github-spec-kit/tests/test_extension_skills.py

"""
Unit tests for extension skill auto-registration.

Tests cover:
- SKILL.md generation when skills mode was used during init
- No skills created when ai_skills not active
- SKILL.md content correctness
- Existing user-modified skills not overwritten
- Skill cleanup on extension removal
- Registry metadata includes registered_skills
"""

import json
import os
import pytest
import tempfile
import shutil
import yaml
from pathlib import Path
from typing import Any

from specify_cli.extensions import (
    ExtensionManifest,
    ExtensionManager,
)


# ===== Helpers =====

def _create_init_options(
    project_root: Path, ai: str = "claude", ai_skills: Any = True
):
    """Write a .specify/init-options.json file."""
    opts_dir = project_root / ".specify"
    opts_dir.mkdir(parents=True, exist_ok=True)
    opts_file = opts_dir / "init-options.json"
    opts_file.write_text(json.dumps({
        "ai": ai,
        "ai_skills": ai_skills,
        "script": "sh",
    }), encoding="utf-8")


def _create_skills_dir(project_root: Path, ai: str = "claude") -> Path:
    """Create and return the expected skills directory for the given agent."""
    # Match the logic in _get_skills_dir() from specify_cli
    from specify_cli import AGENT_CONFIG

    agent_config = AGENT_CONFIG.get(ai, {})
    agent_folder = agent_config.get("folder", "")
    if agent_folder:
        skills_dir = project_root / agent_folder.rstrip("/") / "skills"
    else:
        skills_dir = project_root / ".agents" / "skills"

    skills_dir.mkdir(parents=True, exist_ok=True)
    return skills_dir


def _create_extension_dir(temp_dir: Path, ext_id: str = "test-ext") -> Path:
    """Create a complete extension directory with manifest and command files."""
    ext_dir = temp_dir / ext_id
    ext_dir.mkdir()

    manifest_data = {
        "schema_version": "1.0",
        "extension": {
            "id": ext_id,
            "name": "Test Extension",
            "version": "1.0.0",
            "description": "A test extension for skill registration",
        },
        "requires": {
            "speckit_version": ">=0.1.0",
        },
        "provides": {
            "commands": [
                {
                    "name": f"speckit.{ext_id}.hello",
                    "file": "commands/hello.md",
                    "description": "Test hello command",
                },
                {
                    "name": f"speckit.{ext_id}.world",
                    "file": "commands/world.md",
                    "description": "Test world command",
                },
            ]
        },
    }

    with open(ext_dir / "extension.yml", "w") as f:
        yaml.dump(manifest_data, f)

    commands_dir = ext_dir / "commands"
    commands_dir.mkdir()

    (commands_dir / "hello.md").write_text(
        "---\n"
        "description: \"Test hello command\"\n"
        "---\n"
        "\n"
        "# Hello Command\n"
        "\n"
        "Run this to say hello.\n"
        "$ARGUMENTS\n"
    )

    (commands_dir / "world.md").write_text(
        "---\n"
        "description: \"Test world command\"\n"
        "---\n"
        "\n"
        "# World Command\n"
        "\n"
        "Run this to greet the world.\n"
    )

    return ext_dir


def _can_create_symlink(temp_dir: Path) -> bool:
    """Return True when the current platform/user can create file symlinks."""
    target = temp_dir / "symlink-target.txt"
    link = temp_dir / "symlink-link.txt"
    target.write_text("ok", encoding="utf-8")
    try:
        os.symlink(target, link)
    except OSError:
        return False
    return link.is_symlink()


# ===== Fixtures =====

@pytest.fixture
def temp_dir():
    """Create a temporary directory for tests."""
    tmpdir = tempfile.mkdtemp()
    yield Path(tmpdir)
    shutil.rmtree(tmpdir)


@pytest.fixture
def project_dir(temp_dir):
    """Create a mock spec-kit project directory."""
    proj_dir = temp_dir / "project"
    proj_dir.mkdir()

    # Create .specify directory
    specify_dir = proj_dir / ".specify"
    specify_dir.mkdir()

    return proj_dir


@pytest.fixture
def extension_dir(temp_dir):
    """Create a complete extension directory."""
    return _create_extension_dir(temp_dir)


@pytest.fixture
def skills_project(project_dir):
    """Create a project with skills mode enabled and skills directory."""
    _create_init_options(project_dir, ai="claude", ai_skills=True)
    skills_dir = _create_skills_dir(project_dir, ai="claude")
    return project_dir, skills_dir


@pytest.fixture
def no_skills_project(project_dir):
    """Create a project without skills mode."""
    _create_init_options(project_dir, ai="claude", ai_skills=False)
    return project_dir


# ===== ExtensionManager._get_skills_dir Tests =====

class TestExtensionManagerGetSkillsDir:
    """Test _get_skills_dir() on ExtensionManager."""

    def test_returns_skills_dir_when_active(self, skills_project):
        """Should return skills dir when ai_skills is true and dir exists."""
        project_dir, skills_dir = skills_project
        manager = ExtensionManager(project_dir)
        result = manager._get_skills_dir()
        assert result == skills_dir

    def test_returns_none_when_no_ai_skills(self, no_skills_project):
        """Should return None when ai_skills is false and not create the dir."""
        manager = ExtensionManager(no_skills_project)
        result = manager._get_skills_dir()
        assert result is None
        # Ensure the directory was NOT created on disk
        from specify_cli import _get_skills_dir as resolve_skills_dir
        skills_path = resolve_skills_dir(no_skills_project, "claude")
        assert not skills_path.exists()

    def test_returns_none_when_no_init_options(self, project_dir):
        """Should return None when init-options.json is missing and not create any dir."""
        manager = ExtensionManager(project_dir)
        result = manager._get_skills_dir()
        assert result is None
        # No agent skills directory should have been created
        assert not (project_dir / ".claude" / "skills").exists()
        assert not (project_dir / ".agents" / "skills").exists()

