fix: correct Copilot extension command registration (#1724)

* fix: correct Copilot extension command registration (#copilot)

- Use .agent.md extension for commands in .github/agents/
- Generate companion .prompt.md files in .github/prompts/
- Clean up .prompt.md files on extension removal
- Add tests for Copilot-specific registration behavior

Bumps version to 0.1.7.

* fix: test copilot prompt cleanup via ExtensionManager.remove() instead of manual unlink

---------

Co-authored-by: Ismael <ismael.jimenez-martinez@bmw.de>

CHANGELOG.md

@@ -7,6 +7,15 @@ Recent changes to the Specify CLI and templates are documented here.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.1.13] - 2026-03-03
+
+### Fixed
+
+- **Copilot Extension Commands Not Visible**: Fixed extension commands not appearing in GitHub Copilot when installed via `specify extension add --dev`
+  - Changed Copilot file extension from `.md` to `.agent.md` in `CommandRegistrar.AGENT_CONFIGS` so Copilot recognizes agent files
+  - Added generation of companion `.prompt.md` files in `.github/prompts/` during extension command registration, matching the release packaging behavior
+  - Added cleanup of `.prompt.md` companion files when removing extensions via `specify extension remove`
+
 ## [0.1.12] - 2026-03-02
 
 ### Changed

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.1.12"
+version = "0.1.13"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [

src/specify_cli/extensions.py

@@ -455,6 +455,12 @@ class ExtensionManager:
                     if cmd_file.exists():
                         cmd_file.unlink()
 
+                    # Also remove companion .prompt.md for Copilot
+                    if agent_name == "copilot":
+                        prompt_file = self.project_root / ".github" / "prompts" / f"{cmd_name}.prompt.md"
+                        if prompt_file.exists():
+                            prompt_file.unlink()
+
         if keep_config:
             # Preserve config files, only remove non-config files
             if extension_dir.exists():
@@ -597,7 +603,7 @@ class CommandRegistrar:
             "dir": ".github/agents",
             "format": "markdown",
             "args": "$ARGUMENTS",
-            "extension": ".md"
+            "extension": ".agent.md"
         },
         "cursor": {
             "dir": ".cursor/commands",
@@ -871,16 +877,40 @@ class CommandRegistrar:
             dest_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
             dest_file.write_text(output)
 
+            # Generate companion .prompt.md for Copilot agents
+            if agent_name == "copilot":
+                self._write_copilot_prompt(project_root, cmd_name)
+
             registered.append(cmd_name)
 
             # Register aliases
             for alias in cmd_info.get("aliases", []):
                 alias_file = commands_dir / f"{alias}{agent_config['extension']}"
                 alias_file.write_text(output)
+                # Generate companion .prompt.md for alias too
+                if agent_name == "copilot":
+                    self._write_copilot_prompt(project_root, alias)
                 registered.append(alias)
 
         return registered
 
+    @staticmethod
+    def _write_copilot_prompt(project_root: Path, cmd_name: str) -> None:
+        """Generate a companion .prompt.md file for a Copilot agent command.
+
+        Copilot requires a .prompt.md file in .github/prompts/ that references
+        the corresponding .agent.md file in .github/agents/ via an ``agent:``
+        frontmatter field.
+
+        Args:
+            project_root: Path to project root
+            cmd_name: Command name (used as the file stem, e.g. 'speckit.my-ext.example')
+        """
+        prompts_dir = project_root / ".github" / "prompts"
+        prompts_dir.mkdir(parents=True, exist_ok=True)
+        prompt_file = prompts_dir / f"{cmd_name}.prompt.md"
+        prompt_file.write_text(f"---\nagent: {cmd_name}\n---\n")
+
     def register_commands_for_all_agents(
         self,
         manifest: ExtensionManifest,

tests/test_extensions.py

@@ -520,6 +520,121 @@ $ARGUMENTS
         assert (claude_dir / "speckit.alias.cmd.md").exists()
         assert (claude_dir / "speckit.shortcut.md").exists()
 
