diff --git a/README.md b/README.md
index b389dde795..b426906bdd 100644
--- a/README.md
+++ b/README.md
@@ -50,6 +50,8 @@ Spec-Driven Development **flips the script** on traditional software development
 
 Choose your preferred installation method:
 
+> **Important:** The only official, maintained packages for Spec Kit are published from this GitHub repository. Any packages with the same name on PyPI are **not** affiliated with this project and are not maintained by the Spec Kit maintainers. Always install directly from GitHub as shown below.
+
 #### Option 1: Persistent Installation (Recommended)
 
 Install once and use everywhere. Pin a specific release tag for stability (check [Releases](https://github.com/github/spec-kit/releases) for the latest):
@@ -62,7 +64,13 @@ uv tool install specify-cli --from git+https://github.com/github/spec-kit.git@vX
 uv tool install specify-cli --from git+https://github.com/github/spec-kit.git
 ```
 
-Then use the tool directly:
+Then verify the correct version is installed:
+
+```bash
+specify version
+```
+
+And use the tool directly:
 
 ```bash
 # Create new project
diff --git a/docs/installation.md b/docs/installation.md
index 5d560b6e33..ed253902af 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -10,6 +10,8 @@
 
 ## Installation
 
+> **Important:** The only official, maintained packages for Spec Kit come from the [github/spec-kit](https://github.com/github/spec-kit) GitHub repository. Any packages with the same name available on PyPI (e.g. `specify-cli` on pypi.org) are **not** affiliated with this project and are not maintained by the Spec Kit maintainers. For normal installs, use the GitHub-based commands shown below. For offline or air-gapped environments, locally built wheels created from this repository are also valid.
+
 ### Initialize a New Project
 
 The easiest way to get started is to initialize a new project. Pin a specific release tag for stability (check [Releases](https://github.com/github/spec-kit/releases) for the latest):
@@ -69,6 +71,14 @@ uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <proje
 
 ## Verification
 
+After installation, run the following command to confirm the correct version is installed:
+
+```bash
+specify version
+```
+
+This helps verify you are running the official Spec Kit build from GitHub, not an unrelated package with the same name.
+
 After initialization, you should see the following commands available in your AI agent:
 
 - `/speckit.specify` - Create specifications
diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 11b6e0eda5..4177aa2154 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -3132,6 +3132,10 @@ def extension_add(
         console.print("\n[green]✓[/green] Extension installed successfully!")
         console.print(f"\n[bold]{manifest.name}[/bold] (v{manifest.version})")
         console.print(f"  {manifest.description}")
+
+        for warning in manifest.warnings:
+            console.print(f"\n[yellow]⚠  Compatibility warning:[/yellow] {warning}")
+
         console.print("\n[bold cyan]Provided commands:[/bold cyan]")
         for cmd in manifest.commands:
             console.print(f"  • {cmd['name']} - {cmd.get('description', '')}")
@@ -3185,15 +3189,28 @@ def extension_remove(
 
     # 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)
+    # Derive cmd_count from the registry's registered_commands (includes aliases)
+    # rather than from the manifest (primary commands only). Use max() across
+    # agents to get the per-agent count; sum() would double-count since users
+    # think in logical commands, not per-agent file counts.
+    # Use get() without a default so we can distinguish "key missing" (fall back
+    # to manifest) from "key present but empty dict" (zero commands registered).
+    registered_commands = reg_meta.get("registered_commands") if isinstance(reg_meta, dict) else None
+    if isinstance(registered_commands, dict):
+        cmd_count = max(
+            (len(v) for v in registered_commands.values() if isinstance(v, list)),
+            default=0,
+        )
+    else:
+        cmd_count = len(ext_manifest.commands) if ext_manifest else 0
     raw_skills = reg_meta.get("registered_skills") if reg_meta else None
     skill_count = len(raw_skills) if isinstance(raw_skills, list) else 0
 