    def test_creates_skills_dir_on_demand(self, project_dir):
        """Should create skills dir when ai_skills is enabled but dir is missing."""
        _create_init_options(project_dir, ai="claude", ai_skills=True)
        # Don't create the skills directory — _get_skills_dir should do it
        manager = ExtensionManager(project_dir)
        result = manager._get_skills_dir()
        assert result is not None
        assert result.is_dir()

    def test_returns_kimi_skills_dir_when_ai_skills_disabled(self, project_dir):
        """Kimi should still use its native skills dir when ai_skills is false."""
        _create_init_options(project_dir, ai="kimi", ai_skills=False)
        skills_dir = _create_skills_dir(project_dir, ai="kimi")
        manager = ExtensionManager(project_dir)
        result = manager._get_skills_dir()
        assert result == skills_dir

    def test_returns_none_when_ai_skills_is_non_boolean_truthy(self, project_dir):
        """Corrupted truthy ai_skills values should not enable skills mode."""
        _create_init_options(project_dir, ai="claude", ai_skills="false")

        manager = ExtensionManager(project_dir)
        result = manager._get_skills_dir()
        assert result is None
        assert not (project_dir / ".claude" / "skills").exists()

    def test_returns_none_for_non_dict_init_options(self, project_dir):
        """Corrupted-but-parseable init-options should not crash skill-dir lookup."""
        opts_file = project_dir / ".specify" / "init-options.json"
        opts_file.parent.mkdir(parents=True, exist_ok=True)
        opts_file.write_text("[]", encoding="utf-8")
        _create_skills_dir(project_dir, ai="claude")
        manager = ExtensionManager(project_dir)
        result = manager._get_skills_dir()
        assert result is None


# ===== Extension Skill Registration Tests =====

class TestExtensionSkillRegistration:
    """Test _register_extension_skills() on ExtensionManager."""

    def test_skills_created_when_ai_skills_active(self, skills_project, extension_dir):
        """Skills should be created when ai_skills is enabled."""
        project_dir, skills_dir = skills_project
        manager = ExtensionManager(project_dir)
        manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        # Check that skill directories were created
        skill_dirs = sorted([d.name for d in skills_dir.iterdir() if d.is_dir()])
        assert "speckit-test-ext-hello" in skill_dirs
        assert "speckit-test-ext-world" in skill_dirs

    def test_skill_md_content_correct(self, skills_project, extension_dir):
        """SKILL.md should have correct agentskills.io structure."""
        project_dir, skills_dir = skills_project
        manager = ExtensionManager(project_dir)
        manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
        assert skill_file.exists()
        content = skill_file.read_text()

        # Check structure
        assert content.startswith("---\n")
        assert "name: speckit-test-ext-hello" in content
        assert "description:" in content
        assert "Test hello command" in content
        assert "source: extension:test-ext" in content
        assert "author: github-spec-kit" in content
        assert "compatibility:" in content
        assert "Run this to say hello." in content

    def test_skill_md_has_parseable_yaml(self, skills_project, extension_dir):
        """Generated SKILL.md should contain valid, parseable YAML frontmatter."""
        project_dir, skills_dir = skills_project
        manager = ExtensionManager(project_dir)
        manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
        content = skill_file.read_text()

        assert content.startswith("---\n")
        parts = content.split("---", 2)
        assert len(parts) >= 3
        parsed = yaml.safe_load(parts[1])
        assert isinstance(parsed, dict)
        assert parsed["name"] == "speckit-test-ext-hello"
        assert "description" in parsed
        assert parsed["disable-model-invocation"] is False

    def test_argument_hint_preserved_for_extension_command(
        self, skills_project, temp_dir
    ):
        """argument-hint from an extension command must survive into SKILL.md.

        Regression for #2903: the field was dropped for extension-provided
        commands while being kept for core template commands. The source
        description is intentionally long so it folds across multiple lines
        when serialized, guarding against an in-place string injection that
        would split the folded scalar and produce invalid YAML.
        """
        project_dir, skills_dir = skills_project

        long_description = (
            "Build and maintain a lean, static context/ knowledge folder so "
            "coding agents load only what is relevant and save tokens"
        )
        arg_hint = "<init | update | list | check> [area] [slug] [-- notes]"

        ext_dir = temp_dir / "hint-ext"
        ext_dir.mkdir()
        manifest_data = {
            "schema_version": "1.0",
            "extension": {
                "id": "hint-ext",
                "name": "Hint Extension",
                "version": "1.0.0",
                "description": "Extension exercising argument-hint preservation",
            },
            "requires": {"speckit_version": ">=0.1.0"},
            "provides": {
                "commands": [
                    {
                        "name": "speckit.hint-ext.build-context",
                        "file": "commands/build-context.md",
                        "description": long_description,
                    }
                ]
            },
        }
        with open(ext_dir / "extension.yml", "w") as f:
            yaml.dump(manifest_data, f)
        commands_dir = ext_dir / "commands"
        commands_dir.mkdir()
        (commands_dir / "build-context.md").write_text(
            "---\n"
            f'description: "{long_description}"\n'
            f'argument-hint: "{arg_hint}"\n'
            "---\n"
            "\n"
            "# Build Context\n"
            "\n"
            "Do the thing.\n"
            "$ARGUMENTS\n",
            encoding="utf-8",
        )

        manager = ExtensionManager(project_dir)
        manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)

        skill_file = skills_dir / "speckit-hint-ext-build-context" / "SKILL.md"
        assert skill_file.exists()
        content = skill_file.read_text(encoding="utf-8")

        # Frontmatter must parse cleanly even though the description folds.
        parts = content.split("---", 2)
        assert len(parts) >= 3
        parsed = yaml.safe_load(parts[1])
        assert parsed["argument-hint"] == arg_hint
        assert parsed["description"] == long_description

    def test_argument_hint_not_added_for_non_claude_agent(self, project_dir, temp_dir):
        """argument-hint must stay Claude-only — other skills agents are untouched.

