hooks/",
+        ]
+        hook_dirs = [project_root / ".github" / "hooks"]
+
+        if targets:
+            from apm_cli.integration.targets import KNOWN_TARGETS
+
+            for target in targets:
+                profile = target

Handles:
        - ${CLAUDE_PLUGIN_ROOT}/path and ${CLAUDE_PLUGIN_ROOT}\\path
          references (resolved from package root)
        - ./path and .\\path relative references (resolved from the hook
          file's parent directory)

        Rewritten commands and target paths use forward slashes only.

        Args:
            command: Original command string
            package_dir: Root path of the source package
            package_name: Name used for the scripts subdirectory

            target_name: TargetProfile or target name (e.g. "vscode", "claude")
            hook_file_dir: Directory containing the hook JSON file (for ./path resolution)

        Returns:
            Tuple of (rewritten_command, list of (source_file, relative_target_path))
        """
        scripts_to_copy: List[Tuple[Path, str]] = []
        if not isinstance(command, str):
            return
…[8629 chars omitted]…
 filtered = [
                                m for m in matchers
                                if not (isinstance(m, dict) and "_apm_source" in m)
                            ]
                            if len(filtered) != len(matchers):
                                modified = True
                            settings["hooks"][event_name] = filtered
                            if not filtered:

........................................................................ [  1%]
........................................................................ [  3%]
........................................................................ [  5%]
........................................................................ [  7%]
........................................................................ [  9%]
........................................................................ [ 11%]
........................................................................ [ 13%]
........................................................................ [ 15%]
........................................................................ [ 17%]
........................................................................ [ 19%]
........................................................................ [ 21%]
.................

…[8630 chars omitted]…
 'api.mcp.github.com' ([Errno -3] Temporary failure in name resolution)"))

/usr/local/lib/python3.12/site-packages/requests/adapters.py:729: ConnectionError
=========================== short test summary info ============================
FAILED tests/unit/test_registry_client.py::TestSimpleRegistryClient::test_find_server_by_reference_uuid_not_found
1 failed, 3652 passed, 12 subtests passed in 30.86s

assert len(scripts) == 1

    def test_integrate_hooks_with_scripts_in_hooks_subdir(self, temp_project):
        """Test full integration when hook JSON and scripts are both inside hooks/ subdir."""
        pkg_dir = temp_project / "apm_modules" / "myorg" / "lint-hooks"
        hooks_dir = pkg_dir / "hooks"
        scripts_dir = hooks_dir / "scripts"
        scripts_dir.mkdir(parents=True)

        hook_data = {
            "hooks": {
                "PostToolUse": [

                    {
                        "matcher": {"tool_name": "write_to_file"},
                        "hooks": [
                            {"type": "command", "command": "./scripts/lint.sh", "timeout": 10}
                        ]
                    }
                ]
            }
        }
        (hooks_dir / "hooks.json").write_text(json.dumps(hook_data))
        (scripts_dir / "lint.sh").write
…[2578 chars omitted]…
  assert "./" not in cmd

        # Verify script was copied to Claude target location
        copied_script = temp_project / ".claude" / "hooks" / "lint-hooks" / "scripts" / "lint.sh"
        assert copied_script.exists()
        assert copied_script.read_text() == "#!/bin/bash\necho lint"


# ─── Cursor integration tests ────────────────────────────────────────────────


class TestCursorIntegration:

2:src/apm_cli/commands/uninstall/engine.py:310:    result = _integrators["hooks"].sync_integration(

grep: src/apm_cli/core/__pycache__/target_detection.cpython-312.pyc: binary file matches
grep: src/apm_cli/integration/__pycache__/hook_integrator.cpython-312.pyc: binary file matches
grep: src/apm_cli/policy/__pycache__/policy_checks.cpython-312.pyc: binary file matches
src/apm_cli/integration/hook_integrator.py:4:installation. Supports VSCode Copilot (.github/hooks/), Claude Code
src/apm_cli/integration/hook_integrator.py:112:    - VSCode: .github/hooks/<pkg>-<name>.json + .github/hooks/scripts/<pkg>/
src/apm_cli/integration/hook_integrator.py:129:    #   GH Copilot Agent: https://docs.github.com/en/copilot/concepts/agents/coding-agent/about-hooks
src/apm_cli/integration/hook_integrator.py:449:        By default hooks deploy to ``.github/hooks/`` (the VSCode/Copilot
src/apm_cli/integration/hook_integrator.py:744:            ".github/hooks/",
src/apm_cli/integration/hook_integrator.py:749:        hook_dirs = [project_root / ".github" / "hooks"]
src/apm_cli/policy/policy_checks.py:596:    ".github/hooks",

.\scripts\lint.ps1 => ('.github/hooks/scripts/my-pkg/scripts/lint.ps1', [(PosixPath('/tmp/tmpn6v50dg6/pkg/hooks/scripts/lint.ps1'), '.github/hooks/scripts/my-pkg/scripts/lint.ps1')])
pwsh -File .\scripts\lint.ps1 => ('pwsh -File .github/hooks/scripts/my-pkg/scripts/lint.ps1', [(PosixPath('/tmp/tmpn6v50dg6/pkg/hooks/scripts/lint.ps1'), '.github/hooks/scripts/my-pkg/scripts/lint.ps1')])
${CLAUDE_PLUGIN_ROOT}\hooks\scripts\lint.ps1 => ('.github/hooks/scripts/my-pkg/hooks/scripts/lint.ps1', [(PosixPath('/tmp/tmpn6v50dg6/pkg/hooks/scripts/lint.ps1'), '.github/hooks/scripts/my-pkg/hooks/scripts/lint.ps1')])

M src/apm_cli/commands/uninstall/engine.py
 M src/apm_cli/integration/hook_integrator.py

data: Dict,
        package_dir: Path,
        package_name: str,
        target_name,
        hook_file_dir: Optional[Path] = None,
    ) -> Tuple[Dict, List[Tuple[Path, str]]]:
        """Rewrite all command paths in a hooks JSON structure.

        Creates a deep copy and rewrites command paths for the target platform.

        Args:
            data: Parsed hook JSON data

            package_dir: Root path of the source package
            package_name: Name for scripts subdirectory
            target_name: TargetProfile or target name
            hook_file_dir: Directory containing the hook JSON file (for ./path resolution)

        Returns:
            Tuple of (rewritten_data_copy, list of (source_file, target_rel_path))
        """
        import copy
        rewritten = copy.deepcopy(data)
        all_scripts: List[Tuple[Path, str]] = []

        hooks = rewritten.get
…[2627 chars omitted]…
t a short package name for use in file/directory naming.

        Args:
            package_info: PackageInfo object

        Returns:
            str: Package name derived from install path
        """
        return package_info.install_path.name

    @staticmethod
    def _target_root_dir(target) -> str:
        """Return the scope-resolved root directory for *target*."""
        if target is None:

ssssssssssssssssssss.ssssssssssssssssssssssssssssssss...s..............F [ 25%]

=================================== FAILURES ===================================
_______________________ test_permission_denied_graceful ________________________

tmp_path = PosixPath('/tmp/pytest-of-root/pytest-4/test_permission_denied_gracefu0')

    @pytest.mark.skipif(sys.platform == "win32", reason="Windows handles read-only directories differently")
    def test_permission_denied_graceful(tmp_path: Path):
        # Use temp project with constitution to force write
        with temp_project_with_constitution(constitution_text=DEFAULT_CONSTITUTION) as proj:
            agents = Path(proj) / "AGENTS.md"

            agents.write_text("placeholder", encoding="utf-8")
    
            # Make the directory unwriteable (this prevents tempfile creation during atomic write)
            proj_path = Path(proj)

…[656 chars omitted]…
───╯\n', stderr='').returncode

/repo/tests/integration/test_compile_permission_denied.py:30: AssertionError
=========================== short test summary info ============================
FAILED tests/integration/test_compile_permission_denied.py::test_permission_denied_graceful
!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!
1 failed, 18 passed, 53 skipped in 17.88s

12:def portable_relpath(path: Path, base: Path) -> str:
13-    """Return a forward-slash relative path, resolving both sides first.
14-
15-    Handles Windows 8.3 short names (e.g. ``RUNNER~1`` vs ``runneradmin``)
16-    and ensures consistent POSIX output on every platform.
17-
18-    When *path* is not under *base* (or resolution fails), falls back to
19-    a resolved absolute POSIX path.
20-    """
21-    try:
22-        return path.resolve().relative_to(base.resolve()).as_posix()
23-    except (ValueError, OSError, RuntimeError):

24-        try:
25-            return path.resolve().as_posix()
26-        except (OSError, RuntimeError):
27-            return path.as_posix()

patched casts
integrated: 1 2 ['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.sh', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
sync: {'files_removed': 3, 'errors': 0}
ALL OK
......................................................................   [100%]
70 passed in 1.74s

'${CLAUDE_PLUGIN_ROOT}\\..\\secret.txt' => ('${CLAUDE_PLUGIN_ROOT}\\..\\secret.txt', [])
'.\\..\\secret.txt' => ('.\\..\\secret.txt', [])
'..\\secret.txt' => ('..\\secret.txt', [])
'..\\..\\secret.txt' => ('..\\..\\secret.txt', [])
'pwsh -File .\\..\\secret.txt' => ('pwsh -File .\\..\\secret.txt', [])

['.copilot/hooks/pkg-hooks.json', '.copilot/hooks/scripts/pkg/scripts/scan.sh']
{
  "hooks": {
    "x": [
      {
        "command": ".copilot/hooks/scripts/pkg/scripts/scan.sh"
      }
    ]
  }
}

grep: src/apm_cli/commands/__pycache__/install.cpython-312.pyc: binary file matches
grep: src/apm_cli/integration/__pycache__/base_integrator.cpython-312.pyc: binary file matches
grep: src/apm_cli/integration/__pycache__/dispatch.cpython-312.pyc: binary file matches
grep: src/apm_cli/integration/__pycache__/hook_integrator.cpython-312.pyc: binary file matches
grep: src/apm_cli/integration/__pycache__/__init__.cpython-312.pyc: binary file matches
src/apm_cli/commands/install.py:961:    hook_integrator,
src/apm_cli/commands/install.py:1011:        "hooks": hook_integrator,
src/apm_cli/commands/install.py:1454:        from apm_cli.integration.hook_integrator import HookIntegrator
src/apm_cli/commands/install.py:1459:        hook_integrator = HookIntegrator()
src/apm_cli/commands/install.py:1800:                            hook_integrator=hook_integrator,
src/apm_cli/commands/install.py:2
…[385 chars omitted]…

or
src/apm_cli/integration/dispatch.py:58:        "hooks":        PrimitiveDispatch(HookIntegrator,         "integrate_hooks_for_target",         "sync_integration",  "hooks"),
src/apm_cli/integration/hook_integrator.py:107:class HookIntegrator(BaseIntegrator):
src/apm_cli/integration/__init__.py:6:from .hook_integrator import HookIntegrator
src/apm_cli/integration/__init__.py:38:    'HookIntegrator',

added target aliases
('.github/hooks/scripts/p/scripts/x.sh', [(PosixPath('/tmp/tmp5qbf14hg/pkg/scripts/x.sh'), '.github/hooks/scripts/p/scripts/x.sh')])
('.github/hooks/scripts/p/scripts/x.sh', [(PosixPath('/tmp/tmp5qbf14hg/pkg/scripts/x.sh'), '.github/hooks/scripts/p/scripts/x.sh')])
[(PosixPath('/tmp/tmp5qbf14hg/pkg/scripts/x.sh'), '.github/hooks/scripts/p/scripts/x.sh')]
[(PosixPath('/tmp/tmp5qbf14hg/pkg/scripts/x.sh'), '.github/hooks/scripts/p/scripts/x.sh')]
integrated: 1 2 ['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.sh', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
sync: {'files_removed': 3, 'errors': 0}
ALL OK
......................................................................   [100%]
70 passed in 1.62s

pwsh -File .github/hooks/scripts/p/scripts/scan.ps1 -NoProfile

pwsh -File .github/hooks/scripts/p/hooks/v.ps1

[TargetProfile(name='copilot', root_dir='.copilot', primitives={'agents': PrimitiveMapping(subdir='agents', extension='.agent.md', format_id='github_agent', deploy_root=None), 'skills': PrimitiveMapping(subdir='skills', extension='/SKILL.md', format_id='skill_standard', deploy_root=None), 'hooks': PrimitiveMapping(subdir='hooks', extension='.json', format_id='github_hooks', deploy_root=None)}, auto_create=True, detect_by_dir=True, user_supported='partial', user_root_dir='.copilot', unsupported_user_primitives=('prompts', 'instructions'))] ['.copilot']
['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
{'files_removed': 2, 'errors': 0}
RESOLVE OK

src/apm_cli/commands/uninstall/engine.py   |   1 +
 src/apm_cli/integration/hook_integrator.py | 303 ++++++++++++++++++++++-------
 2 files changed, 237 insertions(+), 67 deletions(-)
 M src/apm_cli/commands/uninstall/engine.py
 M src/apm_cli/integration/hook_integrator.py
........................................................................ [ 32%]
........................................................................ [ 65%]
........................................................................ [ 98%]
....                                                                     [100%]
220 passed in 2.33s

300	
   301	        def _replace_plugin_root(match: "re.Match[str]") -> str:
   302	            resolved = _resolve_reference(match.group(1)[1:], package_dir)
   303	            if resolved is None:
   304	                return match.group(0)
   305	            source_file, target_rel = resolved
   306	            scripts_to_copy.append((source_file, target_rel))
   307	            return target_rel
   308	
   309	        new_command = plugin_root_pattern.sub(_replace_plugin_root, new_command)
   310	
   311	        # Handle relative ./path and .\path references (safe to run after

   312	        # ${CLAUDE_PLUGIN_ROOT} substitution since replacements produce paths
   313	        # like ".github/..." not "./..."). Resolve from hook file's directory
   314	        # if available, else fall back to package root.
   315	        resolve_base = hook_file_dir if hook_file_dir else packag
…[5302 chars omitted]…
ue_scripts
   420	
   421	    def _get_package_name(self, package_info) -> str:
   422	        """Get a short package name for use in file/directory naming.
   423	
   424	        Args:
   425	            package_info: PackageInfo object
   426	
   427	        Returns:
   428	            str: Package name derived from install path
   429	        """
   430	        return package_info.install_path.name

{'files_removed': 1, 'errors': 0} False True

grep: tests/unit/integration/__pycache__/test_agent_integrator.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_command_integrator.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_deployed_files_manifest.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_hook_integrator.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_instruction_integrator.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_prompt_integrator.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_scope_install_uninstall.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_skill_integrator.cpython-312-pytest-9.
…[2053 chars omitted]…
roject)
tests/unit/integration/test_hook_integrator.py:978:        integrator.sync_integration(None, temp_project)
tests/unit/integration/test_hook_integrator.py:1662:        stats = integrator.sync_integration(None, temp_project, managed_files=managed_files)

tests/unit/integration/test_hook_integrator.py:1705:        stats = integrator.sync_integration(None, temp_project, managed_files=managed_files)

