fix(agent): keep explicit skills out of system prompt

tests/agent/test_context_builder.py

@@ -407,15 +407,20 @@ class TestBuildMessages:
         builder = _builder(tmp_path)
 
         messages = builder.build_messages([], "Please $review this patch and use $review carefully.")
+        plain_messages = builder.build_messages([], "Please review this patch carefully.")
 
         system_prompt = messages[0]["content"]
-        assert "# Active Skills" in system_prompt
-        assert "### Skill: review" in system_prompt
-        assert "Follow the unique review checklist." in system_prompt
-        assert system_prompt.count("### Skill: review") == 1
-        assert messages[-1]["content"] == (
-            "Please $review this patch and use $review carefully."
-        )
+        user_prompt = messages[-1]["content"]
+        assert system_prompt == plain_messages[0]["content"]
+        assert "Follow the unique review checklist." not in system_prompt
+        assert "Please $review this patch" in user_prompt
+        assert "[Active Skills — instructions for this user turn]" in user_prompt
+        assert "### Skill: review" in user_prompt
+        assert "Follow the unique review checklist." in user_prompt
+        assert user_prompt.count("### Skill: review") == 1
+        assert messages[-1]["_meta"]["runtime_context"]["sources"] == [
+            "explicit_skills"
+        ]
 
     def test_unknown_skill_reference_does_not_change_active_skills(self, tmp_path):
         messages = _builder(tmp_path).build_messages([], "Keep the shell literal $HOME.")

tests/agent/test_loop_runner_integration.py

@@ -146,6 +146,16 @@ async def test_runtime_context_is_persisted_as_next_turn_prompt_prefix(tmp_path)
     from nanobot.bus.events import InboundMessage
     from nanobot.bus.queue import MessageBus
 
+    skill_dir = tmp_path / "skills" / "review"
+    skill_dir.mkdir(parents=True)
+    (skill_dir / "SKILL.md").write_text(
+        "---\n"
+        "name: review\n"
+        "description: Review changes.\n"
+        "---\n\n"
+        "Follow the unique review checklist.",
+        encoding="utf-8",
+    )
     provider = MagicMock()
     provider.get_default_model.return_value = "test-model"
     provider.generation = GenerationSettings()
@@ -169,7 +179,7 @@ async def test_runtime_context_is_persisted_as_next_turn_prompt_prefix(tmp_path)
         channel="cli",
         sender_id="user",
         chat_id="direct",
-        content="first turn",
+        content="first turn $review",
     ))
     await loop._process_message(InboundMessage(
         channel="cli",
@@ -184,6 +194,9 @@ async def test_runtime_context_is_persisted_as_next_turn_prompt_prefix(tmp_path)
     second_wire = LLMProvider._sanitize_empty_content(second_request)
     assert second_wire[: len(first_wire)] == first_wire
     assert first_wire[1] == second_wire[1]
+    assert first_wire[0] == second_wire[0]
+    assert "Follow the unique review checklist." not in first_wire[0]["content"]
+    assert "Follow the unique review checklist." in first_wire[1]["content"]
     assert second_wire[2]["role"] == "assistant"
     assert second_wire[2]["content"] == "first answer"
     assert second_wire[3]["content"].startswith("second turn")
@@ -191,7 +204,7 @@ async def test_runtime_context_is_persisted_as_next_turn_prompt_prefix(tmp_path)
 
     persisted_first_user = session.messages[0]
     assert persisted_first_user["content"] == first_wire[1]["content"]
-    assert public_history_message(persisted_first_user)["content"] == "first turn"
+    assert public_history_message(persisted_first_user)["content"] == "first turn $review"
 
 
 @pytest.mark.asyncio