        The hint is carried only for integrations that support it (currently
        Claude, the sole integration defining inject_argument_hint). A non-Claude
        skills agent such as kimi must keep the shared build_skill_frontmatter
        shape (name/description/compatibility/metadata) with no argument-hint.
        """
        _create_init_options(project_dir, ai="kimi", ai_skills=True)
        skills_dir = _create_skills_dir(project_dir, ai="kimi")

        arg_hint = "<init | update | list | check> [area]"
        ext_dir = temp_dir / "hint-ext-kimi"
        ext_dir.mkdir()
        manifest_data = {
            "schema_version": "1.0",
            "extension": {
                "id": "hint-ext-kimi",
                "name": "Hint Extension Kimi",
                "version": "1.0.0",
                "description": "Extension exercising argument-hint gating",
            },
            "requires": {"speckit_version": ">=0.1.0"},
            "provides": {
                "commands": [
                    {
                        "name": "speckit.hint-ext-kimi.build-context",
                        "file": "commands/build-context.md",
                        "description": "Build context",
                    }
                ]
            },
        }
        with open(ext_dir / "extension.yml", "w") as f:
            yaml.dump(manifest_data, f)
        commands_dir = ext_dir / "commands"
        commands_dir.mkdir()
        (commands_dir / "build-context.md").write_text(
            "---\n"
            'description: "Build context"\n'
            f'argument-hint: "{arg_hint}"\n'
            "---\n"
            "\n"
            "# Build Context\n"
            "\n"
            "Do the thing.\n"
            "$ARGUMENTS\n",
            encoding="utf-8",
        )

        manager = ExtensionManager(project_dir)
        manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)

        skill_file = skills_dir / "speckit-hint-ext-kimi-build-context" / "SKILL.md"
        assert skill_file.exists()
        parsed = yaml.safe_load(skill_file.read_text(encoding="utf-8").split("---", 2)[1])
        assert "argument-hint" not in parsed

    def test_no_skills_when_ai_skills_disabled(self, no_skills_project, extension_dir):
        """No skills should be created when ai_skills is false."""
        manager = ExtensionManager(no_skills_project)
        manifest = manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        # Verify registry
        metadata = manager.registry.get(manifest.id)
        assert metadata["registered_skills"] == []

    def test_no_skills_when_init_options_missing(self, project_dir, extension_dir):
        """No skills should be created when init-options.json is absent."""
        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        metadata = manager.registry.get(manifest.id)
        assert metadata["registered_skills"] == []

    def test_existing_skill_not_overwritten(self, skills_project, extension_dir):
        """Pre-existing SKILL.md should not be overwritten."""
        project_dir, skills_dir = skills_project

        # Pre-create a custom skill
        custom_dir = skills_dir / "speckit-test-ext-hello"
        custom_dir.mkdir(parents=True)
        custom_content = "# My Custom Hello Skill\nUser-modified content\n"
        (custom_dir / "SKILL.md").write_text(custom_content)

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        # Custom skill should be untouched
        assert (custom_dir / "SKILL.md").read_text() == custom_content

        # But the other skill should still be created
        metadata = manager.registry.get(manifest.id)
        assert "speckit-test-ext-world" in metadata["registered_skills"]
        # The pre-existing one should NOT be in registered_skills (it was skipped)
        assert "speckit-test-ext-hello" not in metadata["registered_skills"]

    def test_dev_skill_symlink_refreshes_existing_cache(
        self, skills_project, extension_dir, temp_dir
    ):
        """Dev-mode skill symlinks should refresh rendered cache content."""
        if not _can_create_symlink(temp_dir):
            pytest.skip("Current platform/user cannot create symlinks")

        project_dir, skills_dir = skills_project
        manager = ExtensionManager(project_dir)
        manifest = ExtensionManifest(extension_dir / "extension.yml")

        manager._register_extension_skills(
            manifest,
            extension_dir,
            link_outputs=True,
        )

        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
        assert skill_file.is_symlink()
        assert "Run this to say hello." in skill_file.read_text(encoding="utf-8")

        (extension_dir / "commands" / "hello.md").write_text(
            "---\n"
            "description: \"Updated test hello command\"\n"
            "---\n"
            "\n"
            "# Hello Command\n"
            "\n"
            "Run this updated hello.\n"
        )

        written = manager._register_extension_skills(
            manifest,
            extension_dir,
            link_outputs=True,
        )

        assert "speckit-test-ext-hello" in written
        assert "Run this updated hello." in skill_file.read_text(encoding="utf-8")

    def test_dev_skill_registration_falls_back_to_copy_when_symlink_fails(
        self, skills_project, extension_dir, monkeypatch
    ):
        """Dev-mode skill registration works when Windows cannot create symlinks."""
        project_dir, skills_dir = skills_project
        manager = ExtensionManager(project_dir)
        manifest = ExtensionManifest(extension_dir / "extension.yml")

        def raise_windows_symlink_error(target, link):
            raise OSError("A required privilege is not held by the client")

        monkeypatch.setattr(
            "specify_cli.extensions.os.symlink", raise_windows_symlink_error
        )

        written = manager._register_extension_skills(
            manifest,
            extension_dir,
            link_outputs=True,
        )

        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
        assert "speckit-test-ext-hello" in written
        assert skill_file.exists()
        assert not skill_file.is_symlink()
        assert "Run this to say hello." in skill_file.read_text(encoding="utf-8")
        assert (
            extension_dir
            / ".specify-dev"
            / "extension-skills"
            / "speckit-test-ext-hello"
            / "SKILL.md"
        ).exists()

    def test_dev_skill_registration_falls_back_to_copy_when_relpath_fails(
        self, skills_project, extension_dir, monkeypatch
    ):
        """Dev-mode skill registration stays functional across Windows drive roots."""
        project_dir, skills_dir = skills_project
        manager = ExtensionManager(project_dir)
        manifest = ExtensionManifest(extension_dir / "extension.yml")

        def raise_relpath_error(path, start=None):
            raise ValueError("path is on mount 'D:', start on mount 'C:'")

        monkeypatch.setattr(
            "specify_cli.extensions.os.path.relpath", raise_relpath_error
        )

        written = manager._register_extension_skills(
            manifest,
            extension_dir,
            link_outputs=True,
        )