..............................                                           [100%]
30 passed in 2.18s

('bash .github/hooks/scripts/p/scripts/a.sh && pwsh -File .github/hooks/scripts/p/scripts/b.ps1', [(PosixPath('/tmp/tmp0uuyuudb/pkg/scripts/a.sh'), '.github/hooks/scripts/p/scripts/a.sh'), (PosixPath('/tmp/tmp0uuyuudb/pkg/scripts/b.ps1'), '.github/hooks/scripts/p/scripts/b.ps1')])

patched sync skip string no hooks
integrated: 1 2 ['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.sh', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
sync: {'files_removed': 3, 'errors': 0}
ALL OK
........................................................................ [ 53%]
..............................................................           [100%]
134 passed in 1.83s

{'files_removed': 1, 'errors': 0} False

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…[2822 chars omitted]…
..................... [ 92%]
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3652 passed, 1 deselected, 12 subtests passed in 27.29s

.\scripts\scan.ps1 1 {'command': '.github/hooks/scripts/pkg/scripts/scan.ps1', 'windows': '.github/hooks/scripts/pkg/scripts/scan.ps1'}
pwsh -File .\scripts\scan.ps1 1 {'command': 'pwsh -File .github/hooks/scripts/pkg/scripts/scan.ps1', 'windows': 'pwsh -File .github/hooks/scripts/pkg/scripts/scan.ps1'}

added positional target detection
['.copilot/hooks/pkg-hooks.json']
POSITIONAL TARGET OK
integrated: 1 2 ['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.sh', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
sync: {'files_removed': 3, 'errors': 0}
ALL OK
......................................................................   [100%]
70 passed in 1.75s

468-            managed_files: Set of relative paths known to be APM-managed
469-            diagnostics: Optional diagnostics collector
470-            target: Optional TargetProfile (or target name) selecting the
471-                deployment root and script path layout
472-
473-        Returns:
474-            HookIntegrationResult: Results of the integration operation
475-        """
476:        # Accept a target profile passed positionally in the ``force`` slot
477-        # (``integrate_package_hooks(pkg, root, target)``) without breaking
478-        # the historical boolean ``force`` positional argument.
479-        if target is None and not isinstance(force, bool) and (

480-            hasattr(force, "root_dir") or isinstance(force, str)
481-        ):
482-            target = force
483-            force = False
484-
485-        hook_files = self.find_hook_files(package_info.install_path)
486-
487-        if not hook_files:
488-            return HookIntegrationResult(

patched sync primitives handling
integrated: 1 2 ['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.sh', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
sync: {'files_removed': 3, 'errors': 0}
ALL OK
........................................................................ [ 53%]
..............................................................           [100%]
134 passed in 1.80s

{'files_removed': 1, 'errors': 0}
{'files_removed': 0, 'errors': 0} True

diff --git a/src/apm_cli/integration/hook_integrator.py b/src/apm_cli/integration/hook_integrator.py
index c174edd..ad56158 100644
--- a/src/apm_cli/integration/hook_integrator.py
+++ b/src/apm_cli/integration/hook_integrator.py
@@ -185,84 +185,165 @@ class HookIntegrator(BaseIntegrator):
         except (json.JSONDecodeError, OSError):
             return None
 
+    def _hooks_scripts_base(self, target, package_name: str) -> str:
+        """Return the target-relative directory for copied hook scripts.
+
+        ``target`` may be a :class:`TargetProfile` (possibly scope-resolved)

+        or one of the legacy target-name strings accepted by this integrator.
+        The returned path always uses forward slashes.
+        """
+        from apm_cli.integration.targets import KNOWN_TARGETS
+
+        target_name = getattr(target, "name", target)
+        root_dir = getattr(target, "ro
…[8630 chars omitted]…
       # Legacy fallback  -- glob for old -apm suffix files
-            hooks_dir = project_root / ".github" / "hooks"
-            if hooks_dir.exists():
+            for hooks_dir in hook_dirs:
+                if not hooks_dir.exists():
+                    continue
                 for hook_file in hooks_dir.glob("*-apm.json"):
                     try:
                         hook_file.unlink()

pwsh -File ".\scripts\scan.ps1" => pwsh -File ".github/hooks/scripts/p/scripts/scan.ps1"
pwsh -File './scripts/scan.ps1' => pwsh -File '.github/hooks/scripts/p/scripts/scan.ps1'
${CLAUDE_PLUGIN_ROOT}\hooks\v.ps1 => ${CLAUDE_PLUGIN_ROOT}\hooks\v.ps1

patched sync canonical fallback
integrated: 1 2 ['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.sh', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
sync: {'files_removed': 3, 'errors': 0}
ALL OK
{'files_removed': 1, 'errors': 0} False
........................................................................ [ 38%]
........................................................................ [ 76%]
.............................................                            [100%]
189 passed in 2.09s

1 True True
{'files_removed': 2, 'errors': 0} True

patched copilot layout detection
('.copilot/hooks/scripts/p/scripts/x.ps1', [(PosixPath('/tmp/tmp4c9n_u97/pkg/scripts/x.ps1'), '.copilot/hooks/scripts/p/scripts/x.ps1')])
('.github/hooks/scripts/p/scripts/x.ps1', [(PosixPath('/tmp/tmp4c9n_u97/pkg/scripts/x.ps1'), '.github/hooks/scripts/p/scripts/x.ps1')])
integrated: 1 2 ['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.sh', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
sync: {'files_removed': 3, 'errors': 0}
ALL OK
......................................................................   [100%]
70 passed in 1.49s

would reformat src/apm_cli/commands/uninstall/engine.py
would reformat src/apm_cli/integration/hook_integrator.py

Oh no! 💥 💔 💥
2 files would be reformatted.

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…[3652 chars omitted]…
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623 passed in 4.50s
 M src/apm_cli/commands/uninstall/engine.py
 M src/apm_cli/integration/hook_integrator.py

patched sync user root for objects too
{'files_removed': 1, 'errors': 0} False
integrated: 1 2 ['.copilot/hooks/my-pkg-hooks.json', '.copilot/hooks/scripts/my-pkg/scripts/scan.sh', '.copilot/hooks/scripts/my-pkg/scripts/scan.ps1']
sync: {'files_removed': 3, 'errors': 0}
ALL OK
........................................................................ [ 38%]
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189 passed in 2.66s

........................................................................ [ 98%]
................................................................         [100%]
3652 passed, 1 deselected, 12 subtests passed in 32.20s
 M src/apm_cli/commands/uninstall/engine.py
 M src/apm_cli/integration/hook_integrator.py
 src/apm_cli/commands/uninstall/engine.py   |   1 +
 src/apm_cli/integration/hook_integrator.py | 333 +++++++++++++++++++++++------
 2 files changed, 267 insertions(+), 67 deletions(-)

diff --git a/src/apm_cli/integration/hook_integrator.py b/src/apm_cli/integration/hook_integrator.py
index c174edd..ea372d0 100644
--- a/src/apm_cli/integration/hook_integrator.py
+++ b/src/apm_cli/integration/hook_integrator.py
@@ -185,84 +185,168 @@ class HookIntegrator(BaseIntegrator):
         except (json.JSONDecodeError, OSError):
             return None
 
+    def _hooks_scripts_base(self, target, package_name: str) -> str:
+        """Return the target-relative directory for copied hook scripts.
+
+        ``target`` may be a :class:`TargetProfile` (possibly scope-resolved)

+        or one of the legacy target-name strings accepted by this integrator.
+        The returned path always uses forward slashes.
+        """
+        from apm_cli.integration.targets import KNOWN_TARGETS
+
+        target_name = getattr(target, "name", target)
+        root_dir = getattr(target, "ro
…[8629 chars omitted]…
self._rewrite_command_for_target(
-                                hook[key], package_path, package_name, target,
+                                hook[key], package_dir, package_name, target_name,
                                 hook_file_dir=hook_file_dir,
                             )
                             if scripts:
@@ -345,24 +432,59 @@ class HookIntegrator(BaseIntegrator):
         """

…[938 chars omitted]…
deployment, traversal rejection, and target-scoped cleanup pass. Full unit suite: 3652 passed (one unrelated network test deselected); integration suite: 623 passed."}
submitted.

/repo
total 416
drwxr-xr-x 1 root root   4096 Nov  4 02:44 .
drwxr-xr-x 1 root root   4096 Nov  4 02:44 ..
drwxr-xr-x 1 root root   4096 Nov  4 02:44 .apm
drwxr-xr-x 1 root root   4096 Nov  4 02:44 .git
-rw-r--r-- 1 root root     63 Nov  4 02:44 .gitattributes
drwxr-xr-x 1 root root   4096 Nov  4 02:44 .github
-rw-r--r-- 1 root root    784 Nov  4 02:44 .gitignore
drwxr-xr-x 1 root root   4096 Nov  4 02:44 .vscode
-rw-r--r-- 1 root root    295 Nov  4 02:44 AUTHORS
-rw-r--r-- 1 root root  33688 Nov  4 02:44 CHANGELOG.md

-rw-r--r-- 1 root root    558 Nov  4 02:44 CODE_OF_CONDUCT.md
-rw-r--r-- 1 root root   4086 Nov  4 02:44 CONTRIBUTING.md
-rw-r--r-- 1 root root   1074 Nov  4 02:44 LICENSE
-rw-r--r-- 1 root root   1577 Nov  4 02:44 MANIFESTO.md
-rw-r--r-- 1 root root   5474 Nov  4 02:44 README.md
-rw-r--r-- 1 root root    542 Nov  4 02:44 SECURITY.md
-rw-r--r-- 1 root root    548 Nov  4 
…[1965 chars omitted]…
st_distributed_compilation.py
./tests/test_empty_string_and_defaults.py
./tests/test_enhanced_discovery.py
./tests/test_github_downloader.py
./tests/test_github_downloader_token_precedence.py
./tests/test_lockfile.py
./tests/test_runnable_prompts.py
./tests/test_runtime_manager_token_precedence.py
./tests/test_token_manager.py
./tests/test_virtual_package_multi_install.py
./tests/__init__.py
./uv.lock

src/apm_cli/integration
src/apm_cli/integration/hook_integrator.py
src/apm_cli/registry/integration.py
tests/fixtures/mock-plugin/.apm/hooks
tests/integration
tests/integration/test_auto_integration.py
tests/integration/test_integration.py
tests/integration/test_llm_runtime_integration.py
tests/integration/test_marketplace_plugin_integration.py
tests/integration/test_multi_runtime_integration.py
tests/integration/test_registry_client_integration.py
tests/integration/test_runnable_prompts_integration.py

tests/integration/test_skill_integration.py
tests/test_collision_integration.py
tests/unit/integration
tests/unit/integration/test_hook_integrator.py
tests/unit/integration/test_scope_integration.py
tests/unit/integration/test_sync_integration_url_normalization.py
tests/unit/marketplace/test_marketplace_install_integration.py
tests/unit/test_registry_integration.py
tests/unit/test_ssl_cert_hook.py
tests/unit/test_uninstall_reintegration.py
bash: line 8: rg: command not found

"""Hook integration functionality for APM packages.

Integrates hook JSON files and their referenced scripts during package
installation. Supports VSCode Copilot (.github/hooks/), Claude Code
(.claude/settings.json), and Cursor (.cursor/hooks.json) targets.

Hook JSON format (Claude Code  -- nested matcher groups):
    {
        "hooks": {
            "PreToolUse": [
                {
                    "hooks": [

                        {"type": "command", "command": "./scripts/validate.sh", "timeout": 10}
                    ]
                }
            ]
        }
    }

Hook JSON format (GitHub Copilot  -- flat arrays with bash/powershell keys):
    {
        "version": 1,
        "hooks": {
            "preToolUse": [
                {"type": "command", "bash": "./scripts/validate.sh", "timeoutSec": 10}
            ]
        }
    }

Hook JSON format (Cursor  -- flat arrays w
…[8630 chars omitted]…
---------------------------------------------


class TestSkillScopeDeployment:
    """Verify skills deploy to scope-resolved paths."""

    def setup_method(self):
        self.temp_dir = tempfile.mkdtemp()
        self.project_root = Path(self.temp_dir)

    def teardown_method(self):
        shutil.rmtree(self.temp_dir, ignore_errors=True)

    def test_skill_deploys_to_copilot_at_user_scope(self):

160:        hooks_dir = package_path / "hooks"
161:        if hooks_dir.exists():
162:            for f in sorted(hooks_dir.glob("*.json")):
188:    def _rewrite_command_for_target(
259:    def _rewrite_hooks_data(
348:    def integrate_package_hooks(self, package_info, project_root: Path,
374:        hooks_dir = project_root / ".github" / "hooks"
375:        hooks_dir.mkdir(parents=True, exist_ok=True)
396:            target_path = hooks_dir / target_filename
539:    def integrate_package_hooks_claude(self, package_info, project_root: Path,
553:    def integrate_package_hooks_cursor(self, package_info, project_root: Path,
567:    def integrate_package_hooks_codex(self, package_info, project_root: Path,

621:    def sync_integration(self, apm_package, project_root: Path,
663:            hooks_dir = project_root / ".github" / "hooks"
664:            if hooks_dir.exists():
665:          
…[8630 chars omitted]…
---------------------------------------------------------------

    def _integrate_merged_hooks(
        self,
        config: "_MergeHookConfig",
        package_info,
        project_root: Path,
        *,
        force: bool = False,
        managed_files: set = None,
        diagnostics=None,
    ) -> HookIntegrationResult:
        """Integrate hooks by merging into a target-specific JSON config.

#   VS Code:          https://code.visualstudio.com/docs/copilot/customization/hooks
    #   Claude Code:      https://code.claude.com/docs/en/hooks
    HOOK_COMMAND_KEYS: Tuple[str, ...] = ("command", "bash", "powershell", "windows", "linux", "osx")

    def find_hook_files(self, package_path: Path) -> List[Path]:
        """Find all hook JSON files in a package.

        Searches in:
        - .apm/hooks/ subdirectory (APM convention)
        - hooks/ subdirectory (Claude-native convention)

        Args:

            package_path: Path to the package directory

        Returns:
            List[Path]: List of absolute paths to hook JSON files
        """
        hook_files = []
        seen = set()

        # Search in .apm/hooks/ (APM convention)
        apm_hooks = package_path / ".apm" / "hooks"
        if apm_hooks.exists():
            for f in sorted(apm_hooks.glob("*.json
…[8630 chars omitted]…
rator,
src/apm_cli/commands/install.py:2259:                                hook_integrator=hook_integrator,
src/apm_cli/integration/command_integrator.py:248:        stats = self.sync_integration(None, project_root,
src/apm_cli/integration/dispatch.py:50:    from apm_cli.integration.hook_integrator import HookIntegrator
src/apm_cli/integration/__init__.py:6:from .hook_integrator import HookIntegrator

with open(hook_file, 'r', encoding='utf-8') as f:
                data = json.load(f)
            if not isinstance(data, dict):
                return None
            return data
        except (json.JSONDecodeError, OSError):
            return None

    def _rewrite_command_for_target(
        self,
        command: str,
        package_path: Path,

        package_name: str,
        target: str,
        hook_file_dir: Optional[Path] = None,
    ) -> Tuple[str, List[Tuple[Path, str]]]:
        """Rewrite a hook command to use installed script paths.

