fix: extract agent markdown body as system instruction

amplifier_foundation/bundle.py

@@ -252,6 +252,10 @@ def resolve_with_overrides(module_id: str, source: str) -> str:
         """
         from amplifier_foundation.modules.activator import ModuleActivator
 
+        # Load full agent metadata (including system instructions from .md files)
+        # Must happen before to_mount_plan() so agent configs include system.instruction
+        self.load_agent_metadata()
+
         # Get mount plan
         mount_plan = self.to_mount_plan()
 
@@ -526,12 +530,12 @@ def _load_agent_file_metadata(path: Path, fallback_name: str) -> dict[str, Any]:
         fallback_name: Name to use if not specified in file
 
     Returns:
-        Dict with name, description, and any other meta fields
+        Dict with name, description, system instruction, and any other meta fields
     """
     from amplifier_foundation.io.frontmatter import parse_frontmatter
 
     text = path.read_text(encoding="utf-8")
-    frontmatter, _body = parse_frontmatter(text)
+    frontmatter, body = parse_frontmatter(text)
 
     # Agents use meta: section (not bundle:)
     meta = frontmatter.get("meta", {})
@@ -542,12 +546,20 @@ def _load_agent_file_metadata(path: Path, fallback_name: str) -> dict[str, Any]:
         else:
             meta = {}
 
-    return {
+    result = {
         "name": meta.get("name", fallback_name),
         "description": meta.get("description", ""),
         **{k: v for k, v in meta.items() if k not in ("name", "description")},
     }
 
+    # Extract markdown body as system instruction
+    # The body contains the agent's behavioral instructions that should be
+    # injected as the system prompt when the agent is spawned
+    if body and body.strip():
+        result["system"] = {"instruction": body.strip()}
+
+    return result
+
 
 def _parse_context(
     context_config: dict[str, Any], base_path: Path | None

tests/test_bundle.py

@@ -256,3 +256,103 @@ def test_pending_context_resolved_after_compose(self) -> None:
         assert "ns2:context/b.md" in result.context
         assert result.context["ns1:context/a.md"] == Path("/ns1/root/context/a.md")
         assert result.context["ns2:context/b.md"] == Path("/ns2/root/context/b.md")
+
+
+class TestAgentMetadataLoading:
+    """Tests for agent metadata loading from .md files."""
+
+    def test_load_agent_metadata_extracts_system_instruction(self) -> None:
+        """Agent markdown body becomes system.instruction."""
+        with TemporaryDirectory() as tmpdir:
+            # Create agent .md file with frontmatter and body
+            agents_dir = Path(tmpdir) / "agents"
+            agents_dir.mkdir()
+            agent_file = agents_dir / "test-agent.md"
+            agent_file.write_text("""---
+meta:
+  name: test-agent
+  description: A test agent
+---
+
+# Test Agent Instructions
+
+You are a test agent. Follow these rules:
+1. Do something
+2. Do something else
+""")
+
+            # Create bundle with agent stub
+            bundle = Bundle(
+                name="test",
+                base_path=Path(tmpdir),
+                agents={"test-agent": {"name": "test-agent"}},
+            )
+
+            # Load metadata
+            bundle.load_agent_metadata()
+
+            # Verify system instruction was extracted from body
+            agent_config = bundle.agents["test-agent"]
+            assert "system" in agent_config
+            assert "instruction" in agent_config["system"]
+            assert "Test Agent Instructions" in agent_config["system"]["instruction"]
+            assert "Follow these rules" in agent_config["system"]["instruction"]
+
+    def test_load_agent_metadata_preserves_existing_system(self) -> None:
+        """Existing system.instruction is not overwritten by file metadata."""
+        with TemporaryDirectory() as tmpdir:
+            # Create agent .md file
+            agents_dir = Path(tmpdir) / "agents"
+            agents_dir.mkdir()
+            agent_file = agents_dir / "test-agent.md"
+            agent_file.write_text("""---
+meta:
+  name: test-agent
+---
+
+File body instructions.
+""")
+
+            # Create bundle with agent that already has system.instruction
+            bundle = Bundle(
+                name="test",
+                base_path=Path(tmpdir),
+                agents={"test-agent": {
+                    "name": "test-agent",
+                    "system": {"instruction": "Explicit inline instruction"}
+                }},
+            )
+
+            # Load metadata
+            bundle.load_agent_metadata()
+
+            # Explicit instruction should be preserved (not overwritten)
+            agent_config = bundle.agents["test-agent"]
+            assert agent_config["system"]["instruction"] == "Explicit inline instruction"
+
+    def test_load_agent_metadata_empty_body_no_system(self) -> None:
+        """Agent with empty body doesn't get system.instruction."""
+        with TemporaryDirectory() as tmpdir:
+            # Create agent .md file with only frontmatter, no body
+            agents_dir = Path(tmpdir) / "agents"
+            agents_dir.mkdir()
+            agent_file = agents_dir / "test-agent.md"
+            agent_file.write_text("""---
+meta:
+  name: test-agent
+  description: Agent with no body
+---
+""")
+
+            bundle = Bundle(
+                name="test",
+                base_path=Path(tmpdir),
+                agents={"test-agent": {"name": "test-agent"}},
+            )
+
+            bundle.load_agent_metadata()
+
+            agent_config = bundle.agents["test-agent"]
+            # Should have description but no system (empty body)
+            assert agent_config.get("description") == "Agent with no body"
+            assert "system" not in agent_config or not agent_config.get("system", {}).get("instruction")