diff --git a/README.md b/README.md
index 006d55227..d1e3cd25e 100644
--- a/README.md
+++ b/README.md
@@ -212,7 +212,7 @@ The `specify` command supports the following options:
 | `--skip-tls`           | Flag     | Skip SSL/TLS verification (not recommended)                                                                                                                                                  |
 | `--debug`              | Flag     | Enable detailed debug output for troubleshooting                                                                                                                                             |
 | `--github-token`       | Option   | GitHub token for API requests (or set GH_TOKEN/GITHUB_TOKEN env variable)                                                                                                                    |
-| `--ai-skills`          | Flag     | Install Prompt.MD templates as agent skills in agent-specific `skills/` directory (requires `--ai`)                                                                                          |
+| `--ai-skills`          | Flag     | Install Prompt.MD templates as agent skills in agent-specific `skills/` directory (requires `--ai`). Extension commands are also auto-registered as skills when extensions are added later.    |
 
 ### Examples
 
diff --git a/extensions/EXTENSION-USER-GUIDE.md b/extensions/EXTENSION-USER-GUIDE.md
index ae77860fe..961c58fe9 100644
--- a/extensions/EXTENSION-USER-GUIDE.md
+++ b/extensions/EXTENSION-USER-GUIDE.md
@@ -187,6 +187,21 @@ Provided commands:
    Check: .specify/extensions/jira/
 ```
 
+### Automatic Agent Skill Registration
+
+If your project was initialized with `--ai-skills`, extension commands are **automatically registered as agent skills** during installation. This ensures that extensions are discoverable by agents that use the [agentskills.io](https://agentskills.io) skill specification.
+
+```text
+✓ Extension installed successfully!
+
+Jira Integration (v1.0.0)
+  ...
+
+✓ 3 agent skill(s) auto-registered
+```
+
+When an extension is removed, its corresponding skills are also cleaned up automatically. Pre-existing skills that were manually customized are never overwritten.
+
 ---
 
 ## Using Extensions
diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index a45535aee..e72257d4c 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -2884,6 +2884,12 @@ def extension_add(
         for cmd in manifest.commands:
             console.print(f"  • {cmd['name']} - {cmd.get('description', '')}")
 
+        # Report agent skills registration
+        reg_meta = manager.registry.get(manifest.id)
+        reg_skills = reg_meta.get("registered_skills", []) if reg_meta else []
+        if reg_skills:
+            console.print(f"\n[green]✓[/green] {len(reg_skills)} agent skill(s) auto-registered")
+
         console.print("\n[yellow]⚠[/yellow]  Configuration may be required")
         console.print(f"   Check: .specify/extensions/{manifest.id}/")
 
@@ -2922,14 +2928,18 @@ def extension_remove(
     installed = manager.list_installed()
     extension_id, display_name = _resolve_installed_extension(extension, installed, "remove")
 
-    # Get extension info for command count
+    # Get extension info for command and skill counts
     ext_manifest = manager.get_extension(extension_id)
     cmd_count = len(ext_manifest.commands) if ext_manifest else 0
+    reg_meta = manager.registry.get(extension_id)
+    skill_count = len(reg_meta.get("registered_skills", [])) if reg_meta else 0
 
     # Confirm removal
     if not force:
         console.print("\n[yellow]⚠  This will remove:[/yellow]")
         console.print(f"   • {cmd_count} commands from AI agent")
+        if skill_count:
+            console.print(f"   • {skill_count} agent skill(s)")
         console.print(f"   • Extension directory: .specify/extensions/{extension_id}/")
         if not keep_config:
             console.print("   • Config files (will be backed up)")
diff --git a/src/specify_cli/extensions.py b/src/specify_cli/extensions.py
index 0dfd40b7c..660d1d1df 100644
--- a/src/specify_cli/extensions.py
+++ b/src/specify_cli/extensions.py
@@ -402,6 +402,185 @@ def _ignore(directory: str, entries: List[str]) -> Set[str]:
 
         return _ignore
 
+    def _get_skills_dir(self) -> Optional[Path]:
+        """Return the skills directory if ``--ai-skills`` was used during init.
+
+        Reads ``.specify/init-options.json`` to determine whether skills
+        are enabled and which agent was selected, then delegates to
+        the module-level ``_get_skills_dir()`` helper for the concrete path.
+
+        Returns:
+            The skills directory ``Path``, or ``None`` if skills were not
+            enabled or the init-options file is missing.