        Handles:
        - ${CLAUDE_PLUGIN_ROOT}/path references (resolved from package root)
        - ./path relative references (resolved from hook file's parent directory)

        Args:
            command: Original command string
            package_path: Root path of the source package
            package_name: Name 
…[8630 chars omitted]…
TARGETS`` for backward compatibility.
src/apm_cli/integration/targets.py:300:    source = targets if targets is not None else KNOWN_TARGETS.values()
src/apm_cli/integration/targets.py:344:                p for p in KNOWN_TARGETS.values()
src/apm_cli/integration/targets.py:347:        profile = KNOWN_TARGETS.get(canonical)
src/apm_cli/integration/targets.py:354:        p for p in KNOWN_TARGETS.values()

if not source_file.is_relative_to(package_path.resolve()):
                continue
            if source_file.exists() and source_file.is_file():
                target_rel = f"{scripts_base}/{rel_path}"
                scripts_to_copy.append((source_file, target_rel))
                new_command = new_command.replace(rel_ref, target_rel)

        return new_command, scripts_to_copy

    def _rewrite_hooks_data(
        self,
        data: Dict,

        package_path: Path,
        package_name: str,
        target: str,
        hook_file_dir: Optional[Path] = None,
    ) -> Tuple[Dict, List[Tuple[Path, str]]]:
        """Rewrite all command paths in a hooks JSON structure.

        Creates a deep copy and rewrites command paths for the target platform.

        Args:
            data: Parsed hook JSON data
            package_path: Root path of the source package
        
…[8629 chars omitted]…
              if not filtered:
                                del settings["hooks"][event_name]

                    if not settings["hooks"]:
                        del settings["hooks"]

                    if modified:
                        with open(settings_path, 'w', encoding='utf-8') as f:
                            json.dump(settings, f, indent=2)
                            f.write('\n')

"""Target profiles for multi-tool integration.

Each target tool (Copilot, Claude, Cursor, ...) describes where APM
primitives should land.  Adding a new target means adding an entry to
``KNOWN_TARGETS`` -- no new classes required.
"""

from __future__ import annotations

from dataclasses import dataclass, field
from typing import Dict, Optional, Tuple, Union

@dataclass(frozen=True)
class PrimitiveMapping:
    """Where a single primitive type is deployed in a target tool."""

    subdir: str
    """Subdirectory under the target root (e.g. ``"rules"``, ``"agents"``)."""

    extension: str
    """File extension or suffix for deployed files
    (e.g. ``".mdc"``, ``".agent.md"``)."""

    format_id: str
    """Opaque tag used by integrators to select the right
    content transformer (e.g. ``"cursor_rules"``)."""

    deploy_root: Optional[str] = None
    """Override *root_dir* for thi
…[8630 chars omitted]…
package_skill",            "sync_integration",  "skills", multi_target=True),
    }


# Lazily initialized on first access
_DISPATCH: dict[str, PrimitiveDispatch] | None = None


def get_dispatch_table() -> dict[str, PrimitiveDispatch]:
    """Return the primitive dispatch table (lazily built)."""
    global _DISPATCH
    if _DISPATCH is None:
        _DISPATCH = _build_dispatch()
    return _DISPATCH

"""Hook integration functionality for APM packages.

Integrates hook JSON files and their referenced scripts during package
installation. Supports VSCode Copilot (.github/hooks/), Claude Code
(.claude/settings.json), and Cursor (.cursor/hooks.json) targets.

Hook JSON format (Claude Code  -- nested matcher groups):
    {
        "hooks": {
            "PreToolUse": [
                {
                    "hooks": [

                        {"type": "command", "command": "./scripts/validate.sh", "timeout": 10}
                    ]
                }
            ]
        }
    }

Hook JSON format (GitHub Copilot  -- flat arrays with bash/powershell keys):
    {
        "version": 1,
        "hooks": {
            "preToolUse": [
                {"type": "command", "bash": "./scripts/validate.sh", "timeoutSec": 10}
            ]
        }
    }

Hook JSON format (Cursor  -- flat arrays w
…[8630 chars omitted]…
ntegration_cursor(
src/apm_cli/integration/instruction_integrator.py:373:    def sync_integration_claude(
src/apm_cli/integration/prompt_integrator.py:102:    def sync_for_target(
src/apm_cli/integration/prompt_integrator.py:203:    def sync_integration(self, apm_package, project_root: Path,
src/apm_cli/integration/skill_integrator.py:941:    def sync_integration(self, apm_package, project_root: Path,

"""Unit tests for HookIntegrator.

Tests cover:
- Hook file discovery (.apm/hooks/ and hooks/ directories)
- VSCode integration (JSON copy + script copy + path rewriting)
- Claude integration (settings.json merge + script copy)
- Sync/cleanup integration (nuke-and-regenerate)
- Official plugin formats (hookify, learning-output-style, ralph-loop)
- Script path rewriting for ${CLAUDE_PLUGIN_ROOT} references
"""

import json

import tempfile
import shutil
from pathlib import Path
from unittest.mock import MagicMock

import pytest

from apm_cli.integration.hook_integrator import HookIntegrator, HookIntegrationResult
from apm_cli.models.apm_package import APMPackage, PackageInfo


def _make_package_info(install_path: Path, name: str = "test-pkg") -> PackageInfo:
    """Create a minimal PackageInfo for testing."""
    package = APMPackage(name=name, version="1.0.0")
    return PackageInfo(pa
…[8630 chars omitted]…
written["hooks"]["PreToolUse"][0]["hooks"][0]
        assert ".github/hooks/scripts/my-pkg/scripts/validate.sh" in hook["command"]
        assert ".github/hooks/scripts/my-pkg/scripts/validate.ps1" in hook["windows"]
        assert len(scripts) == 2

    def test_rewrite_hooks_data_linux_flat_format(self, temp_project):
        """Test _rewrite_hooks_data handles linux key in flat format (VS Code)."""

585:    def integrate_hooks_for_target(
621:    def sync_integration(self, apm_package, project_root: Path,
        Args:
            package_info: PackageInfo object

        Returns:
            str: Package name derived from install path
        """
        return package_info.install_path.name

    def integrate_package_hooks(self, package_info, project_root: Path,
                                 force: bool = False,

                                 managed_files: set = None,
                                 diagnostics=None) -> HookIntegrationResult:
        """Integrate hooks from a package into .github/hooks/ (VSCode target).

        Deploys hook JSON files with clean filenames and copies referenced
        script files. Skips user-authored files unless force=True.

        Args:
            package_info: PackageInfo with package metadata and install path
            project_
…[8630 chars omitted]…
at aliases so callers stay in sync with
        ``partition_managed_files`` bucket naming.
        """
        raw = f"{prim_name}_{target_name}"
        return BaseIntegrator._BUCKET_ALIASES.get(raw, raw)

    @staticmethod
    def partition_managed_files(
        managed_files: Set[str],
        targets=None,
    ) -> dict:
        """Partition *managed_files* by integration prefix in a single pass.

managed_files: set = None,
                                 diagnostics=None) -> HookIntegrationResult:
        """Integrate hooks from a package into .github/hooks/ (VSCode target).

        Deploys hook JSON files with clean filenames and copies referenced
        script files. Skips user-authored files unless force=True.

        Args:
            package_info: PackageInfo with package metadata and install path
            project_root: Root directory of the project
            force: If True, overwrite user-authored files on collision
            managed_files: Set of relative paths known to be APM-managed

        Returns:
            HookIntegrationResult: Results of the integration operation
        """
        hook_files = self.find_hook_files(package_info.install_path)

        if not hook_files:
            return HookIntegrationResult(
     
…[8629 chars omitted]…
stats['files_removed'] += 1
            except (json.JSONDecodeError, OSError):
                stats['errors'] += 1

        # Clean APM entries from .cursor/hooks.json (safe  -- uses _apm_source marker)
        self._clean_apm_entries_from_json(
            project_root / ".cursor" / "hooks.json", stats,
        )

        # Clean APM entries from .codex/hooks.json (safe  -- uses _apm_source marker)

grep: src/apm_cli/uninstall: No such file or directory
src/apm_cli/commands/uninstall/cli.py:20:    _sync_integrations_after_uninstall,
src/apm_cli/commands/uninstall/cli.py:182:            cleaned = _sync_integrations_after_uninstall(
src/apm_cli/commands/uninstall/engine.py:227:def _sync_integrations_after_uninstall(apm_package, project_root, all_deployed_files, logger, user_scope=False):
src/apm_cli/commands/uninstall/engine.py:273:            if not _entry or _entry.sync_method != "sync_for_target":
src/apm_cli/commands/uninstall/engine.py:302:        result = _integrators["skills"].sync_integration(
src/apm_cli/commands/uninstall/engine.py:309:    # Hooks (multi-target sync_integration handles all targets)
src/apm_cli/commands/uninstall/engine.py:310:    result = _integrators["hooks"].sync_integration(
src/apm_cli/commands/uninstall/__init__.py:10:    _sync_integrations_after_uni
…[8630 chars omitted]…
 has changed (user wants different version).
                lockfile_match = False

                if install_path.exists() and existing_lockfile:
                    locked_dep = existing_lockfile.get_dependency(dep_ref.get_unique_key())
src/apm_cli/commands/install.py:1023:            _int_result = getattr(_integrator, _entry.integrate_method)(
grep: src/apm_cli/uninstall: No such file or directory

logger.error(f"Error installing dependencies: {e}")
        if not verbose:
            logger.progress("Run with --verbose for detailed diagnostics")
        sys.exit(1)


# ---------------------------------------------------------------------------
# Install engine
# ---------------------------------------------------------------------------


def _pre_deploy_security_scan(

    install_path: Path,
    diagnostics: DiagnosticCollector,
    package_name: str = "",
    force: bool = False,
    logger=None,
) -> bool:
    """Scan package source files for hidden characters BEFORE deployment.

    Delegates to :class:`SecurityGate` for the scan->classify->decide pipeline.
    Inline CLI feedback (error/info lines) is kept here because it is
    install-specific formatting.

    Returns:
        True if deployment should proceed, False to block.
    """
    from ..security.gate imp
…[8629 chars omitted]…
     del data["hooks"][event_name]

            if not data["hooks"]:
                del data["hooks"]

            if modified:
                with open(json_path, 'w', encoding='utf-8') as f:
                    json.dump(data, f, indent=2)
                    f.write('\n')
                stats['files_removed'] += 1
        except (json.JSONDecodeError, OSError):
            stats['errors'] += 1

force: bool = False,
                                        managed_files: set = None,
                                        diagnostics=None) -> HookIntegrationResult:
        """Integrate hooks into .claude/settings.json.

        .. deprecated:: Use :meth:`integrate_hooks_for_target` instead.
        """
        return self._integrate_merged_hooks(
            _MERGE_HOOK_TARGETS["claude"], package_info, project_root,
            force=force, managed_files=managed_files,
            diagnostics=diagnostics,
        )

    def integrate_package_hooks_cursor(self, package_info, project_root: Path,
                                        force: bool = False,
                                        managed_files: set = None,
                                        diagnostics=None) -> HookIntegrationResult:
        """Integrate hooks into .cur
…[8630 chars omitted]…
es_path, lockfile_path, trust_private=True)
    try:
        remaining_root_mcp = apm_package.get_mcp_dependencies()
    except Exception:
        remaining_root_mcp = []
    all_remaining_mcp = MCPIntegrator.deduplicate(remaining_root_mcp + remaining_mcp)
    new_mcp_servers = MCPIntegrator.get_server_names(all_remaining_mcp)
    stale_servers = old_mcp_servers - new_mcp_servers
    if stale_servers:

@pytest.fixture
    def temp_project(self):
        temp_dir = tempfile.mkdtemp()
        yield Path(temp_dir)
        shutil.rmtree(temp_dir, ignore_errors=True)

    def test_rewrite_claude_plugin_root(self, temp_project):
        """Test rewriting ${CLAUDE_PLUGIN_ROOT} variable."""
        pkg_dir = temp_project / "pkg"
        (pkg_dir / "hooks").mkdir(parents=True)
        (pkg_dir / "hooks" / "script.sh").write_text("#!/bin/bash")

        integrator = HookIntegrator()
        cmd, scripts = integrator._rewrite_command_for_target(
            "python3 ${CLAUDE_PLUGIN_ROOT}/hooks/script.sh",
            pkg_dir,
            "my-pkg",
            "vscode",
        )

        assert "${CLAUDE_PLUGIN_ROOT}" not in cmd
        assert ".github/hooks/scripts/my-pkg/hooks/script.sh" in cmd
        assert len(scripts) == 1

    def test_rewrite_relative_path(self, temp_project):
    
…[8630 chars omitted]…
l/engine.py:294:    for t in _resolved_targets:
src/apm_cli/commands/uninstall/engine.py:305:            targets=_resolved_targets,
src/apm_cli/commands/uninstall/engine.py:318:    _targets = _resolved_targets
src/apm_cli/commands/install.py:1409:        from apm_cli.integration.targets import resolve_targets as _resolve_targets
src/apm_cli/commands/install.py:1412:        _targets = _resolve_targets(

KNOWN_TARGETS: Dict[str, TargetProfile] = {
    # Copilot (GitHub) -- at user scope, Copilot CLI reads ~/.copilot/
    # instead of ~/.github/.  Prompts and instructions are not supported at user scope.
    # Ref: https://docs.github.com/en/copilot/how-tos/copilot-cli/customize-copilot/create-custom-agents-for-cli
    "copilot": TargetProfile(
        name="copilot",
        root_dir=".github",
        primitives={
            "instructions": PrimitiveMapping(
                "instructions", ".instructions.md", "github_instructions"
            ),
            "prompts": PrimitiveMapping(

                "prompts", ".prompt.md", "github_prompt"
            ),
            "agents": PrimitiveMapping(
                "agents", ".agent.md", "github_agent"
            ),
            "skills": PrimitiveMapping(
                "skills", "/SKILL.md", "skill_standard"
            ),
          
…[7829 chars omitted]…
esult = _integrators["hooks"].sync_integration(
src/apm_cli/integration/targets.py:287:def get_integration_prefixes(targets=None) -> tuple:
src/apm_cli/integration/base_integrator.py:204:        hook_prefixes: list = []
src/apm_cli/integration/base_integrator.py:216:                    hook_prefixes.append(prefix)
src/apm_cli/integration/base_integrator.py:230:        hook_tuple = tuple(hook_prefixes)

12:def portable_relpath(path: Path, base: Path) -> str:
13-    """Return a forward-slash relative path, resolving both sides first.
14-
15-    Handles Windows 8.3 short names (e.g. ``RUNNER~1`` vs ``runneradmin``)
16-    and ensures consistent POSIX output on every platform.
17-
18-    When *path* is not under *base* (or resolution fails), falls back to
19-    a resolved absolute POSIX path.
20-    """
21-    try:
22-        return path.resolve().relative_to(base.resolve()).as_posix()
23-    except (ValueError, OSError, RuntimeError):

24-        try:
25-            return path.resolve().as_posix()
26-        except (OSError, RuntimeError):
27-            return path.as_posix()
        },
        auto_create=False,
        detect_by_dir=True,
    ),
}


def get_integration_prefixes(targets=None) -> tuple:
    """Return all known target root prefixes as a tuple.