        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
        assert "speckit-test-ext-hello" in written
        assert skill_file.exists()
        assert not skill_file.is_symlink()
        assert "Run this to say hello." in skill_file.read_text(encoding="utf-8")
        assert (
            extension_dir
            / ".specify-dev"
            / "extension-skills"
            / "speckit-test-ext-hello"
            / "SKILL.md"
        ).exists()

    def test_dev_skill_registration_falls_back_to_copy_when_cache_write_fails(
        self, skills_project, extension_dir, monkeypatch
    ):
        """Dev-mode skill registration stays functional when the dev cache is unwritable."""
        project_dir, skills_dir = skills_project
        manager = ExtensionManager(project_dir)
        manifest = ExtensionManifest(extension_dir / "extension.yml")
        original_write_text = Path.write_text

        def raise_cache_write_error(path, *args, **kwargs):
            if ".specify-dev" in path.parts:
                raise OSError("cache is not writable")
            return original_write_text(path, *args, **kwargs)

        monkeypatch.setattr(Path, "write_text", raise_cache_write_error)

        written = manager._register_extension_skills(
            manifest,
            extension_dir,
            link_outputs=True,
        )

        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
        assert "speckit-test-ext-hello" in written
        assert skill_file.exists()
        assert not skill_file.is_symlink()
        assert "Run this to say hello." in skill_file.read_text(encoding="utf-8")
        assert not (
            extension_dir
            / ".specify-dev"
            / "extension-skills"
            / "speckit-test-ext-hello"
            / "SKILL.md"
        ).exists()

    def test_registered_skills_in_registry(self, skills_project, extension_dir):
        """Registry should contain registered_skills list."""
        project_dir, skills_dir = skills_project
        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        metadata = manager.registry.get(manifest.id)
        assert "registered_skills" in metadata
        assert len(metadata["registered_skills"]) == 2
        assert "speckit-test-ext-hello" in metadata["registered_skills"]
        assert "speckit-test-ext-world" in metadata["registered_skills"]

    def test_kimi_uses_hyphenated_skill_names(self, project_dir, temp_dir):
        """Kimi agent should use the same hyphenated skill names as hooks."""
        _create_init_options(project_dir, ai="kimi", ai_skills=True)
        _create_skills_dir(project_dir, ai="kimi")
        ext_dir = _create_extension_dir(temp_dir, ext_id="test-ext")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=False
        )

        metadata = manager.registry.get(manifest.id)
        assert "speckit-test-ext-hello" in metadata["registered_skills"]
        assert "speckit-test-ext-world" in metadata["registered_skills"]

    def test_kimi_creates_skills_when_ai_skills_disabled(self, project_dir, temp_dir):
        """Kimi should still auto-register extension skills in native-skills mode."""
        _create_init_options(project_dir, ai="kimi", ai_skills=False)
        skills_dir = _create_skills_dir(project_dir, ai="kimi")
        ext_dir = _create_extension_dir(temp_dir, ext_id="test-ext")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=False
        )

        metadata = manager.registry.get(manifest.id)
        assert "speckit-test-ext-hello" in metadata["registered_skills"]
        assert "speckit-test-ext-world" in metadata["registered_skills"]
        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()

    def test_skill_registration_resolves_script_placeholders(self, project_dir, temp_dir):
        """Auto-registered extension skills should resolve script placeholders."""
        _create_init_options(project_dir, ai="claude", ai_skills=True)
        skills_dir = _create_skills_dir(project_dir, ai="claude")

        ext_dir = temp_dir / "scripted-ext"
        ext_dir.mkdir()
        manifest_data = {
            "schema_version": "1.0",
            "extension": {
                "id": "scripted-ext",
                "name": "Scripted Extension",
                "version": "1.0.0",
                "description": "Test",
            },
            "requires": {"speckit_version": ">=0.1.0"},
            "provides": {
                "commands": [
                    {
                        "name": "speckit.scripted-ext.plan",
                        "file": "commands/plan.md",
                        "description": "Scripted plan command",
                    }
                ]
            },
        }
        with open(ext_dir / "extension.yml", "w") as f:
            yaml.dump(manifest_data, f)

        (ext_dir / "commands").mkdir()
        (ext_dir / "commands" / "plan.md").write_text(
            "---\n"
            "description: Scripted plan command\n"
            "scripts:\n"
            "  sh: ../../scripts/bash/setup-plan.sh --json \"{ARGS}\"\n"
            "---\n\n"
            "Run {SCRIPT}\n"
            "Review templates/checklist.md and memory/constitution.md for __AGENT__.\n"
        )

        manager = ExtensionManager(project_dir)
        manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)

        content = (skills_dir / "speckit-scripted-ext-plan" / "SKILL.md").read_text()
        assert "{SCRIPT}" not in content
        assert "{ARGS}" not in content
        assert "__AGENT__" not in content
        assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
        assert ".specify/templates/checklist.md" in content
        assert ".specify/memory/constitution.md" in content

    def test_missing_command_file_skipped(self, skills_project, temp_dir):
        """Commands with missing source files should be skipped gracefully."""
        project_dir, skills_dir = skills_project

        ext_dir = temp_dir / "missing-cmd-ext"
        ext_dir.mkdir()
        manifest_data = {
            "schema_version": "1.0",
            "extension": {
                "id": "missing-cmd-ext",
                "name": "Missing Cmd Extension",
                "version": "1.0.0",
                "description": "Test",
            },
            "requires": {"speckit_version": ">=0.1.0"},
            "provides": {
                "commands": [
                    {
                        "name": "speckit.missing-cmd-ext.exists",
                        "file": "commands/exists.md",
                        "description": "Exists",
                    },
                    {
                        "name": "speckit.missing-cmd-ext.ghost",
                        "file": "commands/ghost.md",
                        "description": "Does not exist",
                    },
                ]
            },
        }
        with open(ext_dir / "extension.yml", "w") as f:
            yaml.dump(manifest_data, f)

