fix(copilot): honor preset command template overrides

src/specify_cli/integrations/copilot/__init__.py

@@ -350,6 +350,10 @@ def _setup_default(
         if not templates:
             return []
 
+        from ...presets import PresetResolver
+
+        preset_resolver = PresetResolver(project_root_resolved)
+
         dest = self.commands_dest(project_root)
         dest_resolved = dest.resolve()
         try:
@@ -367,7 +371,11 @@ def _setup_default(
 
         # 1. Process and write command files as .agent.md
         for src_file in templates:
-            raw = src_file.read_text(encoding="utf-8")
+            resolved_template = preset_resolver.resolve(
+                src_file.stem, template_type="command"
+            )
+            source_path = resolved_template or src_file
+            raw = source_path.read_text(encoding="utf-8")
             processed = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
                 project_root=project_root,

tests/integrations/test_integration_copilot.py

@@ -188,6 +188,43 @@ def test_specify_agent_resolves_active_spec_template(self, tmp_path):
         assert "Copy `.specify/templates/spec-template.md`" not in content
         assert "Load `.specify/templates/spec-template.md`" not in content
 
+    def test_setup_falls_back_to_bundled_command_template_without_preset_override(self, tmp_path):
+        """Copilot should keep using the bundled specify command template when no preset override exists."""
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+
+        copilot.setup(tmp_path, m)
+
+        specify_file = tmp_path / ".github" / "agents" / "speckit.specify.agent.md"
+        content = specify_file.read_text(encoding="utf-8")
+        assert "Create or update the feature specification" in content
+        assert "preset override content" not in content
+
+    def test_setup_uses_preset_command_override_when_present(self, tmp_path):
+        """Copilot should prefer a preset-provided command template over the bundled one."""
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+
+        preset_dir = tmp_path / ".specify" / "presets" / "demo"
+        (preset_dir / "commands").mkdir(parents=True, exist_ok=True)
+        (preset_dir / "commands" / "specify.md").write_text(
+            "preset override content\n",
+            encoding="utf-8",
+        )
+        (tmp_path / ".specify" / "presets" / ".registry").write_text(
+            '{"schema_version": "1.0", "presets": {"demo": {"version": "1.0.0", "source": "local", "enabled": true, "priority": 10}}}',
+            encoding="utf-8",
+        )
+
+        copilot.setup(tmp_path, m)
+
+        specify_file = tmp_path / ".github" / "agents" / "speckit.specify.agent.md"
+        content = specify_file.read_text(encoding="utf-8")
+        assert "preset override content" in content
+        assert "Create or update the feature specification" not in content
+
     def test_plan_command_has_no_context_placeholder(self, tmp_path):
         """The core plan command must not carry a context-file placeholder —
         agent context files are owned by the opt-in agent-context extension."""