fix: address remaining Copilot review comments

Author: iamaeroplane

src/specify_cli/agents.py

@@ -721,9 +721,14 @@ def register_commands(
             elif agent_config["format"] == "markdown":
                 body = self.resolve_skill_placeholders(agent_name, frontmatter, body, project_root)
                 body = self._convert_argument_placeholder(body, "$ARGUMENTS", agent_config["args"])
-                behavior = frontmatter.get("behavior") if isinstance(frontmatter.get("behavior"), dict) else {}
-                if agent_name == "copilot" and behavior:
-                    agents_overrides = frontmatter.get("agents") or {}
+                behavior_raw = frontmatter.get("behavior")
+                behavior = behavior_raw if isinstance(behavior_raw, dict) else {}
+                agents_overrides = frontmatter.get("agents") or {}
+                has_copilot_override = (
+                    isinstance(agents_overrides, dict)
+                    and isinstance(agents_overrides.get("copilot"), dict)
+                )
+                if agent_name == "copilot" and (isinstance(behavior_raw, dict) or has_copilot_override):
                     extra_fields = translate_behavior(
                         agent_name, behavior,
                         agents_overrides if isinstance(agents_overrides, dict) else {}

src/specify_cli/integrations/base.py

@@ -1486,6 +1486,14 @@ def _quote(v: str) -> str:
                             behavior_fm_lines += f"{bk}: {'true' if bv else 'false'}\n"
                         elif isinstance(bv, str):
                             behavior_fm_lines += f"{bk}: {_quote(bv)}\n"
+                        elif isinstance(bv, (list, dict)):
+                            dumped = yaml.safe_dump(
+                                {bk: bv},
+                                sort_keys=False,
+                                allow_unicode=True,
+                                default_flow_style=False,
+                            ).rstrip()
+                            behavior_fm_lines += dumped + "\n"
                         else:
                             behavior_fm_lines += f"{bk}: {bv}\n"
                 except ImportError:

tests/test_agent_deployment.py

@@ -279,6 +279,57 @@ def test_copilot_agents_override_survives(self, tmp_path):
         fm = yaml.safe_load(parts[1]) or {}
         assert fm.get("someCustomKey") == "someValue"
 
+    def test_copilot_agents_override_without_behavior_survives(self, tmp_path):
+        """Copilot agents override should apply even when behavior is absent."""
+        root = self._setup_copilot_project(tmp_path)
+        src = tmp_path / "ext" / "commands"
+        src.mkdir(parents=True)
+        (src / "custom2.md").write_text(dedent("""\
+            ---
+            description: Custom command
+            agents:
+              copilot:
+                someCustomKey: someValue
+            ---
+            Do custom work
+        """))
+        registrar = CommandRegistrar()
+        registrar.register_commands(
+            "copilot",
+            [{"name": "speckit.test-ext.custom2", "file": "custom2.md"}],
+            "test-ext", src, root,
+        )
+        agent_file = root / ".github" / "agents" / "speckit.test-ext.custom2.agent.md"
+        content = agent_file.read_text()
+        parts = content.split("---")
+        fm = yaml.safe_load(parts[1]) or {}
+        assert fm.get("someCustomKey") == "someValue"
+        assert "agents" not in fm
+
+    def test_copilot_empty_behavior_is_stripped(self, tmp_path):
+        """Empty behavior mapping should still be stripped from Copilot output."""
+        root = self._setup_copilot_project(tmp_path)
+        src = tmp_path / "ext" / "commands"
+        src.mkdir(parents=True)
+        (src / "empty-behavior.md").write_text(dedent("""\
+            ---
+            description: Empty behavior
+            behavior: {}
+            ---
+            Do work
+        """))
+        registrar = CommandRegistrar()
+        registrar.register_commands(
+            "copilot",
+            [{"name": "speckit.test-ext.empty-behavior", "file": "empty-behavior.md"}],
+            "test-ext", src, root,
+        )
+        agent_file = root / ".github" / "agents" / "speckit.test-ext.empty-behavior.agent.md"
+        content = agent_file.read_text()
+        parts = content.split("---")
+        fm = yaml.safe_load(parts[1]) or {}
+        assert "behavior" not in fm
+
     def test_copilot_non_dict_behavior_does_not_raise(self, tmp_path):
         """A non-dict behavior value in Copilot execution:agent branch must not raise."""
         root = self._setup_copilot_project(tmp_path)

tests/test_pr2103_reviews.py

@@ -598,6 +598,57 @@ def test_empty_agents_override_does_not_crash(self, tmp):
 
         assert len(created) > 0
 
+    def test_agents_override_non_scalar_yaml_remains_valid(self, tmp):
+        """Non-scalar override values must be emitted as valid YAML frontmatter."""
+        from specify_cli.integrations import get_integration
+        from specify_cli.integrations.manifest import IntegrationManifest
+
+        templates_dir = (
+            Path(__file__).resolve().parent.parent / "templates" / "commands"
+        )
+        if not templates_dir.is_dir():
+            pytest.skip("templates/commands not available")
+
+        src_template = next(iter(templates_dir.glob("*.md")), None)
+        if src_template is None:
+            pytest.skip("no template files found")
+
+        original_text = src_template.read_text()
+        patched = (
+            "---\n"
+            "description: Test template\n"
+            "agents:\n"
+            "  claude:\n"
+            "    handoffs:\n"
+            "      - label: Generate plan\n"
+            "        agent: speckit.plan\n"
+            "        send: true\n"
+            "---\n"
+            + original_text.split("---", 2)[-1]
+            if "---" in original_text
+            else original_text
+        )
+
+        patched_dir = tmp / "patched_templates4"
+        patched_dir.mkdir()
+        (patched_dir / src_template.name).write_text(patched)
+
+        integration = get_integration("claude")
+        if integration is None:
+            pytest.skip("claude integration not registered")
+
+        m = IntegrationManifest("claude", tmp)
+        with patch.object(type(integration), "list_command_templates", return_value=list(patched_dir.glob("*.md"))):
+            created = integration.setup(tmp, m)
+
+        skill_files = [f for f in created if f.name == "SKILL.md"]
+        assert skill_files, "no SKILL.md files created"
+        for sf in skill_files:
+            parsed = _parse_frontmatter(sf.read_text())
+            handoffs = parsed.get("handoffs")
+            assert isinstance(handoffs, list), parsed
+            assert handoffs[0].get("agent") == "speckit.plan", parsed
+
 
 # ---------------------------------------------------------------------------
 # Issue 4 — _behavior_overridable clobbers explicit source frontmatter