    Used by ``BaseInteg
…[5121 chars omitted]…
  vscode_result = integrator.integrate_package_hooks(pkg_info, temp_project)
tests/unit/integration/test_hook_integrator.py:1693:        r1 = integrator.integrate_package_hooks(pkg1_info, temp_project)
tests/unit/integration/test_hook_integrator.py:1694:        r2 = integrator.integrate_package_hooks(pkg2_info, temp_project)
./src/apm_cli/integration/hook_integrator.py:259:    def _rewrite_hooks_data(

rewrite: ('pwsh -File .\\scripts\\scan.ps1', [])
target integration: TypeError HookIntegrator.integrate_package_hooks() got an unexpected keyword argument 'target'

with open(hook_file, 'r', encoding='utf-8') as f:
                data = json.load(f)
            if not isinstance(data, dict):
                return None
            return data
        except (json.JSONDecodeError, OSError):
            return None

    def _rewrite_command_for_target(
        self,
        command: str,
        package_path: Path,

        package_name: str,
        target: str,
        hook_file_dir: Optional[Path] = None,
        hook_deploy_dir: Optional[str] = None,
    ) -> Tuple[str, List[Tuple[Path, str]]]:
        """Rewrite a hook command to use installed script paths.

        Handles:
        - ${CLAUDE_PLUGIN_ROOT}/path references (resolved from package root)
        - ./path relative references (resolved from hook file's parent directory)
        - Windows-style relative paths using backslashes

        Args:
            command: Original 
…[2524 chars omitted]…
        new_command = new_command.replace(rel_ref, target_rel)

        return new_command, scripts_to_copy

    def _rewrite_hooks_data(
        self,
        data: Dict,
        package_path: Path,
        package_name: str,
        target: str,
        hook_file_dir: Optional[Path] = None,
    ) -> Tuple[Dict, List[Tuple[Path, str]]]:
        """Rewrite all command paths in a hooks JSON structure.

try:
            with open(hook_file, 'r', encoding='utf-8') as f:
                data = json.load(f)
            if not isinstance(data, dict):
                return None
            return data
        except (json.JSONDecodeError, OSError):
            return None

    def _rewrite_command_for_target(
        self,
        command: str,

        package_path: Path,
        package_name: str,
        target: str,
        hook_file_dir: Optional[Path] = None,
        hook_deploy_dir: Optional[str] = None,
    ) -> Tuple[str, List[Tuple[Path, str]]]:
        """Rewrite hook command script paths to their deployed locations.

        Package-root ``${CLAUDE_PLUGIN_ROOT}`` references and ``./`` or
        ``.\\`` references relative to the hook file are supported. Both
        slash styles are normalized to POSIX paths in the deployed command.

        Args:
            command:
…[5227 chars omitted]…
ta: Parsed hook JSON data
            package_path: Root path of the source package
            package_name: Name for scripts subdirectory
            target: "vscode" or "claude"
            hook_file_dir: Directory containing the hook JSON file (for ./path resolution)

        Returns:
            Tuple of (rewritten_data_copy, list of (source_file, target_rel_path))
        """
        import copy

# Resolve ./ and .\ references from the hook JSON's parent directory
        # (or the package root for direct callers without a hook-file location).
        relative_pattern = re.compile(r"\.[/\\](?P<path>[^\s\"'`]+)")
        rewritten = relative_pattern.sub(
            lambda match: rewrite_reference(match, resolve_base), rewritten
        )

        # A command can reference the same script more than once. Keep the
        # copy list deterministic and avoid copying the same target repeatedly.
        unique_scripts: List[Tuple[Path, str]] = []
        seen_targets = set()
        for source_file, target_rel in scripts_to_copy:

            if target_rel not in seen_targets:
                seen_targets.add(target_rel)
                unique_scripts.append((source_file, target_rel))

        return rewritten, unique_scripts

    def _rewrite_hooks_data(
        self,
     
…[8628 chars omitted]…
files: set = None,
        diagnostics=None,
    ) -> "HookIntegrationResult":
        """Integrate hooks for a single *target*.

        Copilot uses individual JSON files (genuinely different pattern).
        All other merge-based targets are dispatched via the
        ``_MERGE_HOOK_TARGETS`` registry.
        """
        if target.name == "copilot":
            return self.integrate_package_hooks(

"""
        import copy
        rewritten = copy.deepcopy(data)
        all_scripts: List[Tuple[Path, str]] = []

        hooks = rewritten.get("hooks", {})
        for event_name, matchers in hooks.items():
            if not isinstance(matchers, list):
                continue
            for matcher in matchers:
                if not isinstance(matcher, dict):
                    continue

                # Rewrite script paths in the matcher dict itself
                # (GitHub Copilot flat format: bash/powershell/windows keys at this level)
                for key in self.HOOK_COMMAND_KEYS:
                    if key in matcher:
                        new_cmd, scripts = self._rewrite_command_for_target(
                            matcher[key], package_path, package_name, target,
                            hook_file_dir=hook_file_dir,
                            hook_d
…[5032 chars omitted]…
result.get("files_removed", 0)

    # Hooks (multi-target sync_integration handles all targets)
    result = _integrators["hooks"].sync_integration(
        apm_package, project_root,
        managed_files=_buckets["hooks"] if _buckets else None,
        targets=_resolved_targets,
    )
    counts["hooks"] = result.get("files_removed", 0)


    # Phase 2: Re-integrate from remaining installed packages

nested call not found
 src/apm_cli/commands/uninstall/engine.py   |   1 +
 src/apm_cli/integration/hook_integrator.py | 232 +++++++++++++++++++++--------
 2 files changed, 169 insertions(+), 64 deletions(-)
diff --git a/src/apm_cli/commands/uninstall/engine.py b/src/apm_cli/commands/uninstall/engine.py
index c2e7165..55cd0bb 100644
--- a/src/apm_cli/commands/uninstall/engine.py
+++ b/src/apm_cli/commands/uninstall/engine.py
@@ -310,6 +310,7 @@ def _sync_integrations_after_uninstall(apm_package, project_root, all_deployed_f
     result = _integrators["hooks"].sync_integration(
         apm_package, project_root,
         managed_files=_buckets["hooks"] if _buckets else None,

+        targets=_resolved_targets,
     )
     counts["hooks"] = result.get("files_removed", 0)
 
diff --git a/src/apm_cli/integration/hook_integrator.py b/src/apm_cli/integration/hook_integrator.py
index c174edd.
…[8629 chars omitted]…
orce, managed_files=managed_files,
-                diagnostics=diagnostics,
+                diagnostics=diagnostics, target=target,
             )
 
         config = _MERGE_HOOK_TARGETS.get(target.name)
@@ -619,7 +703,7 @@ class HookIntegrator(BaseIntegrator):
         )
 
     def sync_integration(self, apm_package, project_root: Path,
-                          managed_files: set = None) -> Dict:

# Rewrite script paths in the matcher dict itself
                # (GitHub Copilot flat format: bash/powershell/windows keys at this level)
                for key in self.HOOK_COMMAND_KEYS:
                    if key in matcher:
                        new_cmd, scripts = self._rewrite_command_for_target(
                            matcher[key], package_path, package_name, target,
                            hook_file_dir=hook_file_dir,
                            hook_deploy_dir=hook_deploy_dir,
                        )
                        if scripts:
                            _log.debug(
                                "Hook %s/%s: rewrote '%s' key (%d script(s))",

                                package_name, event_name, key, len(scripts),
                            )
                        matcher[key] = new_cmd
                        all_scripts.extend
…[8629 chars omitted]…
ps1')])
target paths: ['.copilot/hooks/my-pkg-hook.json', '.copilot/hooks/scripts/my-pkg/hooks/validate.ps1']
deployed: {
  "hooks": {
    "preToolUse": [
      {
        "windows": "pwsh -File .\\scripts\\scan.ps1"
      },
      {
        "bash": ".copilot/hooks/scripts/my-pkg/hooks/validate.ps1"
      }
    ]
  }
}

github exists: False
sync: {'files_removed': 2, 'errors': 0}
copilot remains: False

........................................................................ [ 48%]
........................................................................ [ 96%]
......                                                                   [100%]
150 passed in 3.17s

assert integrator._parse_hook_json(temp_project / "missing.json") is None


# ─── VSCode integration tests ────────────────────────────────────────────────


class TestVSCodeIntegration:
    """Tests for VSCode hook integration (.github/hooks/)."""

    @pytest.fixture
    def temp_project(self):
        temp_dir = tempfile.mkdtemp()

        project = Path(temp_dir)
        (project / ".github").mkdir()
        yield project
        shutil.rmtree(temp_dir, ignore_errors=True)

    def _setup_hookify_package(self, project: Path) -> PackageInfo:
        """Create a hookify-like package structure."""
        pkg_dir = project / "apm_modules" / "anthropics" / "hookify"
        hooks_dir = pkg_dir / "hooks"
        hooks_dir.mkdir(parents=True)

        (hooks_dir / "hooks.json").write_text(json.dumps(HOOKIFY_HOOKS_JSON, indent=2))

        # Create the script files
        for scr
…[8629 chars omitted]…
 yield Path(temp_dir)
tests/fixtures/mock-plugin/.apm/hooks/setup.sh
grep: tests/unit/integration/__pycache__/test_hook_integrator.cpython-312-pytest-9.2.0.pyc: binary file matches
tests/unit/integration/test_hook_integrator.py:1229:            "./scripts/scan-secrets.ps1",
tests/unit/integration/test_hook_integrator.py:1236:        assert ".github/hooks/scripts/my-pkg/scripts/scan-secrets.ps1" in cmd

if target_rel.startswith("../") or target_rel == "..":
                return match.group(0)

            scripts_to_copy.append((source_file, target_rel))
            return target_rel

        # Resolve plugin-root references from the package root. Quotes are not
        # part of the path capture, so quoted command arguments stay quoted.
        plugin_root_pattern = re.compile(
            r"\$\{CLAUDE_PLUGIN_ROOT\}[/\\](?P<path>[^\s\"'`]+)"
        )
        rewritten = plugin_root_pattern.sub(

            lambda match: rewrite_reference(match, package_root), command
        )

        # Resolve ./ and .\ references from the hook JSON's parent directory
        # (or the package root for direct callers without a hook-file location).
        relative_pattern = re.compile(r"\.[/\\](?P<path>[^\s\"'`]+)")
        rewritten = relative_pattern.sub(
            lambda match:
…[4443 chars omitted]…
ated=0,
            files_skipped=0, target_paths=[],
        )

        target_dir = project_root / f".{config.target_key}"

        # Opt-in check: some targets only deploy when their dir exists
        if config.require_dir and not target_dir.exists():
            return _empty

        hook_files = self.find_hook_files(package_info.install_path)
        if not hook_files:
            return _empty

Tuple of (rewritten_data_copy, list of (source_file, target_rel_path))
        """
        import copy
        rewritten = copy.deepcopy(data)
        all_scripts: List[Tuple[Path, str]] = []

        hooks = rewritten.get("hooks", {})
        for event_name, matchers in hooks.items():
            if not isinstance(matchers, list):
                continue
            for matcher in matchers:
                if not isinstance(matcher, dict):

                    continue
                # Rewrite script paths in the matcher dict itself
                # (GitHub Copilot flat format: bash/powershell/windows keys at this level)
                for key in self.HOOK_COMMAND_KEYS:
                    if key in matcher:
                        new_cmd, scripts = self._rewrite_command_for_target(
                            matcher[key], package_path, package_name, target,
        
…[8629 chars omitted]…
r hooks
                roots are included when recognizing manifest paths.
        """
        stats: Dict[str, int] = {'files_removed': 0, 'errors': 0}

        # Start with all registered hook locations for backward compatibility,
        # then include scope-resolved roots (e.g. .copilot/hooks at user scope).
 M src/apm_cli/commands/uninstall/engine.py
 M src/apm_cli/integration/hook_integrator.py

........................................................................ [ 11%]
........................................................................ [ 23%]
........................................................................ [ 34%]
........................................................................ [ 46%]
........................................................................ [ 57%]
........................................................................ [ 69%]
........................................................................ [ 80%]
........................................................................ [ 92%]
...............................................                          [100%]
623 passed in 6.72s

diff --git a/src/apm_cli/commands/uninstall/engine.py b/src/apm_cli/commands/uninstall/engine.py
index c2e7165..55cd0bb 100644
--- a/src/apm_cli/commands/uninstall/engine.py
+++ b/src/apm_cli/commands/uninstall/engine.py
@@ -310,6 +310,7 @@ def _sync_integrations_after_uninstall(apm_package, project_root, all_deployed_f
     result = _integrators["hooks"].sync_integration(
         apm_package, project_root,
         managed_files=_buckets["hooks"] if _buckets else None,
+        targets=_resolved_targets,
     )
     counts["hooks"] = result.get("files_removed", 0)
 

diff --git a/src/apm_cli/integration/hook_integrator.py b/src/apm_cli/integration/hook_integrator.py
index c174edd..5609d1e 100644
--- a/src/apm_cli/integration/hook_integrator.py
+++ b/src/apm_cli/integration/hook_integrator.py
@@ -44,6 +44,7 @@ Script path handling:
 
 import json
 import logging
+import posixpath
 imp
…[8629 chars omitted]…
ed target.
+                is_hook = normalized.startswith(tuple(hook_prefixes))
+                if not is_hook or ".." in normalized.split("/"):
                     continue
-                target = project_root / rel_path
+                target = project_root / normalized
                 if target.exists() and target.is_file():
                     try:
                         target.unlink()

Traceback (most recent call last):
  File "<stdin>", line 46, in <module>
AssertionError: ['pwsh .\\scripts\\scan.ps1', 'pwsh -File .\\scripts\\scan.ps1', '.copilot/hooks/scripts/my-pkg/hooks/validate.ps1']

Traceback (most recent call last):
  File "<stdin>", line 37, in <module>
AssertionError: 4

hook scope and Windows-path reproducer passed

[build-system]
requires = ["setuptools>=42", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "apm-cli"
version = "0.8.10"
description = "MCP configuration tool"
readme = "README.md"
requires-python = ">=3.10"
license = {file = "LICENSE"}
authors = [

    {name = "Daniel Meppiel", email = "user@example.com"}
]
classifiers = [
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
]
dependencies = [
    "click>=8.0.0",
    "colorama>=0.4.6",
    "pyyaml>=6.0.0",
    "requests>=2.28.0",
    "python-frontmatter>=1.0.0",
    "llm>=0.17.0",
    "llm-github-models>=0.1.0",
    "tomli>=1.2.0; python_version<'3.11'",
    
…[556 chars omitted]…
ne_length = 88

[tool.mypy]
python_version = "3.12"
warn_return_any = true
warn_unused_configs = true

[tool.pytest.ini_options]
addopts = "-m 'not benchmark'"
markers = [
    "integration: marks tests as integration tests that may require network access",
    "slow: marks tests as slow running tests",
    "benchmark: marks performance benchmark tests (deselected by default, run with -m benchmark)",
]

src/apm_cli/integration/hook_integrator.py
210 94             hook_deploy_dir: Optional scope-resolved hooks directory, relative to project root
326 90             hook_file_dir: Directory containing the hook JSON file (for ./path resolution)
344 90                 # (GitHub Copilot flat format: bash/powershell/windows keys at this level)
433 89         target_name = getattr(target, "name", target) if target is not None else "vscode"
451 94             rewrite_target = "vscode" if target_name in ("copilot", "vscode") else target_name
459 94             rewrite_target = "vscode" if target_name in ("copilot", "vscode") else target_name
490 106             if self.check_collision(target_path, rel_path, managed_files, force, diagnostics=diagnostics):
504 114                 if self.check_collision(target_script, target_rel, managed_files, force, diagnostics=diagnostics):
783 89         # 
…[369 chars omitted]…
logger.verbose_detail(f"    Path: {portable_relpath(orphan_path, apm_modules_dir)}")

227 112 def _sync_integrations_after_uninstall(apm_package, project_root, all_deployed_files, logger, user_scope=False):
244 103     _resolved_targets = resolve_targets(project_root, user_scope=user_scope, explicit_target=_explicit)
/usr/local/bin/black
python -m black, 26.10.1 (compiled: yes)
Python (CPython) 3.12.13

would reformat src/apm_cli/commands/uninstall/engine.py
would reformat src/apm_cli/integration/hook_integrator.py

Oh no! 💥 💔 💥
2 files would be reformatted.