        (ext_dir / "commands").mkdir()
        (ext_dir / "commands" / "exists.md").write_text(
            "---\ndescription: Exists\n---\n\n# Exists\n\nBody.\n"
        )
        # Intentionally do NOT create ghost.md

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=False
        )

        metadata = manager.registry.get(manifest.id)
        assert "speckit-missing-cmd-ext-exists" in metadata["registered_skills"]
        assert "speckit-missing-cmd-ext-ghost" not in metadata["registered_skills"]

    @pytest.mark.parametrize("ai", ["claude", "codex"])
    def test_skills_registered_when_dir_missing(self, project_dir, temp_dir, ai):
        """Extension add should create skills dir on demand and register skills.

        Regression test for https://github.com/github/spec-kit/issues/2682:
        when an extension is installed before the agent skills directory exists,
        skills must still be materialized (the directory is created on demand).
        """
        _create_init_options(project_dir, ai=ai, ai_skills=True)
        # Deliberately do NOT create the skills directory
        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=False
        )

        # Skills dir should have been created automatically
        from specify_cli import _get_skills_dir as resolve_skills_dir
        skills_dir = resolve_skills_dir(project_dir, ai)
        assert skills_dir.is_dir()

        # SKILL.md files should exist
        assert (skills_dir / "speckit-early-ext-hello" / "SKILL.md").exists()
        assert (skills_dir / "speckit-early-ext-world" / "SKILL.md").exists()

        # Registry should record them
        metadata = manager.registry.get(manifest.id)
        assert len(metadata["registered_skills"]) == 2
        assert "speckit-early-ext-hello" in metadata["registered_skills"]
        assert "speckit-early-ext-world" in metadata["registered_skills"]

    def test_commands_registered_when_claude_skills_dir_missing(self, project_dir, temp_dir):
        """Extension install should not silently skip Claude when skills dir is missing."""
        _create_init_options(project_dir, ai="claude", ai_skills=True)
        (project_dir / ".claude").mkdir()
        # Deliberately do NOT create .claude/skills
        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=True
        )

        skills_dir = project_dir / ".claude" / "skills"
        assert skills_dir.is_dir()

        metadata = manager.registry.get(manifest.id)
        assert metadata["registered_commands"] == {
            "claude": [
                "speckit.early-ext.hello",
                "speckit.early-ext.world",
            ]
        }
        assert metadata["registered_skills"] == []

        skill_file = skills_dir / "speckit-early-ext-hello" / "SKILL.md"
        assert skill_file.exists()
        content = skill_file.read_text(encoding="utf-8")
        assert "source: early-ext:commands/hello.md" in content

    def test_hermes_global_skills_dir_used_when_marker_is_recovered(
        self, project_dir, temp_dir, monkeypatch
    ):
        """Hermes recovery must not use the project marker as the output dir."""
        home = temp_dir / "home"
        home.mkdir()
        monkeypatch.setattr(Path, "home", lambda: home)
        _create_init_options(project_dir, ai="hermes", ai_skills=True)
        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=True
        )

        metadata = manager.registry.get(manifest.id)
        assert metadata is not None
        assert metadata["registered_commands"] == {
            "hermes": [
                "speckit.early-ext.hello",
                "speckit.early-ext.world",
            ]
        }
        assert metadata["registered_skills"] == []

        global_skills_dir = home / ".hermes" / "skills"
        assert (
            global_skills_dir / "speckit-early-ext-hello" / "SKILL.md"
        ).exists()
        assert (
            global_skills_dir / "speckit-early-ext-world" / "SKILL.md"
        ).exists()

        marker = project_dir / ".hermes" / "skills"
        assert marker.is_dir()
        assert list(marker.glob("speckit-*/SKILL.md")) == []

    def test_hermes_get_skills_dir_creates_global_output_dir(
        self, project_dir, temp_dir, monkeypatch
    ):
        """ExtensionManager should create the agent-specific output dir it returns."""
        home = temp_dir / "home"
        home.mkdir()
        monkeypatch.setattr(Path, "home", lambda: home)
        _create_init_options(project_dir, ai="hermes", ai_skills=True)

        manager = ExtensionManager(project_dir)
        skills_dir = manager._get_skills_dir()

        assert skills_dir == home / ".hermes" / "skills"
        assert skills_dir.is_dir()
        assert (project_dir / ".hermes" / "skills").is_dir()

    def test_unusable_hermes_global_skills_dir_skips_skill_registration(
        self, project_dir, temp_dir, monkeypatch, capsys
    ):
        """An unusable agent-specific output dir should warn and skip skills."""
        home = temp_dir / "home"
        hermes_dir = home / ".hermes"
        hermes_dir.mkdir(parents=True)
        (hermes_dir / "skills").write_text("not a directory", encoding="utf-8")
        monkeypatch.setattr(Path, "home", lambda: home)
        _create_init_options(project_dir, ai="hermes", ai_skills=True)
        ext_dir = _create_extension_dir(temp_dir, ext_id="blocked-ext")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=False
        )

        metadata = manager.registry.get(manifest.id)
        assert metadata is not None
        assert metadata["registered_skills"] == []
        captured = capsys.readouterr()
        assert "Warning:" in captured.out
        assert "Continuing without skill registration." in captured.out

