fix: address remaining PR2103 review threads

Author: iamaeroplane

src/specify_cli/extensions.py

@@ -22,7 +22,11 @@
 import pathspec
 
 import yaml
-from specify_cli.behavior import get_deployment_type as _get_deployment_type
+from specify_cli.behavior import (
+    get_deployment_type as _get_deployment_type,
+    strip_behavior_keys,
+    translate_behavior,
+)
 from packaging import version as pkg_version
 from packaging.specifiers import SpecifierSet, InvalidSpecifier
 
@@ -930,6 +934,19 @@ def _register_extension_skills(
 
             skill_subdir.mkdir(parents=True, exist_ok=True)
             frontmatter, body = registrar.parse_frontmatter(content)
+
+            for key in ("agents",):
+                if key in cmd_info and key not in frontmatter:
+                    frontmatter[key] = cmd_info[key]
+            if "behavior" in cmd_info:
+                manifest_behavior = cmd_info["behavior"]
+                if isinstance(manifest_behavior, dict):
+                    source_behavior = frontmatter.get("behavior")
+                    if isinstance(source_behavior, dict):
+                        frontmatter["behavior"] = {**manifest_behavior, **source_behavior}
+                    else:
+                        frontmatter["behavior"] = manifest_behavior
+
             frontmatter = registrar._adjust_script_paths(frontmatter)
             body = registrar.rewrite_extension_paths(body, manifest.id, extension_dir)
             body = registrar.resolve_skill_placeholders(
@@ -939,12 +956,27 @@ def _register_extension_skills(
             original_desc = frontmatter.get("description", "")
             description = original_desc or f"Extension command: {cmd_name}"
 
+            clean_frontmatter = strip_behavior_keys(frontmatter)
             frontmatter_data = registrar.build_skill_frontmatter(
                 selected_ai,
                 skill_name,
                 description,
                 f"extension:{manifest.id}",
+                source_frontmatter=clean_frontmatter,
             )
+
+            behavior = frontmatter.get("behavior") if isinstance(frontmatter.get("behavior"), dict) else {}
+            agents_overrides = frontmatter.get("agents") or {}
+            behavior_fields = translate_behavior(
+                selected_ai,
+                behavior,
+                agents_overrides if isinstance(agents_overrides, dict) else {},
+            )
+            overridable_defaults = {"disable-model-invocation", "user-invocable"}
+            for key, value in behavior_fields.items():
+                if key not in frontmatter_data or key in overridable_defaults:
+                    frontmatter_data[key] = value
+
             frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
 
             # Derive a human-friendly title from the command name

src/specify_cli/integrations/base.py

@@ -1465,14 +1465,20 @@ def _quote(v: str) -> str:
             # to produce `disable-model-invocation: false` in the skill.
             # Fields are emitted here so downstream post-processors (e.g.
             # ClaudeIntegration.setup) see them already set and skip injection.
-            behavior = frontmatter.get("behavior") or {}
+            behavior = frontmatter.get("behavior")
+            behavior_dict = behavior if isinstance(behavior, dict) else {}
+            agents_overrides = frontmatter.get("agents") or {}
+            has_agent_override = (
+                isinstance(agents_overrides, dict)
+                and isinstance(agents_overrides.get(self.key), dict)
+            )
             behavior_fm_lines = ""
-            if isinstance(behavior, dict) and behavior:
+            if behavior_dict or has_agent_override:
                 try:
                     from specify_cli.behavior import translate_behavior
-                    agents_overrides = frontmatter.get("agents") or {}
+
                     behavior_fields = translate_behavior(
-                        self.key, behavior,
+                        self.key, behavior_dict,
                         agents_overrides if isinstance(agents_overrides, dict) else {}
                     )
                     for bk, bv in behavior_fields.items():

tests/test_pr2103_reviews.py

@@ -338,6 +338,71 @@ def test_no_behavior_no_manifest_behavior_writes_skill(self, tmp):
         assert skill_file.exists()
 