+        """
+        from . import load_init_options, _get_skills_dir
+
+        opts = load_init_options(self.project_root)
+        if not opts.get("ai_skills"):
+            return None
+
+        agent = opts.get("ai")
+        if not agent:
+            return None
+
+        skills_dir = _get_skills_dir(self.project_root, agent)
+        if not skills_dir.is_dir():
+            return None
+
+        return skills_dir
+
+    def _register_extension_skills(
+        self,
+        manifest: ExtensionManifest,
+        extension_dir: Path,
+    ) -> List[str]:
+        """Generate SKILL.md files for extension commands as agent skills.
+
+        For every command in the extension manifest, creates a SKILL.md
+        file in the agent's skills directory following the agentskills.io
+        specification.  This is only done when ``--ai-skills`` was used
+        during project initialisation.
+
+        Args:
+            manifest: Extension manifest.
+            extension_dir: Installed extension directory.
+
+        Returns:
+            List of skill names that were created (for registry storage).
+        """
+        skills_dir = self._get_skills_dir()
+        if not skills_dir:
+            return []
+
+        from . import load_init_options
+        import yaml
+
+        opts = load_init_options(self.project_root)
+        selected_ai = opts.get("ai", "")
+
+        written: List[str] = []
+
+        for cmd_info in manifest.commands:
+            cmd_name = cmd_info["name"]
+            cmd_file_rel = cmd_info["file"]
+            source_file = extension_dir / cmd_file_rel
+            if not source_file.exists():
+                continue
+
+            # Derive skill name from command name
+            # e.g. "speckit.jira.create" -> "speckit-jira-create" (or dot for kimi)
+            if selected_ai == "kimi":
+                skill_name = cmd_name  # Keep dot notation for kimi
+            else:
+                skill_name = cmd_name.replace(".", "-")
+
+            # Check if skill already exists before creating the directory
+            skill_subdir = skills_dir / skill_name
+            skill_file = skill_subdir / "SKILL.md"
+            if skill_file.exists():
+                # Do not overwrite user-customized skills
+                continue
+
+            # Create skill directory only when we're going to write to it
+            skill_subdir.mkdir(parents=True, exist_ok=True)
+
+            # Parse the command file
+            content = source_file.read_text(encoding="utf-8")
+            if content.startswith("---"):
+                parts = content.split("---", 2)
+                if len(parts) >= 3:
+                    try:
+                        frontmatter = yaml.safe_load(parts[1])
+                    except yaml.YAMLError:
+                        frontmatter = {}
+                    if not isinstance(frontmatter, dict):
+                        frontmatter = {}
+                    body = parts[2].strip()
+                else:
+                    frontmatter = {}
+                    body = content
+            else:
+                frontmatter = {}
+                body = content
+
+            original_desc = frontmatter.get("description", "")
+            description = original_desc or f"Extension command: {cmd_name}"
+
+            frontmatter_data = {
+                "name": skill_name,
+                "description": description,
+                "compatibility": "Requires spec-kit project structure with .specify/ directory",
+                "metadata": {
+                    "author": "github-spec-kit",
+                    "source": f"extension:{manifest.id}",
+                },
+            }
+            frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
+
+            # Derive a human-friendly title from the command name
+            short_name = cmd_name
+            if short_name.startswith("speckit."):
+                short_name = short_name[len("speckit."):]
+
+            skill_content = (
+                f"---\n"
+                f"{frontmatter_text}\n"
+                f"---\n\n"
+                f"# {skill_name.replace('-', ' ').replace('.', ' ').title()} Skill\n\n"
+                f"{body}\n"
+            )
+
+            skill_file.write_text(skill_content, encoding="utf-8")
+            written.append(skill_name)
+
+        return written
+
+    def _unregister_extension_skills(self, skill_names: List[str]) -> None:
+        """Remove SKILL.md directories for extension skills.
+
+        Called during extension removal to clean up skill files that
+        were created by ``_register_extension_skills()``.
+
+        If ``_get_skills_dir()`` returns ``None`` (e.g. the user removed
+        init-options.json or toggled ai_skills after installation), we
+        fall back to scanning all known agent skills directories so that
+        orphaned skill directories are still cleaned up.
+
+        Args:
+            skill_names: List of skill names to remove.
