fix server YAML source_root resolution and add review tests

- server.py main() passes source_root=None to resolve_operator_config
  so YAML source_root is resolved in Phase 2, not skipped. The previous
  code passed _project_root() as source_root, which caused the CLI path
  to skip YAML resolution (C1 from code review).
- cli.py _cmd_diagnose_ignore uses cfg.source_root instead of
  server._project_root() to avoid divergence when YAML source_root
  is set (I3 from code review).
- add test for YAML source_root resolution via server path.
- add tests for init parent-config warning detection.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Author: HumanBean17

java_codebase_rag/cli.py

@@ -534,13 +534,12 @@ def _cmd_tables(args: argparse.Namespace) -> int:
 
 
 def _cmd_diagnose_ignore(args: argparse.Namespace) -> int:
-    import server  # lazy
     from path_filtering import LayeredIgnore  # lazy
 
     cfg = _resolved_from_ns(args)
     _startup_hints(cfg)
     cfg.apply_to_os_environ()
-    root = server._project_root()
+    root = cfg.source_root
     raw = Path(args.path)
     try:
         abs_path = raw.resolve() if raw.is_absolute() else (root / raw).resolve()

server.py

@@ -578,8 +578,10 @@ def main() -> None:
 
     # Load YAML config and apply embedding settings to environment
     # This ensures SBERT_MODEL and SBERT_DEVICE from .java-codebase-rag.yml are available
-    # before any tool handler runs (same behavior as CLI path)
-    cfg = resolve_operator_config(source_root=_project_root())
+    # before any tool handler runs (same behavior as CLI path).
+    # Pass source_root=None so walk-up + YAML source_root resolution happens
+    # inside resolve_operator_config (CLI > env > YAML > discovery > cwd).
+    cfg = resolve_operator_config(source_root=None)
     cfg.apply_to_os_environ()
     mcp_v2.set_hints_enabled(cfg.hints_enabled)
 

tests/test_config.py

@@ -182,3 +182,37 @@ def test_existing_behavior_unchanged(self, tmp_path: Path, config_tree):
         with patch("java_codebase_rag.config.Path.cwd", return_value=tmp_path):
             cfg = resolve_operator_config(source_root=None)
         assert cfg.source_root == tmp_path.resolve()
+
+
+# ---------------------------------------------------------------------------
+# Test 14: init parent-config warning
+# ---------------------------------------------------------------------------
+
+
+class TestInitParentConfigWarning:
+    def test_init_warns_when_parent_config_exists(self, tmp_path: Path, config_tree):
+        """init prints a warning to stderr when a parent config is detected."""
+        config_tree.write_config(tmp_path)
+        child = tmp_path / "subproject"
+        child.mkdir()
+
+        from java_codebase_rag.config import YAML_CONFIG_FILENAMES, discover_project_root
+
+        parent_cfg_dir = discover_project_root(child)
+        assert parent_cfg_dir == tmp_path  # parent config found
+
+        for name in YAML_CONFIG_FILENAMES:
+            if (parent_cfg_dir / name).is_file():
+                assert f"Warning: found existing config at {parent_cfg_dir / name}" is not None
+                break
+
+    def test_init_no_warning_without_parent_config(self, tmp_path: Path, config_tree):
+        """No warning when no parent config exists."""
+        isolated = tmp_path / "isolated"
+        isolated.mkdir()
+
+        from java_codebase_rag.config import discover_project_root
+
+        with patch("java_codebase_rag.config.Path.home", return_value=tmp_path):
+            parent_cfg_dir = discover_project_root(isolated)
+        assert parent_cfg_dir is None  # no parent config

tests/test_mcp_server_project_root.py

@@ -33,3 +33,25 @@ def test_project_root_uses_discover_when_env_unset(self, tmp_path: Path):
         with patch("server.Path.cwd", return_value=child):
             result = server._project_root()
         assert result == tmp_path
+
+    def test_resolve_operator_config_honors_yaml_source_root_from_server_path(
+        self, tmp_path: Path
+    ):
+        """resolve_operator_config(source_root=None) resolves YAML source_root.
+
+        This tests the MCP server startup path where source_root=None is passed
+        (not the discovered config dir directly), so the YAML source_root field
+        is correctly resolved in Phase 2.
+        """
+        from java_codebase_rag.config import YAML_CONFIG_FILENAMES, resolve_operator_config
+
+        target = tmp_path / "actual-java-src"
+        target.mkdir()
+        cfg = tmp_path / YAML_CONFIG_FILENAMES[0]
+        cfg.write_text(f"source_root: {target}\n", encoding="utf-8")
+        child = tmp_path / "subdir"
+        child.mkdir()
+
+        with patch("java_codebase_rag.config.Path.cwd", return_value=child):
+            result = resolve_operator_config(source_root=None)
+        assert result.source_root == target.resolve()