     # Confirm removal
     if not force:
         console.print("\n[yellow]⚠  This will remove:[/yellow]")
-        console.print(f"   • {cmd_count} commands from AI agent")
+        console.print(f"   • {cmd_count} command{'s' if cmd_count != 1 else ''} per agent")
         if skill_count:
             console.print(f"   • {skill_count} agent skill(s)")
         console.print(f"   • Extension directory: .specify/extensions/{extension_id}/")
diff --git a/src/specify_cli/agents.py b/src/specify_cli/agents.py
index ec7af88768..d9f3388a28 100644
--- a/src/specify_cli/agents.py
+++ b/src/specify_cli/agents.py
@@ -563,6 +563,15 @@ def unregister_commands(
                 cmd_file = commands_dir / f"{output_name}{agent_config['extension']}"
                 if cmd_file.exists():
                     cmd_file.unlink()
+                    # For SKILL.md agents each command lives in its own subdirectory
+                    # (e.g. .agents/skills/speckit-ext-cmd/SKILL.md). Remove the
+                    # parent dir when it becomes empty to avoid orphaned directories.
+                    parent = cmd_file.parent
+                    if parent != commands_dir and parent.exists():
+                        try:
+                            parent.rmdir()  # no-op if dir still has other files
+                        except OSError:
+                            pass
 
                 if agent_name == "copilot":
                     prompt_file = project_root / ".github" / "prompts" / f"{cmd_name}.prompt.md"
diff --git a/src/specify_cli/extensions.py b/src/specify_cli/extensions.py
index da1a5f4472..15b954bdf7 100644
--- a/src/specify_cli/extensions.py
+++ b/src/specify_cli/extensions.py
@@ -130,6 +130,7 @@ def __init__(self, manifest_path: Path):
             ValidationError: If manifest is invalid
         """
         self.path = manifest_path
+        self.warnings: List[str] = []
         self.data = self._load_yaml(manifest_path)
         self._validate()
 
@@ -215,18 +216,107 @@ def _validate(self):
                         f"Hook '{hook_name}' missing required 'command' field"
                     )
 
-        # Validate commands (if present)
+        # Validate commands; track renames so hook references can be rewritten.
+        rename_map: Dict[str, str] = {}
         for cmd in commands:
             if "name" not in cmd or "file" not in cmd:
                 raise ValidationError("Command missing 'name' or 'file'")
 
             # Validate command name format
-            if EXTENSION_COMMAND_NAME_PATTERN.match(cmd["name"]) is None:
+            if not EXTENSION_COMMAND_NAME_PATTERN.match(cmd["name"]):
+                corrected = self._try_correct_command_name(cmd["name"], ext["id"])
+                if corrected:
+                    self.warnings.append(
+                        f"Command name '{cmd['name']}' does not follow the required pattern "
+                        f"'speckit.{{extension}}.{{command}}'. Registering as '{corrected}'. "
+                        f"The extension author should update the manifest to use this name."
+                    )
+                    rename_map[cmd["name"]] = corrected
+                    cmd["name"] = corrected
+                else:
+                    raise ValidationError(
+                        f"Invalid command name '{cmd['name']}': "
+                        "must follow pattern 'speckit.{extension}.{command}'"
+                    )
+
+            # Validate and auto-correct alias name formats
+            aliases = cmd.get("aliases")
+            if aliases is None:
+                aliases = []
+            if not isinstance(aliases, list):
+                raise ValidationError(
+                    f"Aliases for command '{cmd['name']}' must be a list"
+                )
+            for i, alias in enumerate(aliases):
+                if not isinstance(alias, str):
+                    raise ValidationError(
+                        f"Aliases for command '{cmd['name']}' must be strings"
+                    )
+                if not EXTENSION_COMMAND_NAME_PATTERN.match(alias):
+                    corrected = self._try_correct_command_name(alias, ext["id"])
+                    if corrected:
+                        self.warnings.append(
+                            f"Alias '{alias}' does not follow the required pattern "
+                            f"'speckit.{{extension}}.{{command}}'. Registering as '{corrected}'. "
+                            f"The extension author should update the manifest to use this name."
+                        )
+                        rename_map[alias] = corrected
+                        aliases[i] = corrected
+                    else:
+                        raise ValidationError(
+                            f"Invalid alias '{alias}': "
+                            "must follow pattern 'speckit.{extension}.{command}'"
+                        )
+
+        # Rewrite any hook command references that pointed at a renamed command or
+        # an alias-form ref (ext.cmd → speckit.ext.cmd).  Always emit a warning when
+        # the reference is changed so extension authors know to update the manifest.
+        for hook_name, hook_data in self.data.get("hooks", {}).items():
+            if not isinstance(hook_data, dict):
                 raise ValidationError(
-                    f"Invalid command name '{cmd['name']}': "
-                    "must follow pattern 'speckit.{extension}.{command}'"
+                    f"Hook '{hook_name}' must be a mapping, got {type(hook_data).__name__}"
+                )
+            command_ref = hook_data.get("command")
+            if not isinstance(command_ref, str):
+                continue
+            # Step 1: apply any rename from the auto-correction pass.
+            after_rename = rename_map.get(command_ref, command_ref)
+            # Step 2: lift alias-form '{ext_id}.cmd' to canonical 'speckit.{ext_id}.cmd'.
+            parts = after_rename.split(".")
+            if len(parts) == 2 and parts[0] == ext["id"]:
+                final_ref = f"speckit.{ext['id']}.{parts[1]}"
+            else:
+                final_ref = after_rename
+            if final_ref != command_ref:
+                hook_data["command"] = final_ref
+                self.warnings.append(
+                    f"Hook '{hook_name}' referenced command '{command_ref}'; "
+                    f"updated to canonical form '{final_ref}'. "
+                    f"The extension author should update the manifest."
                 )
 