+        """
+        if not skill_names:
+            return
+
+        skills_dir = self._get_skills_dir()
+
+        if skills_dir:
+            # Fast path: we know the exact skills directory
+            for skill_name in skill_names:
+                skill_subdir = skills_dir / skill_name
+                if skill_subdir.exists():
+                    shutil.rmtree(skill_subdir)
+        else:
+            # Fallback: scan all possible agent skills directories
+            from . import AGENT_CONFIG, AGENT_SKILLS_DIR_OVERRIDES, DEFAULT_SKILLS_DIR
+
+            candidate_dirs: set[Path] = set()
+            for override_path in AGENT_SKILLS_DIR_OVERRIDES.values():
+                candidate_dirs.add(self.project_root / override_path)
+            for cfg in AGENT_CONFIG.values():
+                folder = cfg.get("folder", "")
+                if folder:
+                    candidate_dirs.add(self.project_root / folder.rstrip("/") / "skills")
+            candidate_dirs.add(self.project_root / DEFAULT_SKILLS_DIR)
+
+            for skills_candidate in candidate_dirs:
+                if not skills_candidate.is_dir():
+                    continue
+                for skill_name in skill_names:
+                    skill_subdir = skills_candidate / skill_name
+                    if skill_subdir.exists():
+                        shutil.rmtree(skill_subdir)
+
     def check_compatibility(
         self,
         manifest: ExtensionManifest,
@@ -487,6 +666,10 @@ def install_from_directory(
                 manifest, dest_dir, self.project_root
             )
 
+        # Auto-register extension commands as agent skills when --ai-skills
+        # was used during project initialisation (feature parity).
+        registered_skills = self._register_extension_skills(manifest, dest_dir)
+
         # Register hooks
         hook_executor = HookExecutor(self.project_root)
         hook_executor.register_hooks(manifest)
@@ -497,7 +680,8 @@ def install_from_directory(
             "source": "local",
             "manifest_hash": manifest.get_hash(),
             "enabled": True,
-            "registered_commands": registered_commands
+            "registered_commands": registered_commands,
+            "registered_skills": registered_skills,
         })
 
         return manifest
@@ -569,9 +753,10 @@ def remove(self, extension_id: str, keep_config: bool = False) -> bool:
         if not self.registry.is_installed(extension_id):
             return False
 
-        # Get registered commands before removal
+        # Get registered commands and skills before removal
         metadata = self.registry.get(extension_id)
         registered_commands = metadata.get("registered_commands", {})
+        registered_skills = metadata.get("registered_skills", [])
 
         extension_dir = self.extensions_dir / extension_id
 
@@ -580,6 +765,9 @@ def remove(self, extension_id: str, keep_config: bool = False) -> bool:
             registrar = CommandRegistrar()
             registrar.unregister_commands(registered_commands, self.project_root)
 
+        # Unregister agent skills
+        self._unregister_extension_skills(registered_skills)
+
         if keep_config:
             # Preserve config files, only remove non-config files
             if extension_dir.exists():
diff --git a/tests/test_extension_skills.py b/tests/test_extension_skills.py
new file mode 100644
index 000000000..f011c059f
--- /dev/null
+++ b/tests/test_extension_skills.py
@@ -0,0 +1,640 @@
+"""
+Unit tests for extension skill auto-registration.
+
+Tests cover:
+- SKILL.md generation when --ai-skills 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 pytest
+import tempfile
+import shutil
+import yaml
+from pathlib import Path
+
+from specify_cli.extensions import (
+    ExtensionManifest,
+    ExtensionManager,
+    ExtensionError,
+)
+
+
+# ===== Helpers =====
+
+def _create_init_options(project_root: Path, ai: str = "claude", ai_skills: bool = 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",
+    }))
+
+
+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_SKILLS_DIR_OVERRIDES, DEFAULT_SKILLS_DIR
+
+    if ai in AGENT_SKILLS_DIR_OVERRIDES:
+        skills_dir = project_root / AGENT_SKILLS_DIR_OVERRIDES[ai]
+    else:
+        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 / DEFAULT_SKILLS_DIR
+
+    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
+
+
+# ===== 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 --ai-skills 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 --ai-skills."""
+    _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."""
+        manager = ExtensionManager(no_skills_project)
+        result = manager._get_skills_dir()
+        assert result is None
+
+    def test_returns_none_when_no_init_options(self, project_dir):
+        """Should return None when init-options.json is missing."""
+        manager = ExtensionManager(project_dir)
+        result = manager._get_skills_dir()
+        assert result is None
+
+    def test_returns_none_when_skills_dir_missing(self, project_dir):
+        """Should return None when skills dir doesn't exist on disk."""
+        _create_init_options(project_dir, ai="claude", ai_skills=True)
+        # Don't create the skills directory
+        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)
+        manifest = 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
+
+    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_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_dot_notation(self, project_dir, temp_dir):
+        """Kimi agent should use dot notation for skill names."""
+        _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)
+        # Kimi should use dots, not hyphens
+        assert "speckit.test-ext.hello" in metadata["registered_skills"]
+        assert "speckit.test-ext.world" in metadata["registered_skills"]
+
+    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"]
+
+
+# ===== 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_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)
+        manifest = 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)
+        manifest = 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)
+        manifest_a = manager.install_from_directory(
+            ext_dir_a, "0.1.0", register_commands=False
+        )
+        manifest_b = 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
+        manifest = 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()