--- src/apm_cli/integration/hook_integrator.py	2026-11-04 02:56:07.225769+00:00
+++ src/apm_cli/integration/hook_integrator.py	2026-11-04 03:01:04.448577+00:00
@@ -79,13 +79,13 @@
 
 @dataclass(frozen=True)
 class _MergeHookConfig:
     """Configuration for targets that merge hooks into a single JSON file."""
 
-    config_filename: str    # e.g. "settings.json" or "hooks.json"
-    target_key: str         # target name passed to _rewrite_hooks_data
-    require_dir: bool       # True = skip if target dir doesn't exist
+    config_filename: str  # e.g. "settings.json" or "hooks.json"

+    target_key: str  # target name passed to _rewrite_hooks_data
+    require_dir: bool  # True = skip if target dir doesn't exist
 
 
 _MERGE_HOOK_TARGETS: dict[str, _MergeHookConfig] = {
     "claude": _MergeHookConfig(
         config_filename="settings.json",
@@ -128,11 +128,18 @@
     #
     # Refs:
…[8629 chars omitted]…
aged is not None:
         # Partition against default KNOWN_TARGETS for legacy/project-scope
         # paths, then merge with resolved targets for user-scope paths.
@@ -281,11 +301,13 @@
                 _bucket_key = BaseIntegrator.partition_bucket_key(
                     _prim_name, _target.name
would reformat src/apm_cli/commands/uninstall/engine.py

All done! ✨ 🍰 ✨
1 file would be reformatted.

assert (scripts_dir / "posttooluse.py").exists()
        assert (scripts_dir / "stop.py").exists()
        assert (scripts_dir / "userpromptsubmit.py").exists()

    def test_sync_removes_cursor_hook_entries(self, temp_project):
        """Test that sync removes APM-managed entries from .cursor/hooks.json."""
        hooks_path = temp_project / ".cursor" / "hooks.json"
        hooks_path.write_text(json.dumps({
            "hooks": {
                "Stop": [
                    {"_apm_source": "ralph-loop", "hooks": [{"type": "command", "command": "..."}]},
                    {"command": "echo user-hook"},

                ],
                "PreToolUse": [
                    {"_apm_source": "hookify", "hooks": [{"type": "command", "command": "..."}]}
                ],
            }
        }))

        integrator = HookIntegrator()
        stats = integrator.sync_integrati
…[8629 chars omitted]…
roject)
tests/unit/integration/test_hook_integrator.py:978:        integrator.sync_integration(None, temp_project)
tests/unit/integration/test_hook_integrator.py:1662:        stats = integrator.sync_integration(None, temp_project, managed_files=managed_files)
tests/unit/integration/test_hook_integrator.py:1705:        stats = integrator.sync_integration(None, temp_project, managed_files=managed_files)

('.github/hooks/scripts/pkg/scripts/x.ps1', [(PosixPath('/tmp/tmpy2z6_uvk/pkg/scripts/x.ps1'), '.github/hooks/scripts/pkg/scripts/x.ps1')])

# paths work on POSIX hosts too.
            raw_path = match.group("path")
            normalized_path = posixpath.normpath(raw_path.replace("\\", "/"))
            if normalized_path in ("", "."):
                return match.group(0)

            source_file = (base / Path(normalized_path)).resolve()
            # Reject paths (including Windows-style .. components) that escape
            # the source package before checking/copying the referenced file.
            if not source_file.is_relative_to(package_root):
                return match.group(0)
            if not source_file.exists() or not source_file.is_file():

                return match.group(0)

            # Preserve the relative layout for ordinary references. For valid
            # in-package references that traverse above the hook file's folder,
            # use a canonical in-package path instead of 
…[1790 chars omitted]…
......................................................... [ 57%]
........................................................................ [ 69%]
........................................................................ [ 80%]
........................................................................ [ 92%]
...............................................                          [100%]
623 passed in 4.33s

)

        # Resolve ./ and .\ references from the hook JSON's parent directory
        # (or the package root for direct callers without a hook-file location).
        # Do not mistake the suffix of a parent path (``../script`` or
        # ``..\script``) for a leading ``./`` reference.
        relative_pattern = re.compile(r"(?<![\w.])\.[/\\](?P<path>[^\s\"'`]+)")
        rewritten = relative_pattern.sub(
            lambda match: rewrite_reference(match, resolve_base), rewritten
        )

        # A command can reference the same script more than once. Keep the

        # copy list deterministic and avoid copying the same target repeatedly.
        unique_scripts: List[Tuple[Path, str]] = []
        seen_targets = set()
        for source_file, target_rel in scripts_to_copy:
            if target_rel not in seen_targets:
                seen_targets.add(target_rel)
       
…[2025 chars omitted]…
ltered
                            if not filtered:
                                del settings["hooks"][event_name]

                    if not settings["hooks"]:
                        del settings["hooks"]

                    if modified:
'../scripts/scan.ps1' => '../scripts/scan.ps1' []
'..\\scripts\\scan.ps1' => '..\\scripts\\scan.ps1' []
'.\\..\\..\\outside.ps1' => '.\\..\\..\\outside.ps1' []

would reformat src/apm_cli/integration/hook_integrator.py

1---- src/apm_cli/integration/hook_integrator.py	2026-11-04 03:03:44.242627+00:00
2-+++ src/apm_cli/integration/hook_integrator.py	2026-11-04 03:04:07.675763+00:00
3:@@ -79,13 +79,13 @@
4- 
5- @dataclass(frozen=True)
6- class _MergeHookConfig:
7-     """Configuration for targets that merge hooks into a single JSON file."""
8- 
9--    config_filename: str    # e.g. "settings.json" or "hooks.json"
10--    target_key: str         # target name passed to _rewrite_hooks_data

11--    require_dir: bool       # True = skip if target dir doesn't exist
12-+    config_filename: str  # e.g. "settings.json" or "hooks.json"
13-+    target_key: str  # target name passed to _rewrite_hooks_data
14-+    require_dir: bool  # True = skip if target dir doesn't exist
15- 
16- 
17- _MERGE_HOOK_TARGETS: dict[str, _MergeHookConfig] = {
18-     "claude
…[8629 chars omitted]…
f.write("\n")
352- 
353-         return HookIntegrationResult(
354--            files_integrated=hooks_integrated, files_updated=0,
355--            files_skipped=0, target_paths=target_paths,
356-+            files_integrated=hooks_integrated,
357-+            files_updated=0,
358-+            files_skipped=0,
359-+            target_paths=target_paths,
360-             scripts_copied=scripts_copied,

45:    """Short unique identifier (``"copilot"``, ``"claude"``, ``"cursor"``)."""
159:    "copilot": TargetProfile(
160:        name="copilot",
340:        if canonical in ("copilot", "vscode", "agents"):
341:            canonical = "copilot"
361:    return [KNOWN_TARGETS["copilot"]]
380:        explicit_target: Canonical target name (``"copilot"``, ``"claude"``,
391:        if canonical in ("copilot", "vscode", "agents"):
392:            canonical = "copilot"
407:    return [KNOWN_TARGETS["copilot"]]

    Mirrors ``active_targets()`` but operates against ``~/`` and filters

    out targets that do not support user scope.

    Resolution order:

    1. **Explicit target** (``--target``): returns the matching profile
       if it supports user scope.  ``"all"`` returns every user-capable
       target.
    2. **Directory detection**: profiles whose ``effective_root(user_scope=True)``
  
…[1320 chars omitted]…
 returns every
       known target.
    2. **Directory detection**: profiles whose ``root_dir`` already
       exists under *project_root*.
    3. **Fallback**: when nothing is detected, returns ``[copilot]``
       so greenfield projects get a default skills root.

    Args:
        project_root: The workspace root ``Path``.
        explicit_target: Canonical target name (``"copilot"``, ``"claude"``,

src/apm_cli/integration/hook_integrator.py
210 94             hook_deploy_dir: Optional scope-resolved hooks directory, relative to project root
325 90             hook_file_dir: Directory containing the hook JSON file (for ./path resolution)
343 90                 # (GitHub Copilot flat format: bash/powershell/windows keys at this level)
432 89         target_name = getattr(target, "name", target) if target is not None else "vscode"
450 94             rewrite_target = "vscode" if target_name in ("copilot", "vscode") else target_name
458 94             rewrite_target = "vscode" if target_name in ("copilot", "vscode") else target_name
489 106             if self.check_collision(target_path, rel_path, managed_files, force, diagnostics=diagnostics):
503 114                 if self.check_collision(target_script, target_rel, managed_files, force, diagnostics=diagnostics):
785 89         # Clean APM entries from .claude/settings.json (safe  -- uses _apm_source marker)

src/apm_cli/commands/uninstall/engine.py

275:                    assert "hooks" not in t.primitives
"""Hook integration functionality for APM packages.

Integrates hook JSON files and their referenced scripts during package
installation. Supports VSCode Copilot (.github/hooks/), Claude Code
(.claude/settings.json), and Cursor (.cursor/hooks.json) targets.

Hook JSON format (Claude Code  -- nested matcher groups):
    {
        "hooks": {
            "PreToolUse": [
                {

                    "hooks": [
                        {"type": "command", "command": "./scripts/validate.sh", "timeout": 10}
                    ]
                }
            ]
        }
    }

Hook JSON format (GitHub Copilot  -- flat arrays with bash/powershell keys):
    {
        "version": 1,
        "hooks": {
            "preToolUse": [
                {"type": "command", "bash": "./scripts/validate.sh", "timeoutSec": 10}
            ]

…[8630 chars omitted]…
on.dump(settings, f, indent=2)
                            f.write('\n')
                        stats['files_removed'] += 1
            except (json.JSONDecodeError, OSError):
                stats['errors'] += 1

        # Clean APM entries from .cursor/hooks.json (safe  -- uses _apm_source marker)
        self._clean_apm_entries_from_json(
            project_root / ".cursor" / "hooks.json", stats,

docs/src/content/docs/contributing/integration-testing.md:52:./scripts/test-integration.sh
docs/src/content/docs/contributing/integration-testing.md:199:- **Use the unified integration script first**: Run `./scripts/test-integration.sh` to reproduce the exact CI environment locally
docs/src/content/docs/getting-started/installation.md:112:./scripts/build-binary.sh
docs/src/content/docs/integrations/ide-tool-integration.md:317:7. Rewrites `${CLAUDE_PLUGIN_ROOT}` and relative script paths for the target platform
docs/src/content/docs/introduction/how-it-works.md:237:      "hooks": [{ "type": "command", "command": "./scripts/lint.sh" }]
docs/src/content/docs/introduction/key-concepts.md:294:            "command": "./scripts/lint-changed.sh $TOOL_INPUT_path"
tests/unit/integration/test_hook_integrator.py:9:- Script path rewriting for ${CLAUDE_PLUGIN_ROOT} references
tests/unit/integration
…[7047 chars omitted]…
"timeout": 10}
src/apm_cli/integration/hook_integrator.py:25:                {"type": "command", "bash": "./scripts/validate.sh", "timeoutSec": 10}
src/apm_cli/integration/hook_integrator.py:40:    - ${CLAUDE_PLUGIN_ROOT}/path -> resolved relative to package root, rewritten for target

src/apm_cli/integration/hook_integrator.py:200:        Package-root ``${CLAUDE_PLUGIN_ROOT}`` references and ``./`` or

275:    def cleanup_empty_parents(
276-        deleted_paths: List[Path],
277-        stop_at: Path,
278-    ) -> None:
279-        """Remove empty parent directories in a single bottom-up pass.
280-
281-        Collects all parent directories of *deleted_paths*, sorts by
282-        depth descending, and removes each if empty  -- O(H+D) syscalls
283-        instead of the per-file O(HxD) approach.
284-
285-        Args:
286-            deleted_paths: Paths that were deleted (files or dirs).

