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.

cli/tests/conftest.py

@@ -9,10 +9,23 @@ import pytest
 import yaml
 
 
+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": 18000},
         "programs": {
@@ -61,7 +74,7 @@ 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)
 
     # Create project directories
     svc_dir = tmp_path / "test-svc"