    def test_detect_dir_marker_file_does_not_register_hermes_commands(
        self, project_dir, temp_dir, monkeypatch
    ):
        """Regular files at detect_dir marker paths should not detect agents."""
        home = temp_dir / "home"
        global_skills_dir = home / ".hermes" / "skills"
        global_skills_dir.mkdir(parents=True)
        monkeypatch.setattr(Path, "home", lambda: home)
        _create_init_options(project_dir, ai="hermes", ai_skills=True)
        marker_parent = project_dir / ".hermes"
        marker_parent.mkdir()
        marker_file = marker_parent / "skills"
        marker_file.write_text("not a directory", encoding="utf-8")
        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=True
        )

        assert marker_file.is_file()
        assert marker_file.read_text(encoding="utf-8") == "not a directory"
        assert not (
            global_skills_dir / "speckit-early-ext-hello" / "SKILL.md"
        ).exists()
        assert not (
            global_skills_dir / "speckit-early-ext-world" / "SKILL.md"
        ).exists()

        metadata = manager.registry.get(manifest.id)
        assert metadata is not None
        assert metadata["registered_commands"] == {}
        assert metadata["registered_skills"] == []

    def test_non_boolean_ai_skills_does_not_recover_missing_skills_dir(
        self, project_dir, temp_dir
    ):
        """Corrupted truthy ai_skills values should not recover skills dirs."""
        _create_init_options(project_dir, ai="claude", ai_skills="false")
        (project_dir / ".claude").mkdir()
        # Deliberately do NOT create .claude/skills.
        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=True
        )

        metadata = manager.registry.get(manifest.id)
        assert metadata is not None
        assert metadata["registered_commands"] == {}
        assert metadata["registered_skills"] == []
        assert not (project_dir / ".claude" / "skills").exists()

    def test_non_boolean_ai_skills_does_not_skip_default_agent_reregistration(
        self, project_dir, temp_dir
    ):
        """Corrupted ai_skills values should not trigger skills-mode skips."""
        _create_init_options(project_dir, ai="copilot", ai_skills="false")
        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=False
        )
        manager.register_enabled_extensions_for_agent("copilot")

        metadata = manager.registry.get(manifest.id)
        assert metadata is not None
        assert metadata["registered_commands"] == {
            "copilot": [
                "speckit.early-ext.hello",
                "speckit.early-ext.world",
            ]
        }
        assert metadata["registered_skills"] == []
        assert (project_dir / ".github" / "agents").is_dir()

    def test_existing_agent_command_path_file_is_not_detected(
        self, project_dir, temp_dir
    ):
        """Existing files at command-dir paths should not count as detected agents."""
        _create_init_options(project_dir, ai="claude", ai_skills=False)
        claude_dir = project_dir / ".claude"
        claude_dir.mkdir()
        skills_file = claude_dir / "skills"
        skills_file.write_text("not a directory", encoding="utf-8")
        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=True
        )

        assert skills_file.read_text(encoding="utf-8") == "not a directory"
        metadata = manager.registry.get(manifest.id)
        assert metadata is not None
        assert metadata["registered_commands"] == {}
        assert metadata["registered_skills"] == []

    def test_missing_shared_skills_dir_registers_only_active_agent(self, project_dir, temp_dir):
        """Recreating shared skills dirs should not activate unrelated agents."""
        _create_init_options(project_dir, ai="agy", ai_skills=True)
        (project_dir / ".agents").mkdir()
        # Deliberately do NOT create .agents/skills, shared by agy and codex.
        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=True
        )

        skills_dir = project_dir / ".agents" / "skills"
        assert skills_dir.is_dir()

        metadata = manager.registry.get(manifest.id)
        assert metadata["registered_commands"] == {
            "agy": [
                "speckit.early-ext.hello",
                "speckit.early-ext.world",
            ]
        }
        assert metadata["registered_skills"] == []

    def test_missing_shared_skills_dir_uses_normalized_guard_for_later_agents(
        self, project_dir, temp_dir, monkeypatch
    ):
        """Shared-dir suppression should tolerate lexical path differences."""
        _create_init_options(project_dir, ai="agy", ai_skills=True)
        (project_dir / ".agents").mkdir()
        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")

        from specify_cli.agents import CommandRegistrar as AgentRegistrar

        original_resolve_agent_dir = AgentRegistrar._resolve_agent_dir
        original_register_commands = AgentRegistrar.register_commands
        attempted_agents = []

        def resolve_codex_with_parent_segment(self, agent_name, agent_config, root):
            if agent_name == "codex":
                return root / ".agents" / ".." / ".agents" / "skills"
            return original_resolve_agent_dir(agent_name, agent_config, root)

        def record_registration(self, agent_name, *args, **kwargs):
            attempted_agents.append(agent_name)
            return original_register_commands(self, agent_name, *args, **kwargs)

        monkeypatch.setattr(
            AgentRegistrar, "_resolve_agent_dir", resolve_codex_with_parent_segment
        )
        monkeypatch.setattr(AgentRegistrar, "register_commands", record_registration)

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=True
        )

        assert attempted_agents == ["agy"]
        metadata = manager.registry.get(manifest.id)
        assert metadata is not None
        assert metadata["registered_commands"] == {
            "agy": [
                "speckit.early-ext.hello",
                "speckit.early-ext.world",
            ]
        }
        assert metadata["registered_skills"] == []

    def test_missing_shared_skills_dir_write_oserror_does_not_register_other_agents(
        self, project_dir, temp_dir, monkeypatch
    ):
        """Failed active registration must not make shared skills dirs detected."""
        _create_init_options(project_dir, ai="agy", ai_skills=True)
        (project_dir / ".agents").mkdir()
        # Deliberately do NOT create .agents/skills, shared by agy and codex.
        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")

        from specify_cli.agents import CommandRegistrar as AgentRegistrar

        original_register_commands = AgentRegistrar.register_commands
        attempted_agents = []

        def fail_recovered_agy_registration(self, agent_name, *args, **kwargs):
            attempted_agents.append(agent_name)
            if agent_name == "agy":
                raise PermissionError("denied")
            return original_register_commands(self, agent_name, *args, **kwargs)

        monkeypatch.setattr(
            AgentRegistrar, "register_commands", fail_recovered_agy_registration
        )