+    @staticmethod
+    def _try_correct_command_name(name: str, ext_id: str) -> Optional[str]:
+        """Try to auto-correct a non-conforming command name to the required pattern.
+
+        Handles the two legacy formats used by community extensions:
+          - 'speckit.command'  → 'speckit.{ext_id}.command'
+          - '{ext_id}.command' → 'speckit.{ext_id}.command'
+
+        The 'X.Y' form is only corrected when X matches ext_id to ensure the
+        result passes the install-time namespace check. Any other prefix is
+        uncorrectable and will produce a ValidationError at the call site.
+
+        Returns the corrected name, or None if no safe correction is possible.
+        """
+        parts = name.split('.')
+        if len(parts) == 2:
+            if parts[0] == 'speckit' or parts[0] == ext_id:
+                candidate = f"speckit.{ext_id}.{parts[1]}"
+                if EXTENSION_COMMAND_NAME_PATTERN.match(candidate):
+                    return candidate
+        return None
+
     @property
     def id(self) -> str:
         """Get extension ID."""
diff --git a/tests/test_extensions.py b/tests/test_extensions.py
index c5aed03dcf..d9342887ef 100644
--- a/tests/test_extensions.py
+++ b/tests/test_extensions.py
@@ -243,7 +243,7 @@ def test_invalid_version(self, temp_dir, valid_manifest_data):
             ExtensionManifest(manifest_path)
 
     def test_invalid_command_name(self, temp_dir, valid_manifest_data):
-        """Test manifest with invalid command name format."""
+        """Test manifest with command name that cannot be auto-corrected raises ValidationError."""
         import yaml
 
         valid_manifest_data["provides"]["commands"][0]["name"] = "invalid-name"
@@ -255,6 +255,85 @@ def test_invalid_command_name(self, temp_dir, valid_manifest_data):
         with pytest.raises(ValidationError, match="Invalid command name"):
             ExtensionManifest(manifest_path)
 
