Refactor configuration handling to use directory-per-resource layout

- Introduced `_write_castle_config` function to scatter nested config into separate YAML files for programs, services, and jobs.
- Updated `castle_root` fixture to utilize the new config writing method.
- Added tests for configuration aggregation and scattering in `test_health.py`.
- Removed legacy unit handling from `manifest.py` and refactored related code in `config.py`.
- Updated documentation to reflect new configuration directory structure.
- Removed obsolete unit tests related to unit expansion.

castle-api/tests/conftest.py

@@ -17,10 +17,25 @@ from castle_core.registry import (
 )
 
 
+def _write_castle_config(root: Path, config: dict) -> None:
+    """Scatter a nested castle config dict into the directory-per-resource layout."""
+    globals_data = {k: v for k, v in config.items() if k in ("gateway", "repo")}
+    (root / "castle.yaml").write_text(yaml.dump(globals_data, default_flow_style=False))
+    for section in ("programs", "services", "jobs"):
+        entries = config.get(section) or {}
+        if not entries:
+            continue
+        section_dir = root / section
+        section_dir.mkdir(parents=True, exist_ok=True)
+        for name, spec in entries.items():
+            (section_dir / f"{name}.yaml").write_text(
+                yaml.dump(spec, default_flow_style=False)
+            )
+
+
 @pytest.fixture
 def castle_root(tmp_path: Path) -> Generator[Path, None, None]:
-    """Create a temporary castle root with castle.yaml."""
-    castle_yaml = tmp_path / "castle.yaml"
+    """Create a temporary castle root with directory-per-resource config."""
     config = {
         "gateway": {"port": 9000},
         "programs": {
@@ -77,7 +92,7 @@ def castle_root(tmp_path: Path) -> Generator[Path, None, None]:
             },
         },
     }
-    castle_yaml.write_text(yaml.dump(config, default_flow_style=False))
+    _write_castle_config(tmp_path, config)
     yield tmp_path
 
 
@@ -143,7 +158,14 @@ def registry_path(tmp_path: Path, castle_root: Path) -> Generator[Path, None, No
         "config_editor.get_castle_root": config_editor_mod.get_castle_root,
     }
 
-    for mod in [api_config, routes_mod, services_mod, nodes_mod, stream_mod, config_editor_mod]:
+    for mod in [
+        api_config,
+        routes_mod,
+        services_mod,
+        nodes_mod,
+        stream_mod,
+        config_editor_mod,
+    ]:
         if hasattr(mod, "get_registry"):
             mod.get_registry = _get_registry
         if hasattr(mod, "get_castle_root"):

castle-api/tests/test_health.py

@@ -268,3 +268,36 @@ class TestGateway:
         assert data["routes"]
         for r in data["routes"]:
             assert r["kind"] in ("static", "proxy", "remote")
+
+
+class TestConfigEditor:
+    """Virtual castle.yaml aggregation/scatter endpoints."""
+
+    def test_get_aggregates_resources(self, client: TestClient) -> None:
+        """GET /config returns a unified YAML aggregating all resource files."""
+        import yaml
+
+        response = client.get("/config")
+        assert response.status_code == 200
+        data = yaml.safe_load(response.json()["yaml_content"])
+        assert "test-tool" in data["programs"]
+        assert "test-svc" in data["services"]
+        assert "test-job" in data["jobs"]
+
+    def test_put_scatters_and_prunes(self, client: TestClient, castle_root) -> None:
+        """PUT /config writes resource files and prunes removed ones."""
+        import yaml
+
+        current = yaml.safe_load(client.get("/config").json()["yaml_content"])
+        current["services"].pop("test-svc")
+        current["programs"]["new-tool"] = {
+            "description": "Brand new",
+            "behavior": "tool",
+        }
+        resp = client.put("/config", json={"yaml_content": yaml.dump(current)})
+        assert resp.status_code == 200, resp.text
+        assert not (castle_root / "services" / "test-svc.yaml").exists()
+        assert (castle_root / "programs" / "new-tool.yaml").exists()
+        after = yaml.safe_load(client.get("/config").json()["yaml_content"])
+        assert "new-tool" in after["programs"]
+        assert "test-svc" not in (after.get("services") or {})