+    def test_register_commands_for_copilot(self, extension_dir, project_dir):
+        """Test registering commands for Copilot agent with .agent.md extension."""
+        # Create .github/agents directory (Copilot project)
+        agents_dir = project_dir / ".github" / "agents"
+        agents_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(extension_dir / "extension.yml")
+
+        registrar = CommandRegistrar()
+        registered = registrar.register_commands_for_agent(
+            "copilot", manifest, extension_dir, project_dir
+        )
+
+        assert len(registered) == 1
+        assert "speckit.test.hello" in registered
+
+        # Verify command file uses .agent.md extension
+        cmd_file = agents_dir / "speckit.test.hello.agent.md"
+        assert cmd_file.exists()
+
+        # Verify NO plain .md file was created
+        plain_md_file = agents_dir / "speckit.test.hello.md"
+        assert not plain_md_file.exists()
+
+        content = cmd_file.read_text()
+        assert "description: Test hello command" in content
+        assert "<!-- Extension: test-ext -->" in content
+
+    def test_copilot_companion_prompt_created(self, extension_dir, project_dir):
+        """Test that companion .prompt.md files are created in .github/prompts/."""
+        agents_dir = project_dir / ".github" / "agents"
+        agents_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(extension_dir / "extension.yml")
+
+        registrar = CommandRegistrar()
+        registrar.register_commands_for_agent(
+            "copilot", manifest, extension_dir, project_dir
+        )
+
+        # Verify companion .prompt.md file exists
+        prompt_file = project_dir / ".github" / "prompts" / "speckit.test.hello.prompt.md"
+        assert prompt_file.exists()
+
+        # Verify content has correct agent frontmatter
+        content = prompt_file.read_text()
+        assert content == "---\nagent: speckit.test.hello\n---\n"
+
+    def test_copilot_aliases_get_companion_prompts(self, project_dir, temp_dir):
+        """Test that aliases also get companion .prompt.md files for Copilot."""
+        import yaml
+
+        ext_dir = temp_dir / "ext-alias-copilot"
+        ext_dir.mkdir()
+
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "ext-alias-copilot",
+                "name": "Extension with Alias",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.alias-copilot.cmd",
+                        "file": "commands/cmd.md",
+                        "aliases": ["speckit.shortcut-copilot"],
+                    }
+                ]
+            },
+        }
+
+        with open(ext_dir / "extension.yml", "w") as f:
+            yaml.dump(manifest_data, f)
+
+        (ext_dir / "commands").mkdir()
+        (ext_dir / "commands" / "cmd.md").write_text(
+            "---\ndescription: Test\n---\n\nTest"
+        )
+
+        # Set up Copilot project
+        (project_dir / ".github" / "agents").mkdir(parents=True)
+
+        manifest = ExtensionManifest(ext_dir / "extension.yml")
+        registrar = CommandRegistrar()
+        registered = registrar.register_commands_for_agent(
+            "copilot", manifest, ext_dir, project_dir
+        )
+
+        assert len(registered) == 2
+
+        # Both primary and alias get companion .prompt.md
+        prompts_dir = project_dir / ".github" / "prompts"
+        assert (prompts_dir / "speckit.alias-copilot.cmd.prompt.md").exists()
+        assert (prompts_dir / "speckit.shortcut-copilot.prompt.md").exists()
+
+    def test_non_copilot_agent_no_companion_file(self, extension_dir, project_dir):
+        """Test that non-copilot agents do NOT create .prompt.md files."""
+        claude_dir = project_dir / ".claude" / "commands"
+        claude_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(extension_dir / "extension.yml")
+
+        registrar = CommandRegistrar()
+        registrar.register_commands_for_agent(
+            "claude", manifest, extension_dir, project_dir
+        )
+
+        # No .github/prompts directory should exist
+        prompts_dir = project_dir / ".github" / "prompts"
+        assert not prompts_dir.exists()
+
 
 # ===== Utility Function Tests =====
 
@@ -596,6 +711,31 @@ class TestIntegration:
         assert not cmd_file.exists()
         assert len(manager.list_installed()) == 0
 
+    def test_copilot_cleanup_removes_prompt_files(self, extension_dir, project_dir):
+        """Test that removing a Copilot extension also removes .prompt.md files."""
+        agents_dir = project_dir / ".github" / "agents"
+        agents_dir.mkdir(parents=True)
+
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=True)
+
+        # Verify copilot was detected and registered
+        metadata = manager.registry.get("test-ext")
+        assert "copilot" in metadata["registered_commands"]
+
+        # Verify files exist before cleanup
+        agent_file = agents_dir / "speckit.test.hello.agent.md"
+        prompt_file = project_dir / ".github" / "prompts" / "speckit.test.hello.prompt.md"
+        assert agent_file.exists()
+        assert prompt_file.exists()
+
+        # Use the extension manager to remove — exercises the copilot prompt cleanup code
+        result = manager.remove("test-ext")
+        assert result is True
+
+        assert not agent_file.exists()
+        assert not prompt_file.exists()
+
     def test_multiple_extensions(self, temp_dir, project_dir):
         """Test installing multiple extensions."""
         import yaml