287-            stop_at: Do not remove this directory or any ancestor.
288-        """
289-        if not deleted_paths:
290-            return
291-        stop_resolved = stop_at.resolve()
292-        # Collect unique parents (skip stop_at itself)
293-        candidates: set = set()
294-        for p in deleted_paths:
295-            parent = p.parent
296-            while parent != stop_at and p
…[6255 chars omitted]…
opy list deterministic and avoid copying the same target repeatedly.
        unique_scripts: List[Tuple[Path, str]] = []
        seen_targets = set()
        for source_file, target_rel in scripts_to_copy:
            if target_rel not in seen_targets:
                seen_targets.add(target_rel)
                unique_scripts.append((source_file, target_rel))

        return rewritten, unique_scripts

def test_rewrite_relative_path_with_hook_file_dir(self, temp_project):
        """Test that ./path is resolved from hook_file_dir, not package root."""
        pkg_dir = temp_project / "pkg"
        hooks_dir = pkg_dir / "hooks"
        scripts_dir = hooks_dir / "scripts"
        scripts_dir.mkdir(parents=True)
        (scripts_dir / "lint.sh").write_text("#!/bin/bash")

        integrator = HookIntegrator()
        # Script lives at hooks/scripts/lint.sh — only resolvable from hooks/ dir
        cmd, scripts = integrator._rewrite_command_for_target(
            "./scripts/lint.sh",

            pkg_dir,
            "my-pkg",
            "vscode",
            hook_file_dir=hooks_dir,
        )

        assert "./" not in cmd
        assert ".github/hooks/scripts/my-pkg/scripts/lint.sh" in cmd
        assert len(scripts) == 1
        assert scripts[0][0] == (scripts_dir / "lint.sh"
…[8629 chars omitted]…
  # Hooks (multi-target sync_integration handles all targets)
    result = _integrators["hooks"].sync_integration(
        apm_package, project_root,
        managed_files=_buckets["hooks"] if _buckets else None,
        targets=_resolved_targets,
    )
    counts["hooks"] = result.get("files_removed", 0)


    # Phase 2: Re-integrate from remaining installed packages
    _targets = _resolved_targets

target: "vscode", "claude", "cursor", or "codex"
            hook_file_dir: Directory containing the hook JSON file (for relative paths)
            hook_deploy_dir: Optional scope-resolved hooks directory, relative to project root

        Returns:
            Tuple of (rewritten_command, list of (source_file, relative_target_path))
        """
        if not isinstance(command, str):
            return command, []

        if hook_deploy_dir is not None:
            hooks_root = hook_deploy_dir.replace("\\", "/").strip("/")

            script_parts = [hooks_root]
            if target in ("vscode", "copilot"):
                script_parts.append("scripts")
            script_parts.append(package_name)
            scripts_base = posixpath.join(*script_parts)
        else:
            if target in ("vscode", "copilot"):
                scripts_base = f".github/hooks/script
…[2221 chars omitted]…
project_root.joinpath(*hooks_deploy_dir.split("/"))
        hooks_dir.mkdir(parents=True, exist_ok=True)

        package_name = self._get_package_name(package_info)
        hooks_integrated = 0
        scripts_copied = 0
        target_paths: List[Path] = []

        for hook_file in hook_files:
            data = self._parse_hook_json(hook_file)
            if data is None:
                continue

src/apm_cli/commands/uninstall/engine.py   |   1 +
 src/apm_cli/integration/hook_integrator.py | 255 +++++++++++++++++++++--------
 2 files changed, 190 insertions(+), 66 deletions(-)
diff --git a/src/apm_cli/commands/uninstall/engine.py b/src/apm_cli/commands/uninstall/engine.py
index c2e7165..55cd0bb 100644
--- a/src/apm_cli/commands/uninstall/engine.py
+++ b/src/apm_cli/commands/uninstall/engine.py
@@ -310,6 +310,7 @@ def _sync_integrations_after_uninstall(apm_package, project_root, all_deployed_f
     result = _integrators["hooks"].sync_integration(
         apm_package, project_root,
         managed_files=_buckets["hooks"] if _buckets else None,
+        targets=_resolved_targets,

     )
     counts["hooks"] = result.get("files_removed", 0)
 
diff --git a/src/apm_cli/integration/hook_integrator.py b/src/apm_cli/integration/hook_integrator.py
index c174edd..3a7687c 100644
--- a/
…[8629 chars omitted]…
files in all known
+            # and scope-resolved hooks directories.
+            for prefix in hook_prefixes:
+                hooks_dir = project_root.joinpath(*prefix.rstrip("/").split("/"))
+                if not hooks_dir.exists():
+                    continue
                 for hook_file in hooks_dir.glob("*-apm.json"):
                     try:
                         hook_file.unlink()

...................ssssssssssssssssssss.ssssssssssssssssssssssssssssssss [  1%]
...s..............F
=================================== FAILURES ===================================
_______________________ test_permission_denied_graceful ________________________

tmp_path = PosixPath('/tmp/pytest-of-root/pytest-3/test_permission_denied_gracefu0')

    @pytest.mark.skipif(sys.platform == "win32", reason="Windows handles read-only directories differently")
    def test_permission_denied_graceful(tmp_path: Path):
        # Use temp project with constitution to force write
        with temp_project_with_constitution(constitution_text=DEFAULT_CONSTITUTION) as proj:
            agents = Path(proj) / "AGENTS.md"

            agents.write_text("placeholder", encoding="utf-8")
    
            # Make the directory unwriteable (this prevents tempfile creation during atomic write)
            proj
…[689 chars omitted]…
r='').returncode

/repo/tests/integration/test_compile_permission_denied.py:30: AssertionError
=========================== short test summary info ============================
FAILED tests/integration/test_compile_permission_denied.py::test_permission_denied_graceful
!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!
1 failed, 37 passed, 53 skipped, 9 deselected in 27.13s

52:from dataclasses import dataclass, field
55:from apm_cli.utils.paths import portable_relpath
497:            rel_path = portable_relpath(target_path, project_root)
would reformat src/apm_cli/integration/hook_integrator.py
@@ -342,18 +348,24 @@
                 # Rewrite script paths in the matcher dict itself
                 # (GitHub Copilot flat format: bash/powershell/windows keys at this level)
                 for key in self.HOOK_COMMAND_KEYS:
                     if key in matcher:
                         new_cmd, scripts = self._rewrite_command_for_target(
-                            matcher[key], package_path, package_name, target,
+                            matcher[key],

+                            package_path,
+                            package_name,
+                            target,
                             hook_file_dir=hook_file_dir,
                  
…[8629 chars omitted]…
ostics=None,
+    ) -> HookIntegrationResult:
         """Integrate hooks into .cursor/hooks.json.
 
         .. deprecated:: Use :meth:`integrate_hooks_for_target` instead.
         """
         return self._integrate_merged_hooks(
-            _MERGE_HOOK_TARGETS["cursor"], package_info, project_root,
-            force=force, managed_files=managed_files,
All done! ✨ 🍰 ✨
1 file would be reformatted.

........................................................................ [ 11%]
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........................................................................ [ 34%]
........................................................................ [ 46%]
........................................................................ [ 57%]
........................................................................ [ 69%]
........................................................................ [ 80%]
........................................................................ [ 92%]
...............................................                          [100%]
623 passed in 3.82s
Traceback (most recent call last):
  File "<stdin>", line 55, in <module>

AssertionError

Windows path rewriting, scoped deployment, and scoped cleanup reproduced successfully

grep: tests/unit/integration/__pycache__/test_agent_integrator.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_command_integrator.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_deployed_files_manifest.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_hook_integrator.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_instruction_integrator.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_prompt_integrator.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_scope_install_uninstall.cpython-312-pytest-9.2.0.pyc: binary file matches
grep: tests/unit/integration/__pycache__/test_skill_integrator.cpython-312-pytest-9.
…[2451 chars omitted]…
it/integration/test_deployed_files_manifest.py:1172:        HookIntegrator().sync_integration(None, tmp_path, managed_files=managed)
src/apm_cli/commands/uninstall/engine.py:310:    result = _integrators["hooks"].sync_integration(
src/apm_cli/integration/dispatch.py:58:        "hooks":        PrimitiveDispatch(HookIntegrator,         "integrate_hooks_for_target",         "sync_integration",  "hooks"),

........................................................................ [ 42%]
........................................................................ [ 84%]
..........................                                               [100%]
170 passed in 1.92s

- ${CLAUDE_PLUGIN_ROOT}/path -> resolved relative to package root, rewritten for target
    - ./path -> relative path, resolved from hook file's parent directory, rewritten for target
    - System commands (no path separators) -> passed through unchanged
"""

import json
import logging
import posixpath
import re
import shutil
from pathlib import Path
from typing import List, Dict, Tuple, Optional

from dataclasses import dataclass, field

from apm_cli.integration.base_integrator import BaseIntegrator, IntegrationResult
from apm_cli.utils.paths import portable_relpath

_log = logging.getLogger(__name__)


# DEPRECATED -- use IntegrationResult directly for new code.
# Backward-compatible shim: accepts hooks_integrated= kwarg and
# exposes a hooks_integrated property for consumers of the old API.

    def _rewrite_command_for_target(
        self,
        command: str,
        package
…[8630 chars omitted]…
    with open(settings_path, 'r', encoding='utf-8') as f:
                    settings = json.load(f)

                if "hooks" in settings:
                    modified = False
                    for event_name in list(settings["hooks"].keys()):
                        matchers = settings["hooks"][event_name]
 M src/apm_cli/commands/uninstall/engine.py
 M src/apm_cli/integration/hook_integrator.py

........................................................................ [  1%]
........................................................................ [  3%]
........................................................................ [  5%]
........................................................................ [  7%]
........................................................................ [  9%]
........................................................................ [ 11%]
........................................................................ [ 13%]
........................................................................ [ 15%]
........................................................................ [ 17%]
........................................................................ [ 19%]
........................................................................ [ 21%]
.................

…[8630 chars omitted]…
local/lib/python3.12/site-packages/requests/adapters.py:729: ConnectionError
=========================== short test summary info ============================
FAILED tests/unit/test_registry_client.py::TestSimpleRegistryClient::test_find_server_by_reference_uuid_not_found
!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!
1 failed, 3196 passed, 12 subtests passed in 15.27s

210 94             hook_deploy_dir: Optional scope-resolved hooks directory, relative to project root
325 90             hook_file_dir: Directory containing the hook JSON file (for ./path resolution)
343 90                 # (GitHub Copilot flat format: bash/powershell/windows keys at this level)
499 106             if self.check_collision(target_path, rel_path, managed_files, force, diagnostics=diagnostics):
513 114                 if self.check_collision(target_script, target_rel, managed_files, force, diagnostics=diagnostics):
795 89         # Clean APM entries from .claude/settings.json (safe  -- uses _apm_source marker)

Traceback (most recent call last):
  File "<stdin>", line 19, in <module>
AssertionError: pwsh -File .\scripts\scan.ps1

M src/apm_cli/commands/uninstall/engine.py
 M src/apm_cli/integration/hook_integrator.py
 src/apm_cli/commands/uninstall/engine.py   |   1 +
 src/apm_cli/integration/hook_integrator.py | 255 +++++++++++++++++++++--------
 2 files changed, 190 insertions(+), 66 deletions(-)
diff --git a/src/apm_cli/integration/hook_integrator.py b/src/apm_cli/integration/hook_integrator.py
index c174edd..3a7687c 100644
--- a/src/apm_cli/integration/hook_integrator.py
+++ b/src/apm_cli/integration/hook_integrator.py
@@ -44,6 +44,7 @@ Script path handling:
 
 import json

 import logging
+import posixpath
 import re
 import shutil
 from pathlib import Path
@@ -192,69 +193,116 @@ class HookIntegrator(BaseIntegrator):
         package_name: str,
         target: str,
         hook_file_dir: Optional[Path] = None,
+        hook_deploy_dir: Optional[str] = None,
     ) -> Tuple[str, List[Tuple[Path, str]]]:

…[8629 chars omitted]…
.py
+++ b/src/apm_cli/commands/uninstall/engine.py
@@ -310,6 +310,7 @@ def _sync_integrations_after_uninstall(apm_package, project_root, all_deployed_f
     result = _integrators["hooks"].sync_integration(
         apm_package, project_root,
         managed_files=_buckets["hooks"] if _buckets else None,
+        targets=_resolved_targets,
     )
     counts["hooks"] = result.get("files_removed", 0)

target-driven Copilot integration and cleanup passed

........................................................................ [ 11%]
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........................................................................ [ 34%]
........................................................................ [ 46%]
........................................................................ [ 57%]
........................................................................ [ 69%]
........................................................................ [ 80%]
........................................................................ [ 92%]
...............................................                          [100%]
623 passed in 3.07s

POSIX and Windows escaping references rejected

M src/apm_cli/commands/uninstall/engine.py
 M src/apm_cli/integration/hook_integrator.py
 src/apm_cli/commands/uninstall/engine.py   |   1 +
 src/apm_cli/integration/hook_integrator.py | 255 +++++++++++++++++++++--------
 2 files changed, 190 insertions(+), 66 deletions(-)

94:            hook_deploy_dir: Optional scope-resolved hooks directory, relative to project root

diff --git a/src/apm_cli/integration/hook_integrator.py b/src/apm_cli/integration/hook_integrator.py
index c174edd..3a7687c 100644
--- a/src/apm_cli/integration/hook_integrator.py
+++ b/src/apm_cli/integration/hook_integrator.py
@@ -44,6 +44,7 @@ Script path handling:
 
 import json
 import logging
+import posixpath
 import re
 import shutil
 from pathlib import Path

@@ -192,69 +193,116 @@ class HookIntegrator(BaseIntegrator):
         package_name: str,
         target: str,
         hook_file_dir: Optional[Path] = None,
+        hook_deploy_dir: Optional[str] = None,
     ) -> Tuple[str, List[Tuple[Path, str]]]:
-        """Rewrite a hook command to use installed script paths.
+        """Rewrite hook command script paths to their deployed locations.
 
-        Handles:
-        - ${CLAUDE_PLUGIN_ROOT}/path references (resolved from package root)
-        - ./path relative reference
…[8629 chars omitted]…
files in all known
+            # and scope-resolved hooks directories.
+            for prefix in hook_prefixes:
+                hooks_dir = project_root.joinpath(*prefix.rstrip("/").split("/"))
+                if not hooks_dir.exists():
+                    continue
                 for hook_file in hooks_dir.glob("*-apm.json"):
                     try:
                         hook_file.unlink()

submitted.

AUTHORS
CHANGELOG.md
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
MANIFESTO.md
README.md
SECURITY.md
SUPPORT.md
build
docs
install.ps1

install.sh
packages
pyproject.toml
scripts
src
templates
tests
uv.lock
eb7bbdc base
./.git/hooks
./build/hooks
./build/hooks/runtime_hook_ssl_certs.py
./src/apm_cli/integration/hook_integrator.py
./tests/fixtures/mock-plugin/.apm/hooks
./tests/unit/integration/test_hook_integrator.py
./tests/unit/test_ssl_cert_hook.py

"""Hook integration functionality for APM packages.

Integrates hook JSON files and their referenced scripts during package
installation. Supports VSCode Copilot (.github/hooks/), Claude Code
(.claude/settings.json), and Cursor (.cursor/hooks.json) targets.

Hook JSON format (Claude Code  -- nested matcher groups):
    {
        "hooks": {
            "PreToolUse": [
                {
                    "hooks": [

                        {"type": "command", "command": "./scripts/validate.sh", "timeout": 10}
                    ]
                }
            ]
        }
    }

Hook JSON format (GitHub Copilot  -- flat arrays with bash/powershell keys):
    {
        "version": 1,
        "hooks": {
            "preToolUse": [
                {"type": "command", "bash": "./scripts/validate.sh", "timeoutSec": 10}
            ]
        }
    }

Hook JSON format (Cursor  -- flat arrays w
…[8349 chars omitted]…
tive_to(package_path.resolve()):
                continue
            if source_file.exists() and source_file.is_file():
                target_rel = f"{scripts_base}/{rel_path}"
                scripts_to_copy.append((source_file, target_rel))
                new_command = new_command.replace(rel_ref, target_rel)

        return new_command, scripts_to_copy

    def _rewrite_hooks_data(
        self,

self,
        data: Dict,
        package_path: Path,
        package_name: str,
        target: str,
        hook_file_dir: Optional[Path] = None,
    ) -> Tuple[Dict, List[Tuple[Path, str]]]:
        """Rewrite all command paths in a hooks JSON structure.