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=True
        )

        skills_dir = project_dir / ".agents" / "skills"
        assert skills_dir.is_dir()
        assert attempted_agents == ["agy"]

        metadata = manager.registry.get(manifest.id)
        assert metadata is not None
        assert metadata["registered_commands"] == {}
        assert "speckit-early-ext-hello" in metadata["registered_skills"]
        assert "speckit-early-ext-world" in metadata["registered_skills"]

    def test_missing_active_skills_dir_does_not_follow_symlinked_parent(
        self, project_dir, temp_dir
    ):
        """Recovered command registration must reuse active skills-dir safety checks."""
        if not hasattr(os, "symlink"):
            pytest.skip("symlinks are unavailable")

        _create_init_options(project_dir, ai="claude", ai_skills=True)
        outside = temp_dir / "outside-claude"
        outside.mkdir()
        try:
            os.symlink(outside, project_dir / ".claude", target_is_directory=True)
        except OSError:
            pytest.skip("Current platform/user cannot create directory symlinks")
        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=True
        )

        metadata = manager.registry.get(manifest.id)
        assert metadata["registered_commands"] == {}
        assert metadata["registered_skills"] == []
        assert not (outside / "skills").exists()

    def test_missing_active_skills_dir_invalid_parent_skips_without_aborting(
        self, project_dir, temp_dir
    ):
        """Invalid active skill parents should not abort extension installation."""
        _create_init_options(project_dir, ai="claude", ai_skills=True)
        (project_dir / ".claude").write_text("not a directory", encoding="utf-8")
        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=True
        )

        metadata = manager.registry.get(manifest.id)
        assert metadata["registered_commands"] == {}
        assert metadata["registered_skills"] == []

    def test_missing_active_skills_dir_write_oserror_skips_without_aborting(
        self, project_dir, temp_dir, monkeypatch
    ):
        """Filesystem failures in recovered command registration should skip safely."""
        _create_init_options(project_dir, ai="claude", ai_skills=True)
        (project_dir / ".claude").mkdir()
        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")

        from specify_cli.agents import CommandRegistrar as AgentRegistrar

        original_register_commands = AgentRegistrar.register_commands

        def fail_recovered_claude_registration(self, agent_name, *args, **kwargs):
            if agent_name == "claude":
                raise PermissionError("denied")
            return original_register_commands(self, agent_name, *args, **kwargs)

        monkeypatch.setattr(
            AgentRegistrar, "register_commands", fail_recovered_claude_registration
        )

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=True
        )

        metadata = manager.registry.get(manifest.id)
        assert metadata["registered_commands"] == {}
        assert "speckit-early-ext-hello" in metadata["registered_skills"]
        assert "speckit-early-ext-world" in metadata["registered_skills"]


# ===== Extension Skill Unregistration Tests =====

class TestExtensionSkillUnregistration:
    """Test _unregister_extension_skills() on ExtensionManager."""

    def test_skills_removed_on_extension_remove(self, skills_project, extension_dir):
        """Removing an extension should clean up its skill directories."""
        project_dir, skills_dir = skills_project
        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        # Verify skills exist
        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()
        assert (skills_dir / "speckit-test-ext-world" / "SKILL.md").exists()

        # Remove extension
        result = manager.remove(manifest.id, keep_config=False)
        assert result is True

        # Skills should be gone
        assert not (skills_dir / "speckit-test-ext-hello").exists()
        assert not (skills_dir / "speckit-test-ext-world").exists()

    def test_other_skills_preserved_on_remove(self, skills_project, extension_dir):
        """Non-extension skills should not be affected by extension removal."""
        project_dir, skills_dir = skills_project

        # Pre-create a custom skill
        custom_dir = skills_dir / "my-custom-skill"
        custom_dir.mkdir(parents=True)
        (custom_dir / "SKILL.md").write_text("# My Custom Skill\n")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        manager.remove(manifest.id, keep_config=False)

        # Custom skill should still exist
        assert (custom_dir / "SKILL.md").exists()
        assert (custom_dir / "SKILL.md").read_text() == "# My Custom Skill\n"

    def test_remove_handles_already_deleted_skills(self, skills_project, extension_dir):
        """Gracefully handle case where skill dirs were already deleted."""
        project_dir, skills_dir = skills_project
        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        # Manually delete skill dirs before calling remove
        shutil.rmtree(skills_dir / "speckit-test-ext-hello")
        shutil.rmtree(skills_dir / "speckit-test-ext-world")

        # Should not raise
        result = manager.remove(manifest.id, keep_config=False)
        assert result is True

    def test_remove_no_skills_when_not_active(self, no_skills_project, extension_dir):
        """Removal without active skills should not attempt skill cleanup."""
        manager = ExtensionManager(no_skills_project)
        manifest = manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        # Should not raise even though no skills exist
        result = manager.remove(manifest.id, keep_config=False)
        assert result is True


# ===== Command File Without Frontmatter =====

class TestExtensionSkillEdgeCases:
    """Test edge cases in extension skill registration."""

    def test_install_with_non_dict_init_options_does_not_crash(self, project_dir, extension_dir):
        """Corrupted init-options payloads should disable skill registration, not crash install."""
        opts_file = project_dir / ".specify" / "init-options.json"
        opts_file.parent.mkdir(parents=True, exist_ok=True)
        opts_file.write_text("[]", encoding="utf-8")
        _create_skills_dir(project_dir, ai="claude")