 
+class TestExtensionSkillFrontmatterPropagation:
+    """Issue 6: extension skill rendering must preserve merged source frontmatter."""
+
+    @pytest.fixture
+    def tmp(self):
+        d = tempfile.mkdtemp()
+        yield Path(d)
+        shutil.rmtree(d)
+
+    def test_manifest_behavior_is_applied_to_skill_frontmatter(self, tmp):
+        """Manifest-level behavior must affect generated SKILL.md frontmatter."""
+        ext_dir = _make_ext_dir(tmp, "ext3", [{
+            "name": "speckit.ext3.cmd",
+            "file": "commands/cmd.md",
+            "behavior": {"invocation": "automatic"},
+        }])
+        (ext_dir / "commands" / "cmd.md").write_text(
+            "---\n"
+            "description: Test\n"
+            "---\n\n"
+            "Body"
+        )
+
+        proj = _make_project(tmp, ai="claude", ai_skills=True)
+        (proj / ".claude" / "skills").mkdir(parents=True)
+
+        from specify_cli.extensions import ExtensionManifest, ExtensionManager
+
+        manifest = ExtensionManifest(ext_dir / "extension.yml")
+        mgr = ExtensionManager(proj)
+        created = mgr._register_extension_skills(manifest, ext_dir)
+        assert created == ["speckit-ext3-cmd"]
+
+        skill_file = proj / ".claude" / "skills" / "speckit-ext3-cmd" / "SKILL.md"
+        parsed = _parse_frontmatter(skill_file.read_text())
+        assert parsed.get("disable-model-invocation") is False, parsed
+
+    def test_source_frontmatter_passthrough_is_preserved(self, tmp):
+        """Passthrough keys like model must be preserved in generated SKILL.md."""
+        ext_dir = _make_ext_dir(tmp, "ext4", [{
+            "name": "speckit.ext4.cmd",
+            "file": "commands/cmd.md",
+        }])
+        (ext_dir / "commands" / "cmd.md").write_text(
+            "---\n"
+            "description: Test\n"
+            "model: claude-opus-4-6\n"
+            "---\n\n"
+            "Body"
+        )
+
+        proj = _make_project(tmp, ai="claude", ai_skills=True)
+        (proj / ".claude" / "skills").mkdir(parents=True)
+
+        from specify_cli.extensions import ExtensionManifest, ExtensionManager
+
+        manifest = ExtensionManifest(ext_dir / "extension.yml")
+        mgr = ExtensionManager(proj)
+        mgr._register_extension_skills(manifest, ext_dir)
+
+        skill_file = proj / ".claude" / "skills" / "speckit-ext4-cmd" / "SKILL.md"
+        parsed = _parse_frontmatter(skill_file.read_text())
+        assert parsed.get("model") == "claude-opus-4-6", parsed
+
+
 # ---------------------------------------------------------------------------
 # Issue 3 — SkillsIntegration.setup() ignores agents: override
 # ---------------------------------------------------------------------------
@@ -406,6 +471,49 @@ def test_agents_override_applied_in_skills_integration(self, tmp):
                 f"agents: override not applied; got frontmatter: {parsed}"
             )
 
+    def test_agents_override_without_behavior_is_applied(self, tmp):
+        """agents-only template frontmatter must still apply for the target agent."""
+        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 = src_template.read_text()
+        patched = (
+            "---\n"
+            "description: Test patched template\n"
+            "agents:\n"
+            "  codex:\n"
+            "    effort: max\n"
+            "---\n" + original.split("---", 2)[-1] if "---" in original else original
+        )
+
+        patched_dir = tmp / "patched_templates_agents_only"
+        patched_dir.mkdir()
+        (patched_dir / src_template.name).write_text(patched)
+
+        integration = get_integration("codex")
+        if integration is None:
+            pytest.skip("codex integration not registered")
+
+        m = IntegrationManifest("codex", 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())
+            assert parsed.get("effort") == "max", parsed
+
     def test_agents_override_for_other_agent_not_applied(self, tmp):
         """agents: override for a different agent must not bleed into codex output."""
         from specify_cli.integrations import get_integration