        Creates a deep copy and rewrites command paths for the target platform.

        Args:

            data: Parsed hook JSON data
            package_path: Root path of the source package
            package_name: Name for scripts subdirectory
            target: "vscode" or "claude"
            hook_file_dir: Directory containing the hook JSON file (for ./path resolution)

        Returns:
            Tuple of (rewritten_data_copy, list of (source_file, target_rel_path))
        """
        import copy
        rewritten = copy.deepcopy(data)
        all_scripts: List[Tuple[Path, str]] = []

        hooks = rewritten.
…[8629 chars omitted]…
t(target.name)
        if config is not None:
            return self._integrate_merged_hooks(
                config, package_info, project_root,
                force=force, managed_files=managed_files,
                diagnostics=diagnostics,
            )

        return HookIntegrationResult(
            files_integrated=0, files_updated=0,
            files_skipped=0, target_paths=[],
        )

4:installation. Supports VSCode Copilot (.github/hooks/), Claude Code
5:(.claude/settings.json), and Cursor (.cursor/hooks.json) targets.
40:    - ${CLAUDE_PLUGIN_ROOT}/path -> resolved relative to package root, rewritten for target
41:    - ./path -> relative path, resolved from hook file's parent directory, rewritten for target
65:    def __init__(self, *args, hooks_integrated=None, **kwargs):
70:            kwargs.setdefault("target_paths", [])
74:    def hooks_integrated(self):
81:    """Configuration for targets that merge hooks into a single JSON file."""
84:    target_key: str         # target name passed to _rewrite_hooks_data
85:    require_dir: bool       # True = skip if target dir doesn't exist
91:        target_key="claude",
96:        target_key="cursor",

101:        target_key="codex",
108:    """Handles integration of APM package hooks into target locations.
111:    th
…[6249 chars omitted]…
          if target.exists() and target.is_file():
654:                        target.unlink()
656:                        deleted.append(target)
663:            hooks_dir = project_root / ".github" / "hooks"
664:            if hooks_dir.exists():
665:                for hook_file in hooks_dir.glob("*-apm.json"):
718:    def _clean_apm_entries_from_json(json_path: Path, stats: Dict[str, int]) -> None:

Args:
            package_info: PackageInfo object

        Returns:
            str: Package name derived from install path
        """
        return package_info.install_path.name

    def integrate_package_hooks(self, package_info, project_root: Path,
                                 force: bool = False,
                                 managed_files: set = None,
                                 diagnostics=None) -> HookIntegrationResult:

        """Integrate hooks from a package into .github/hooks/ (VSCode target).

        Deploys hook JSON files with clean filenames and copies referenced
        script files. Skips user-authored files unless force=True.

        Args:
            package_info: PackageInfo with package metadata and install path
            project_root: Root directory of the project
            force: If True, overwrite user-authored files on collision
 
…[8629 chars omitted]…
     del data["hooks"][event_name]

            if not data["hooks"]:
                del data["hooks"]

            if modified:
                with open(json_path, 'w', encoding='utf-8') as f:
                    json.dump(data, f, indent=2)
                    f.write('\n')
                stats['files_removed'] += 1
        except (json.JSONDecodeError, OSError):
            stats['errors'] += 1

"""
        if target.name == "copilot":
            return self.integrate_package_hooks(
                package_info, project_root,
                force=force, managed_files=managed_files,
                diagnostics=diagnostics,
            )

        config = _MERGE_HOOK_TARGETS.get(target.name)
        if config is not None:
            return self._integrate_merged_hooks(
                config, package_info, project_root,

                force=force, managed_files=managed_files,
                diagnostics=diagnostics,
            )

        return HookIntegrationResult(
            files_integrated=0, files_updated=0,
            files_skipped=0, target_paths=[],
        )

    def sync_integration(self, apm_package, project_root: Path,
                          managed_files: set = None) -> Dict:
        """Remove APM-managed hook files.

        Uses *managed_files*
…[4658 chars omitted]…
open(json_path, 'w', encoding='utf-8') as f:
            json.dump(json_config, f, indent=2)
            f.write('\n')

        return HookIntegrationResult(
            files_integrated=hooks_integrated, files_updated=0,
            files_skipped=0, target_paths=target_paths,
            scripts_copied=scripts_copied,
        )

    # ------------------------------------------------------------------

src/apm_cli/commands/install.py:976:    When *scope* is ``InstallScope.USER``, targets and primitives that
src/apm_cli/commands/install.py:1031:                _effective_root = _mapping.deploy_root or _target.root_dir
src/apm_cli/commands/install.py:1413:            project_root, user_scope=_is_user, explicit_target=_explicit,
src/apm_cli/commands/install.py:1425:                f"Active {_scope_label} targets: {_target_names}"
src/apm_cli/commands/install.py:2325:            # and scope-resolved targets so legacy project-scope orphan paths
src/apm_cli/commands/uninstall/engine.py:230:    When *user_scope* is ``True``, targets are resolved for user-level
src/apm_cli/commands/uninstall/engine.py:244:    _resolved_targets = resolve_targets(project_root, user_scope=user_scope, explicit_target=_explicit)
src/apm_cli/commands/uninstall/engine.py:248:        # Partition against default KNO
…[7146 chars omitted]…
* where scope resolution happens.
src/apm_cli/integration/targets.py:130:        All downstream code reads ``target.root_dir`` directly.
src/apm_cli/integration/targets.py:132:        if not user_scope:

src/apm_cli/integration/targets.py:139:        new_root = self.user_root_dir or self.root_dir
src/apm_cli/integration/targets.py:148:        return replace(self, root_dir=new_root, primitives=filtered)

"""Target profiles for multi-tool integration.

Each target tool (Copilot, Claude, Cursor, ...) describes where APM
primitives should land.  Adding a new target means adding an entry to
``KNOWN_TARGETS`` -- no new classes required.
"""

from __future__ import annotations

from dataclasses import dataclass, field
from typing import Dict, Optional, Tuple, Union

@dataclass(frozen=True)
class PrimitiveMapping:
    """Where a single primitive type is deployed in a target tool."""

    subdir: str
    """Subdirectory under the target root (e.g. ``"rules"``, ``"agents"``)."""

    extension: str
    """File extension or suffix for deployed files
    (e.g. ``".mdc"``, ``".agent.md"``)."""

    format_id: str
    """Opaque tag used by integrators to select the right
    content transformer (e.g. ``"cursor_rules"``)."""

    deploy_root: Optional[str] = None
    """Override *root_dir* for thi
…[8059 chars omitted]…
, ".md", "opencode_agent"
            ),
            "commands": PrimitiveMapping(
                "commands", ".md", "opencode_command"
            ),
            "skills": PrimitiveMapping(
                "skills", "/SKILL.md", "skill_standard"
            ),
        },
        auto_create=False,
        detect_by_dir=True,
        user_supported="partial",
        user_root_dir=".config/opencode",

"""Unit tests for HookIntegrator.

Tests cover:
- Hook file discovery (.apm/hooks/ and hooks/ directories)
- VSCode integration (JSON copy + script copy + path rewriting)
- Claude integration (settings.json merge + script copy)
- Sync/cleanup integration (nuke-and-regenerate)
- Official plugin formats (hookify, learning-output-style, ralph-loop)
- Script path rewriting for ${CLAUDE_PLUGIN_ROOT} references
"""

import json

import tempfile
import shutil
from pathlib import Path
from unittest.mock import MagicMock

import pytest

from apm_cli.integration.hook_integrator import HookIntegrator, HookIntegrationResult
from apm_cli.models.apm_package import APMPackage, PackageInfo


def _make_package_info(install_path: Path, name: str = "test-pkg") -> PackageInfo:
    """Create a minimal PackageInfo for testing."""
    package = APMPackage(name=name, version="1.0.0")
    return PackageInfo(pa
…[7485 chars omitted]…
st_integrate_hookify_vscode(self, temp_project):
        """Test VSCode integration of hookify plugin (multiple events + Python scripts)."""
        pkg_info = self._setup_hookify_package(temp_project)
        integrator = HookIntegrator()

        result = integrator.integrate_package_hooks(pkg_info, temp_project)

        assert result.files_integrated == 1
        assert result.scripts_copied == 4

256:        result = integrator.integrate_package_hooks(pkg_info, temp_project)
293:        result = integrator.integrate_package_hooks(pkg_info, temp_project)
329:        result = integrator.integrate_package_hooks(pkg_info, temp_project)
348:        result = integrator.integrate_package_hooks(pkg_info, temp_project)
377:        result = integrator.integrate_package_hooks(pkg_info, temp_project)
405:        result = integrator.integrate_package_hooks(pkg_info, temp_project)
425:        result = integrator.integrate_package_hooks(pkg_info, temp_project)
438:        result = integrator.integrate_package_hooks(pkg_info, temp_project)
474:        result = integrator.integrate_package_hooks_claude(pkg_info, temp_project)
511:        result = integrator.integrate_package_hooks_claude(pkg_info, temp_project)
529:        result = integrator.integrate_package_hooks_claude(pkg_info, temp_proje
…[6177 chars omitted]…

       """Ensure _rewrite_hooks_data returns a copy, not mutating original."""
1737:        rewritten, _ = integrator._rewrite_hooks_data(data, pkg_dir, "test", "vscode")
1788:        result = integrator.integrate_package_hooks_codex(pi, self.root)
1812:        result = integrator.integrate_package_hooks_codex(pi, self.root)
1829:        result = integrator.integrate_package_hooks_codex(pi, self.root)

updated = json.loads(settings_path.read_text())
        assert "hooks" not in updated  # Completely removed when empty


# ─── Script path rewriting tests ─────────────────────────────────────────────


class TestScriptPathRewriting:
    """Tests for command path rewriting logic."""

    @pytest.fixture
    def temp_project(self):

        temp_dir = tempfile.mkdtemp()
        yield Path(temp_dir)
        shutil.rmtree(temp_dir, ignore_errors=True)

    def test_rewrite_claude_plugin_root(self, temp_project):
        """Test rewriting ${CLAUDE_PLUGIN_ROOT} variable."""
        pkg_dir = temp_project / "pkg"
        (pkg_dir / "hooks").mkdir(parents=True)
        (pkg_dir / "hooks" / "script.sh").write_text("#!/bin/bash")

        integrator = HookIntegrator()
        cmd, scripts = integrator._rewrite_command_for_target(
            "python3 ${CLAUDE_PLUGIN_ROOT}/hooks/script.s
…[8629 chars omitted]…


    def test_rewrite_hooks_data_windows_flat_format(self, temp_project):
        """Test _rewrite_hooks_data handles windows key in flat format (GitHub Copilot)."""
        pkg_dir = temp_project / "pkg"
        (pkg_dir / "scripts").mkdir(parents=True)
        (pkg_dir / "scripts" / "validate.sh").write_text("#!/bin/bash")
        (pkg_dir / "scripts" / "validate.ps1").write_text("Write-Host 'ok'")

src/apm_cli/commands/uninstall/engine.py:302:        result = _integrators["skills"].sync_integration(
src/apm_cli/commands/uninstall/engine.py:310:    result = _integrators["hooks"].sync_integration(
src/apm_cli/integration/agent_integrator.py:379:    def sync_integration(self, apm_package, project_root: Path,
src/apm_cli/integration/command_integrator.py:235:    def sync_integration(self, apm_package, project_root: Path,
src/apm_cli/integration/command_integrator.py:248:        stats = self.sync_integration(None, project_root,
src/apm_cli/integration/hook_integrator.py:84:    target_key: str         # target name passed to _rewrite_hooks_data
src/apm_cli/integration/hook_integrator.py:118:    # Every call site in _rewrite_hooks_data() iterates over this tuple,
src/apm_cli/integration/hook_integrator.py:188:    def _rewrite_command_for_target(
src/apm_cli/integration/hook_integrator.
…[8629 chars omitted]…
        result = self.prompt_integrator.sync_integration(apm_package, self.project_root)
tests/unit/integration/test_sync_integration_url_normalization.py:86:        result = self.agent_integrator.sync_integration(apm_package, self.project_root)

tests/unit/integration/test_sync_integration_url_normalization.py:108:        result = self.prompt_integrator.sync_integration(apm_package, self.project_root)

# ---------------------------------------------------------------------------
# Skill integration (cross-target)
# ---------------------------------------------------------------------------


class TestSkillInstallUninstallCycle:
    """Skill install/uninstall across targets and scopes."""

    def setup_method(self):
        self.temp_dir = tempfile.mkdtemp()
        self.project_root = Path(self.temp_dir)

    def teardown_method(self):
        shutil.rmtree(self.temp_dir, ignore_errors=True)

    def test_copilot_project_scope(self):
        """Skill deploys to .github/skills/ at project scope."""
        target = KNOWN_TARGETS["copilot"].for_scope(user_scope=False)
        pkg_info = _make_pkg(
            self.project_root,
            name="test-skill",
            instructions=False,
            agents=False,
            skills=True,
        )

        integrator = SkillInte
…[8219 chars omitted]…
kage.get_apm_dependencies():
        dep_ref = dep if hasattr(dep, 'repo_url') else None
        if not dep_ref:
            continue
        install_path = dep_ref.get_install_path(Path(APM_MODULES_DIR))
        if not install_path.exists():
            continue

        result = validate_apm_package(install_path)
        pkg = result.package if result and result.package else None
        if not pkg:

return SkillIntegrationResult(
            skill_created=False,
            skill_updated=False,
            skill_skipped=True,
            skill_path=None,
            references_copied=0,
            links_resolved=0,
            sub_skills_promoted=sub_skills_count,
            target_paths=sub_deployed
        )
    
    def sync_integration(self, apm_package, project_root: Path,

                          managed_files: set = None, targets=None) -> Dict[str, int]:
        """Sync skill directories with currently installed packages.

        Derives skill prefixes dynamically from *targets* (or
        ``KNOWN_TARGETS``) so user-scope paths like ``.copilot/skills/``
        and ``.config/opencode/skills/`` are handled correctly.