        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        metadata = manager.registry.get(manifest.id)
        assert metadata["registered_skills"] == []

    def test_command_without_frontmatter(self, skills_project, temp_dir):
        """Commands without YAML frontmatter should still produce valid skills."""
        project_dir, skills_dir = skills_project

        ext_dir = temp_dir / "nofm-ext"
        ext_dir.mkdir()
        manifest_data = {
            "schema_version": "1.0",
            "extension": {
                "id": "nofm-ext",
                "name": "No Frontmatter Extension",
                "version": "1.0.0",
                "description": "Test",
            },
            "requires": {"speckit_version": ">=0.1.0"},
            "provides": {
                "commands": [
                    {
                        "name": "speckit.nofm-ext.plain",
                        "file": "commands/plain.md",
                        "description": "Plain command",
                    }
                ]
            },
        }
        with open(ext_dir / "extension.yml", "w") as f:
            yaml.dump(manifest_data, f)

        (ext_dir / "commands").mkdir()
        (ext_dir / "commands" / "plain.md").write_text(
            "# Plain Command\n\nBody without frontmatter.\n"
        )

        manager = ExtensionManager(project_dir)
        manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=False
        )

        skill_file = skills_dir / "speckit-nofm-ext-plain" / "SKILL.md"
        assert skill_file.exists()
        content = skill_file.read_text()
        assert "name: speckit-nofm-ext-plain" in content
        # Fallback description when no frontmatter description
        assert "Extension command: speckit.nofm-ext.plain" in content
        assert "Body without frontmatter." in content

    def test_gemini_agent_skills(self, project_dir, temp_dir):
        """Gemini agent should use .gemini/skills/ for skill directory."""
        _create_init_options(project_dir, ai="gemini", ai_skills=True)
        _create_skills_dir(project_dir, ai="gemini")
        ext_dir = _create_extension_dir(temp_dir, ext_id="test-ext")

        manager = ExtensionManager(project_dir)
        manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=False
        )

        skills_dir = project_dir / ".gemini" / "skills"
        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()
        assert (skills_dir / "speckit-test-ext-world" / "SKILL.md").exists()

    def test_multiple_extensions_independent_skills(self, skills_project, temp_dir):
        """Installing and removing different extensions should be independent."""
        project_dir, skills_dir = skills_project

        ext_dir_a = _create_extension_dir(temp_dir, ext_id="ext-a")
        ext_dir_b = _create_extension_dir(temp_dir, ext_id="ext-b")

        manager = ExtensionManager(project_dir)
        manager.install_from_directory(
            ext_dir_a, "0.1.0", register_commands=False
        )
        manager.install_from_directory(
            ext_dir_b, "0.1.0", register_commands=False
        )

        # Both should have skills
        assert (skills_dir / "speckit-ext-a-hello" / "SKILL.md").exists()
        assert (skills_dir / "speckit-ext-b-hello" / "SKILL.md").exists()

        # Remove ext-a
        manager.remove("ext-a", keep_config=False)

        # ext-a skills gone, ext-b skills preserved
        assert not (skills_dir / "speckit-ext-a-hello").exists()
        assert (skills_dir / "speckit-ext-b-hello" / "SKILL.md").exists()

    def test_malformed_frontmatter_handled(self, skills_project, temp_dir):
        """Commands with invalid YAML frontmatter should still produce valid skills."""
        project_dir, skills_dir = skills_project

        ext_dir = temp_dir / "badfm-ext"
        ext_dir.mkdir()
        manifest_data = {
            "schema_version": "1.0",
            "extension": {
                "id": "badfm-ext",
                "name": "Bad Frontmatter Extension",
                "version": "1.0.0",
                "description": "Test",
            },
            "requires": {"speckit_version": ">=0.1.0"},
            "provides": {
                "commands": [
                    {
                        "name": "speckit.badfm-ext.broken",
                        "file": "commands/broken.md",
                        "description": "Broken frontmatter",
                    }
                ]
            },
        }
        with open(ext_dir / "extension.yml", "w") as f:
            yaml.dump(manifest_data, f)

        (ext_dir / "commands").mkdir()
        # Malformed YAML: invalid key-value syntax
        (ext_dir / "commands" / "broken.md").write_text(
            "---\n"
            "description: [invalid yaml\n"
            "  unclosed: bracket\n"
            "---\n"
            "\n"
            "# Broken Command\n"
            "\n"
            "This body should still be used.\n"
        )

        manager = ExtensionManager(project_dir)
        # Should not raise
        manager.install_from_directory(
            ext_dir, "0.1.0", register_commands=False
        )

        skill_file = skills_dir / "speckit-badfm-ext-broken" / "SKILL.md"
        assert skill_file.exists()
        content = skill_file.read_text()
        # Fallback description since frontmatter was invalid
        assert "Extension command: speckit.badfm-ext.broken" in content
        assert "This body should still be used." in content

    def test_remove_cleans_up_when_init_options_deleted(self, skills_project, extension_dir):
        """Skills should be cleaned up even if init-options.json is deleted after install."""
        project_dir, skills_dir = skills_project
        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        # Verify skills exist
        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()

        # Delete init-options.json to simulate user change
        init_opts = project_dir / ".specify" / "init-options.json"
        init_opts.unlink()

        # Remove should still clean up via fallback scan
        result = manager.remove(manifest.id, keep_config=False)
        assert result is True
        assert not (skills_dir / "speckit-test-ext-hello").exists()
        assert not (skills_dir / "speckit-test-ext-world").exists()

    def test_remove_cleans_up_when_ai_skills_toggled(self, skills_project, extension_dir):
        """Skills should be cleaned up even if ai_skills is toggled to false after install."""
        project_dir, skills_dir = skills_project
        manager = ExtensionManager(project_dir)
        manifest = manager.install_from_directory(
            extension_dir, "0.1.0", register_commands=False
        )

        # Verify skills exist
        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()

        # Toggle ai_skills to false
        _create_init_options(project_dir, ai="claude", ai_skills=False)

        # Remove should still clean up via fallback scan
        result = manager.remove(manifest.id, keep_config=False)
        assert result is True
        assert not (skills_dir / "speckit-test-ext-hello").exists()
        assert not (skills_dir / "speckit-test-ext-world").exists()