+    def test_command_name_autocorrect_speckit_prefix(self, temp_dir, valid_manifest_data):
+        """Test that 'speckit.command' is auto-corrected to 'speckit.{ext_id}.command'."""
+        import yaml
+
+        valid_manifest_data["provides"]["commands"][0]["name"] = "speckit.hello"
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        manifest = ExtensionManifest(manifest_path)
+
+        assert manifest.commands[0]["name"] == "speckit.test-ext.hello"
+        assert len(manifest.warnings) == 1
+        assert "speckit.hello" in manifest.warnings[0]
+        assert "speckit.test-ext.hello" in manifest.warnings[0]
+
+    def test_command_name_autocorrect_matching_ext_id_prefix(self, temp_dir, valid_manifest_data):
+        """Test that '{ext_id}.command' is auto-corrected to 'speckit.{ext_id}.command'."""
+        import yaml
+
+        # Set ext_id to match the legacy namespace so correction is valid
+        valid_manifest_data["extension"]["id"] = "docguard"
+        valid_manifest_data["provides"]["commands"][0]["name"] = "docguard.guard"
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        manifest = ExtensionManifest(manifest_path)
+
+        assert manifest.commands[0]["name"] == "speckit.docguard.guard"
+        assert len(manifest.warnings) == 1
+        assert "docguard.guard" in manifest.warnings[0]
+        assert "speckit.docguard.guard" in manifest.warnings[0]
+
+    def test_command_name_mismatched_namespace_not_corrected(self, temp_dir, valid_manifest_data):
+        """Test that 'X.command' is NOT corrected when X doesn't match ext_id."""
+        import yaml
+
+        # ext_id is "test-ext" but command uses a different namespace
+        valid_manifest_data["provides"]["commands"][0]["name"] = "docguard.guard"
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        with pytest.raises(ValidationError, match="Invalid command name"):
+            ExtensionManifest(manifest_path)
+
+    def test_alias_autocorrect_speckit_prefix(self, temp_dir, valid_manifest_data):
+        """Test that a legacy 'speckit.command' alias is auto-corrected."""
+        import yaml
+
+        valid_manifest_data["provides"]["commands"][0]["aliases"] = ["speckit.hello"]
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        manifest = ExtensionManifest(manifest_path)
+
+        assert manifest.commands[0]["aliases"] == ["speckit.test-ext.hello"]
+        assert len(manifest.warnings) == 1
+        assert "speckit.hello" in manifest.warnings[0]
+        assert "speckit.test-ext.hello" in manifest.warnings[0]
+
+    def test_valid_command_name_has_no_warnings(self, temp_dir, valid_manifest_data):
+        """Test that a correctly-named command produces no warnings."""
+        import yaml
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        manifest = ExtensionManifest(manifest_path)
+
+        assert manifest.warnings == []
+
     def test_no_commands_no_hooks(self, temp_dir, valid_manifest_data):
         """Test manifest with no commands and no hooks provided."""
         import yaml
@@ -317,6 +396,19 @@ def test_hooks_not_dict_rejected(self, temp_dir, valid_manifest_data):
         with pytest.raises(ValidationError, match="Invalid hooks"):
             ExtensionManifest(manifest_path)
 
+    def test_non_dict_hook_entry_raises_validation_error(self, temp_dir, valid_manifest_data):
+        """Non-mapping hook entries must raise ValidationError, not silently skip."""
+        import yaml
+
+        valid_manifest_data["hooks"]["after_tasks"] = "speckit.test-ext.hello"
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        with pytest.raises(ValidationError, match="Invalid hook 'after_tasks'"):
+            ExtensionManifest(manifest_path)
+
     def test_manifest_hash(self, extension_dir):
         """Test manifest hash calculation."""
         manifest_path = extension_dir / "extension.yml"
@@ -686,8 +778,8 @@ def test_install_rejects_extension_id_in_core_namespace(self, temp_dir, project_
         with pytest.raises(ValidationError, match="conflicts with core command namespace"):
             manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
 
-    def test_install_accepts_short_alias(self, temp_dir, project_dir):
-        """Install should accept legacy short aliases for community extension compat."""
+    def test_install_autocorrects_alias_without_extension_namespace(self, temp_dir, project_dir):
+        """Legacy short aliases are auto-corrected to 'speckit.{ext_id}.{cmd}' with a warning."""
         import yaml
 
         ext_dir = temp_dir / "alias-shortcut"
@@ -718,8 +810,12 @@ def test_install_accepts_short_alias(self, temp_dir, project_dir):
         (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nBody")
 
         manager = ExtensionManager(project_dir)
-        # Should not raise — short aliases are allowed
-        manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
+        manifest = manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
+
+        assert manifest.commands[0]["aliases"] == ["speckit.alias-shortcut.shortcut"]
+        assert len(manifest.warnings) == 1
+        assert "speckit.shortcut" in manifest.warnings[0]
+        assert "speckit.alias-shortcut.shortcut" in manifest.warnings[0]
 
     def test_install_rejects_namespace_squatting(self, temp_dir, project_dir):
         """Install should reject commands and aliases outside the extension namespace."""
@@ -1619,6 +1715,54 @@ def test_non_copilot_agent_no_companion_file(self, extension_dir, project_dir):
         prompts_dir = project_dir / ".github" / "prompts"
         assert not prompts_dir.exists()
 