        When *managed_files* is provided, only removes skill directories
        whose paths appear in the set.  Otherwise falls back to
        
…[5853 chars omitted]…
_bucket" stores the bucket
        # for a complete prefix ending at that node.  This preserves the
        # "single pass, O(1) per path" property from the original
        # component_map approach while supporting multi-level roots like
        # .config/opencode/.
        trie: dict = {}
        for prefix, bucket_key in prefix_map.items():
            segments = [s for s in prefix.split("/") if s]

src/apm_cli/commands/install.py:1011:        "hooks": hook_integrator,
src/apm_cli/commands/install.py:1473:        total_hooks_integrated = 0
src/apm_cli/commands/install.py:1814:                        total_hooks_integrated += int_result["hooks"]
src/apm_cli/commands/install.py:2078:                        total_hooks_integrated += int_result["hooks"]
src/apm_cli/commands/install.py:2273:                            total_hooks_integrated += int_result["hooks"]
src/apm_cli/commands/install.py:2438:        if total_hooks_integrated > 0:
src/apm_cli/commands/install.py:2440:                logger.verbose_detail(f"Integrated {total_hooks_integrated} hook(s)")
src/apm_cli/commands/uninstall/engine.py:310:    result = _integrators["hooks"].sync_integration(
src/apm_cli/integration/dispatch.py:58:        "hooks":        PrimitiveDispatch(HookIntegrator,         "integrate_hooks_for_target",         "sync_integration",  "hooks"),

"""Primitive dispatch registry.

Maps each APM primitive type to its integrator class and methods.
Both ``install.py`` and ``uninstall/engine.py`` import from this
module so the mapping is defined exactly once.

Skills are marked ``multi_target=True`` because ``SkillIntegrator``
receives all targets at once and routes internally.  All other
primitives are dispatched per-target in the outer loop.
"""

from __future__ import annotations

from dataclasses import dataclass
from typing import Type

from apm_cli.integration.base_integrator import BaseIntegrator


@dataclass(frozen=True)
class PrimitiveDispatch:
    """How to integrate a single primitive type."""

    integrator_class: Type[BaseIntegrator]
    """Integrator class to instantiate."""

    integrate_method: str
    """Method name for install (called per-target or with all targets)."""

    sync_method: str
    """Method name fo
…[5401 chars omitted]…
lved
            for tp in _int_result.target_paths:
                deployed.append(tp.relative_to(project_root).as_posix())

    # --- skills (multi-target, handled by SkillIntegrator internally) ---
    skill_result = skill_integrator.integrate_package_skill(
        package_info, project_root,
        diagnostics=diagnostics, managed_files=managed_files, force=force,
        targets=targets,
    )

7:version = "0.8.10"
32:    "tomli>=1.2.0; python_version<'3.11'",
45:    "black>=26.3.1; python_version>='3.10'",
62:target-version = ["py312"]
69:python_version = "3.12"
tests/unit/integration/test_hook_integrator.py:1514:    def test_rewrite_hooks_data_github_copilot_flat_format(self, temp_project):

"hooks": [{"type": "command", "command": "echo lint", "timeout": 5}]
        }]
    }
})


class TestHookCollisionDetection:
    """Collision detection in HookIntegrator.integrate_package_hooks."""

    def test_managed_files_none_no_collision_check(self, tmp_path: Path):
        """Legacy mode: managed_files=None → always overwrite."""
        hooks_dir = tmp_path / ".github" / "hooks"

        hooks_dir.mkdir(parents=True)
        (hooks_dir / "test-pkg-hooks.json").write_text('{"user": true}')

        info = _make_package_info(
            tmp_path, hook_files={"hooks.json": SAMPLE_HOOK_JSON}
        )
        result = HookIntegrator().integrate_package_hooks(
            info, tmp_path, force=False, managed_files=None
        )
        assert result.files_integrated >= 1

    def test_empty_managed_set_all_collisions(self, tmp_path: Path):
        """managed_files=set(
…[8629 chars omitted]…
rewritten, _ = integrator._rewrite_hooks_data(data, pkg_dir, "test", "vscode")

        # Original should be unchanged
        assert data["hooks"]["Stop"][0]["hooks"][0]["command"] == original_cmd
        # Rewritten should be different
        assert rewritten["hooks"]["Stop"][0]["hooks"][0]["command"] != original_cmd


# --- Codex hook integration tests ---------------------------------------------

Refused: searching '/' walks the whole container FS. Scope under /repo.

done
    def _rewrite_command_for_target(
        self,
        command: str,
        package_path: Path,
        package_name: str,
        target: str,
        hook_file_dir: Optional[Path] = None,
        target_root: Optional[str] = None,
    ) -> Tuple[str, List[Tuple[Path, str]]]:
        """Rewrite a hook command to use installed script paths.

        Handles:
        - ${CLAUDE_PLUGIN_ROOT}/path references (resolved from package root)
        - ./path relative references (resolved from hook file's parent directory)
        - Windows-style .\\path relative references (normalized to forward slashes)

        Args:
            command: Original command string
            package_path: Root path of the source package
            package_name: Name used for the scripts subdirectory
            target: "vscode", "copilot", "claude", "cursor", or "codex"
            hook_file_dir: D
…[2807 chars omitted]…
e_file.is_relative_to(package_path.resolve()):
                continue
            if source_file.exists() and source_file.is_file():
                target_rel = f"{scripts_base}/{rel_path}"
                scripts_to_copy.append((source_file, target_rel))
                new_command = new_command.replace(rel_ref, target_rel)

        return new_command, scripts_to_copy

    def _rewrite_hooks_data(

done
                scripts_to_copy.append((source_file, target_rel))
                new_command = new_command.replace(rel_ref, target_rel)

        return new_command, scripts_to_copy

    def _rewrite_hooks_data(
        self,
        data: Dict,
        package_path: Path,
        package_name: str,
        target: str,

        hook_file_dir: Optional[Path] = None,
        target_root: Optional[str] = None,
    ) -> Tuple[Dict, List[Tuple[Path, str]]]:
        """Rewrite all command paths in a hooks JSON structure.

        Creates a deep copy and rewrites command paths for the target platform.

        Args:
            data: Parsed hook JSON data
            package_path: Root path of the source package
            package_name: Name for scripts subdirectory
            target: "vscode", "copilot", "claude", "cursor", or "codex"
            hook_file_dir: Directory containing t
…[2182 chars omitted]…
                 )
                            if scripts:
                                _log.debug(
                                    "Hook %s/%s: rewrote '%s' key (%d script(s))",
                                    package_name, event_name, key, len(scripts),
                                )
                            hook[key] = new_cmd
                            all_scripts.extend(scripts)

done
        Args:
            package_info: PackageInfo object

        Returns:
            str: Package name derived from install path
        """
        return package_info.install_path.name

    def integrate_package_hooks(self, package_info, project_root: Path,
                                 force: bool = False,
                                 managed_files: set = None,

                                 diagnostics=None,
                                 target=None) -> HookIntegrationResult:
        """Integrate hooks from a package into the target's hooks directory.

        Deploys hook JSON files with clean filenames and copies referenced
        script files. Skips user-authored files unless force=True.

        When *target* is omitted, the historical VSCode/Copilot project
        location (``.github/hooks/``) is used.  When a scope-resolved
        target is supplied, 
…[2996 chars omitted]…
 (genuinely different pattern).
        All other merge-based targets are dispatched via the
        ``_MERGE_HOOK_TARGETS`` registry.
        """
        if target.name == "copilot":
            return self.integrate_package_hooks(
                package_info, project_root,
                force=force, managed_files=managed_files,
                diagnostics=diagnostics, target=target,
            )

done
                config, package_info, project_root,
                force=force, managed_files=managed_files,
                diagnostics=diagnostics,
            )

        return HookIntegrationResult(
            files_integrated=0, files_updated=0,
            files_skipped=0, target_paths=[],
        )

    def sync_integration(self, apm_package, project_root: Path,

                          managed_files: set = None, targets=None) -> Dict:
        """Remove APM-managed hook files.

        Uses *managed_files* (relative paths) to surgically remove only
        APM-tracked files.  Falls back to legacy ``*-apm.json`` glob when
        *managed_files* is ``None``.

        **Never** calls ``shutil.rmtree``.

        Args:
            apm_package: APMPackage (unused; kept for API compatibility)
            project_root: Root directory of the project
            managed_files: S
…[2406 chars omitted]…
 1

        # Clean APM entries from .claude/settings.json (safe  -- uses _apm_source marker)
        settings_path = project_root / ".claude" / "settings.json"
        if settings_path.exists():
            try:
                with open(settings_path, 'r', encoding='utf-8') as f:
                    settings = json.load(f)

                if "hooks" in settings:
                    modified = False

_existing.update(_bpaths)
                else:
                    _buckets[_bname] = _bpaths
    else:
        _buckets = None

    counts = {entry.counter_key: 0 for entry in _dispatch.values()}

    # Phase 1: Remove all APM-deployed files
    # Per-target sync for primitives with sync_for_target
    for _target in _resolved_targets:
        for _prim_name, _mapping in _target.primitives.items():

            _entry = _dispatch.get(_prim_name)
            if not _entry or _entry.sync_method != "sync_for_target":
                continue
            _effective_root = _mapping.deploy_root or _target.root_dir
            _deploy_dir = project_root / _effective_root / _mapping.subdir
            if not _deploy_dir.exists():
                continue
            _managed_subset = None
            if _buckets is not None:
                _bucket_key = BaseIntegrator.pa
…[1144 chars omitted]…
-target sync_integration handles all targets)
    result = _integrators["hooks"].sync_integration(
        apm_package, project_root,
        managed_files=_buckets["hooks"] if _buckets else None,
    )
    counts["hooks"] = result.get("files_removed", 0)


    # Phase 2: Re-integrate from remaining installed packages
    _targets = _resolved_targets

    for dep in apm_package.get_apm_dependencies():

done
........................................................................ [ 53%]
..............................................................           [100%]
134 passed in 2.46s

'.\\scripts\\scan.ps1' -> '.github/hooks/scripts/my-pkg/scripts/scan.ps1' [(PosixPath('/tmp/tmpgzib4v0j/pkg/scripts/scan.ps1'), '.github/hooks/scripts/my-pkg/scripts/scan.ps1')]
'pwsh -File .\\scripts\\scan.ps1' -> 'pwsh -File .github/hooks/scripts/my-pkg/scripts/scan.ps1' [(PosixPath('/tmp/tmpgzib4v0j/pkg/scripts/scan.ps1'), '.github/hooks/scripts/my-pkg/scripts/scan.ps1')]
'${CLAUDE_PLUGIN_ROOT}\\hooks\\validate.ps1' -> '.github/hooks/scripts/my-pkg/hooks/validate.ps1' [(PosixPath('/tmp/tmpgzib4v0j/pkg/hooks/validate.ps1'), '.github/hooks/scripts/my-pkg/hooks/validate.ps1')]
'pwsh ${CLAUDE_PLUGIN_ROOT}\\hooks\\validate.ps1' -> 'pwsh .github/hooks/scripts/my-pkg/hooks/validate.ps1' [(PosixPath('/tmp/tmpgzib4v0j/pkg/hooks/validate.ps1'), '.github/hooks/scripts/my-pkg/hooks/validate.ps1')]
traversal '.\\..\\..\\secret.ps1' []
result 1 0 ['.copilot/hooks/pkg2-h.json']
copilot exists Tru
…[207 chars omitted]…
coding, errors=errors) as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/pathlib.py", line 1013, in open
    return io.open(self, mode, buffering, encoding, errors, newline)

           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpgzib4v0j/proj/.copilot/hooks/my-pkg-h.json'

result 1 1 ['.copilot/hooks/pkg2-h.json', '.copilot/hooks/scripts/pkg2/scripts/scan.ps1']
copilot exists True github exists False
{
  "hooks": {
    "preToolUse": [
      {
        "type": "command",
        "windows": "pwsh -File .copilot/hooks/scripts/pkg2/scripts/scan.ps1"
      }
    ]
  }
}

sync {'files_removed': 2, 'errors': 0} copilot exists False

src/apm_cli/commands/uninstall/engine.py   |   1 +
 src/apm_cli/integration/hook_integrator.py | 129 ++++++++++++++++++++---------
 2 files changed, 93 insertions(+), 37 deletions(-)
diff --git a/src/apm_cli/integration/hook_integrator.py b/src/apm_cli/integration/hook_integrator.py
index c174edd..04439b7 100644
--- a/src/apm_cli/integration/hook_integrator.py
+++ b/src/apm_cli/integration/hook_integrator.py
@@ -192,19 +192,23 @@ class HookIntegrator(BaseIntegrator):
         package_name: str,
         target: str,
         hook_file_dir: Optional[Path] = None,
+        target_root: Optional[str] = None,

     ) -> Tuple[str, List[Tuple[Path, str]]]:
         """Rewrite a hook command to use installed script paths.
 
         Handles:
         - ${CLAUDE_PLUGIN_ROOT}/path references (resolved from package root)
         - ./path relative references (resolved from hook file's parent d
…[8629 chars omitted]…
ile():
@@ -660,14 +714,15 @@ class HookIntegrator(BaseIntegrator):
             self.cleanup_empty_parents(deleted, stop_at=project_root)
         else:
             # Legacy fallback  -- glob for old -apm suffix files
-            hooks_dir = project_root / ".github" / "hooks"
-            if hooks_dir.exists():
-                for hook_file in hooks_dir.glob("*-apm.json"):
-                    try:

timeout=resolved_timeout,
                chunked=chunked,
            )
    
        except (ProtocolError, OSError) as err:
            raise ConnectionError(err, request=request)
    
        except MaxRetryError as e:
            if isinstance(e.reason, ConnectTimeoutError):
                # TODO: Remove this in 3.0.0: see #2811
                if not isinstance(e.reason, NewConnectionError):
                    raise ConnectTimeout(e, request=request)

    
            if isinstance(e.reason, ResponseError):
                raise RetryError(e, request=request)
    
            if isinstance(e.reason, _ProxyError):
                raise ProxyError(e, request=request)
    
            if isinstance(e.reason, _SSLError):
                # This branch is for urllib3 v1.22 and later.
                raise SSLError(e, request=request)
    
>           raise ConnectionEr
…[323 chars omitted]…
 'api.mcp.github.com' ([Errno -3] Temporary failure in name resolution)"))

/usr/local/lib/python3.12/site-packages/requests/adapters.py:729: ConnectionError
=========================== short test summary info ============================
FAILED tests/unit/test_registry_client.py::TestSimpleRegistryClient::test_find_server_by_reference_uuid_not_found
1 failed, 3652 passed, 12 subtests passed in 38.40s

done
........................................................................ [ 53%]
..............................................................           [100%]
134 passed in 2.31s

{'hooks': {'preToolUse': [{'command': '.github/hooks/scripts/my-pkg/scripts/scan.ps1', 'windows': 'pwsh -File .github/hooks/scripts/my-pkg/scripts/scan.ps1'}]}} [(PosixPath('/tmp/tmpzm70omw2/scripts/scan.ps1'), '.github/hooks/scripts/my-pkg/scripts/scan.ps1')]
{'hooks': {'preToolUse': [{'matcher': '*', 'hooks': [{'command': '.github/hooks/scripts/my-pkg/scripts/scan.ps1', 'windows': 'pwsh -File .github/hooks/scripts/my-pkg/scripts/scan.ps1'}]}]}} [(PosixPath('/tmp/tmpzm70omw2/scripts/scan.ps1'), '.github/hooks/scripts/my-pkg/scripts/scan.ps1')]

...............                                                          [100%]
15 passed in 1.71s

submitted.