+    def test_unregister_skill_removes_parent_directory(self, project_dir, temp_dir):
+        """Unregistering a SKILL.md command should remove the empty parent subdirectory."""
+        import yaml
+
+        ext_dir = temp_dir / "cleanup-ext"
+        ext_dir.mkdir()
+        (ext_dir / "commands").mkdir()
+
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "cleanup-ext",
+                "name": "Cleanup Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.cleanup-ext.run",
+                        "file": "commands/run.md",
+                        "description": "Run",
+                    }
+                ]
+            },
+        }
+        with open(ext_dir / "extension.yml", "w") as f:
+            yaml.dump(manifest_data, f)
+        (ext_dir / "commands" / "run.md").write_text("---\ndescription: Run\n---\n\nBody")
+
+        skills_dir = project_dir / ".agents" / "skills"
+        skills_dir.mkdir(parents=True)
+
+        registrar = CommandRegistrar()
+        from specify_cli.extensions import ExtensionManifest
+        manifest = ExtensionManifest(ext_dir / "extension.yml")
+        registered = registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
+
+        skill_subdir = skills_dir / "speckit-cleanup-ext-run"
+        assert skill_subdir.exists(), "Skill subdirectory should exist after registration"
+        assert (skill_subdir / "SKILL.md").exists()
+
+        registrar.unregister_commands({"codex": ["speckit.cleanup-ext.run"]}, project_dir)
+
+        assert not (skill_subdir / "SKILL.md").exists(), "SKILL.md should be removed"
+        assert not skill_subdir.exists(), "Empty parent subdirectory should be removed"
+
 
 # ===== Utility Function Tests =====
 
@@ -3737,3 +3881,58 @@ def test_hook_message_falls_back_when_invocation_is_empty(self, project_dir):
         assert "Executing: `/<missing command>`" in message
         assert "EXECUTE_COMMAND: <missing command>" in message
         assert "EXECUTE_COMMAND_INVOCATION: /<missing command>" in message
+
+
+class TestExtensionRemoveCLI:
+    """CLI tests for `specify extension remove` confirmation prompt wording."""
+
+    def _install_ext(self, project_dir, ext_dir):
+        """Install extension and return the manager."""
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
+        return manager
+
+    def test_remove_confirmation_singular_command(self, tmp_path, extension_dir):
+        """Confirmation prompt should say '1 command' (singular) when one command registered."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        project_dir = tmp_path / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        manager = self._install_ext(project_dir, extension_dir)
+        # Inject registered_commands with 1 entry so cmd_count == 1
+        manager.registry.update("test-ext", {"registered_commands": {"claude": ["speckit.test-ext.hello"]}})
+
+        runner = CliRunner()
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(
+                app, ["extension", "remove", "test-ext"], input="n\n", catch_exceptions=False
+            )
+
+        assert "1 command" in result.output
+        assert "1 commands" not in result.output
+
+    def test_remove_confirmation_plural_commands(self, tmp_path, extension_dir):
+        """Confirmation prompt should say '2 commands' (plural) when two commands registered."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        project_dir = tmp_path / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        manager = self._install_ext(project_dir, extension_dir)
+        # Inject registered_commands with 2 entries so cmd_count == 2
+        manager.registry.update("test-ext", {"registered_commands": {"claude": ["speckit.test-ext.hello", "speckit.test-ext.run"]}})
+
+        runner = CliRunner()
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(
+                app, ["extension", "remove", "test-ext"], input="n\n", catch_exceptions=False
+            )
+
+        assert "2 commands" in result.output
diff --git a/tests/test_presets.py b/tests/test_presets.py
index d22264f806..57e209f407 100644
--- a/tests/test_presets.py
+++ b/tests/test_presets.py
@@ -1175,8 +1175,7 @@ def test_search_with_cached_data(self, project_dir, monkeypatch):
         """Test search with cached catalog data."""
         from unittest.mock import patch
 
-        # Only use the default catalog to prevent fetching the community catalog from the network
-        monkeypatch.setenv("SPECKIT_PRESET_CATALOG_URL", PresetCatalog.DEFAULT_CATALOG_URL)
+        monkeypatch.delenv("SPECKIT_PRESET_CATALOG_URL", raising=False)
         catalog = PresetCatalog(project_dir)
         catalog.cache_dir.mkdir(parents=True, exist_ok=True)