fix walk-up discovery to also detect index directory

discover_project_root() only looked for .java-codebase-rag.yml config
files, missing .java-codebase-rag/ index directories. This caused MCP
tools to fail when started from a microservice subdirectory because
walk-up returned None and fell back to cwd (no index there).

Empty index directories are skipped to avoid stale artifacts from
falsely anchoring discovery.

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

Author: HumanBean17

java_codebase_rag/cli.py

@@ -229,18 +229,23 @@ def _add_verbosity_flags(p: argparse.ArgumentParser) -> None:
 
 def _cmd_init(args: argparse.Namespace) -> int:
     cfg = _resolved_from_ns(args)
-    # Check for parent config
-    from java_codebase_rag.config import discover_project_root, YAML_CONFIG_FILENAMES
+    # Check for parent config or index
+    from java_codebase_rag.config import discover_project_root, find_yaml_config_file
     parent_config_dir = discover_project_root(cfg.source_root.parent)
     if parent_config_dir is not None:
-        parent_config = parent_config_dir / YAML_CONFIG_FILENAMES[0]
-        if not parent_config.is_file():
-            parent_config = parent_config_dir / YAML_CONFIG_FILENAMES[1]
-        print(
-            f"Warning: found existing config at {parent_config}. "
-            f"Creating a new project here will create a separate index.",
-            file=sys.stderr,
-        )
+        parent_config = find_yaml_config_file(parent_config_dir)
+        if parent_config is not None:
+            print(
+                f"Warning: found existing config at {parent_config}. "
+                f"Creating a new project here will create a separate index.",
+                file=sys.stderr,
+            )
+        else:
+            print(
+                f"Warning: found existing index at {parent_config_dir / '.java-codebase-rag'}. "
+                f"Creating a new project here will create a separate index.",
+                file=sys.stderr,
+            )
     _startup_hints(cfg)
     cfg.apply_to_os_environ()
     occupied, paths = index_dir_has_existing_artifacts(cfg.index_dir)

java_codebase_rag/config.py

@@ -123,20 +123,33 @@ def find_yaml_config_file(source_root: Path) -> Path | None:
     return None
 
 
+def _has_index_dir(directory: Path) -> bool:
+    """True if *directory* contains a non-empty ``.java-codebase-rag/`` index directory."""
+    idx = directory / ".java-codebase-rag"
+    return idx.is_dir() and any(idx.iterdir())
+
+
 def discover_project_root(start: Path) -> Path | None:
-    """Walk up from start to find the directory containing a config file.
+    """Walk up from start to find the directory containing a config file or index.
 
-    First match wins (closest to start). Stops at $HOME inclusive — checks $HOME
-    itself but does not walk past it. Returns None if no config found.
+    Looks for ``.java-codebase-rag.yml`` / ``.java-codebase-rag.yaml`` (preferred)
+    or the ``.java-codebase-rag/`` index directory as a project boundary marker.
+
+    First match wins (closest to start). Config file takes priority over index
+    directory at the same level. Stops at $HOME inclusive — checks $HOME itself
+    but does not walk past it. Returns None if no marker found.
     """
     start = start.resolve()
     home = Path.home().resolve()
 
     current = start
     while True:
-        # Check if current directory contains a config file
+        # Config file is the primary anchor
         if find_yaml_config_file(current) is not None:
             return current
+        # Index directory is the secondary anchor (supports indexes without config)
+        if _has_index_dir(current):
+            return current
 
         # Stop if we've reached home (check home itself, but don't walk past it)
         if current == home:

tests/test_config.py

@@ -80,6 +80,62 @@ def test_discover_project_root_first_match_wins(self, tmp_path):
         # Should find the closest config (subdir), not the parent (tmp_path)
         assert result == subdir
 
+    def test_discover_project_root_finds_nonempty_index_dir(self, tmp_path):
+        """Non-empty .java-codebase-rag/ directory acts as project anchor."""
+        subdir = tmp_path / "microservice"
+        subdir.mkdir()
+        idx = tmp_path / ".java-codebase-rag"
+        idx.mkdir()
+        (idx / "code_graph.kuzu").write_bytes(b"\x00" * 16)
+
+        result = discover_project_root(subdir)
+        assert result == tmp_path
+
+    def test_discover_project_root_skips_empty_index_dir(self, tmp_path):
+        """Empty .java-codebase-rag/ directory does not anchor the project."""
+        subdir = tmp_path / "microservice"
+        subdir.mkdir()
+        # Empty index dir at subdir level
+        empty_idx = subdir / ".java-codebase-rag"
+        empty_idx.mkdir()
+        # Real index at parent level
+        real_idx = tmp_path / ".java-codebase-rag"
+        real_idx.mkdir()
+        (real_idx / "code_graph.kuzu").write_bytes(b"\x00" * 16)
+
+        result = discover_project_root(subdir)
+        assert result == tmp_path
+
+    def test_discover_project_root_config_wins_over_index_dir(self, tmp_path):
+        """Config file takes priority over index dir at the same level."""
+        subdir = tmp_path / "subdir"
+        subdir.mkdir()
+        # Index dir at tmp_path level
+        idx = tmp_path / ".java-codebase-rag"
+        idx.mkdir()
+        (idx / "code_graph.kuzu").write_bytes(b"\x00" * 16)
+        # Config at subdir level
+        config_file = subdir / YAML_CONFIG_FILENAMES[0]
+        config_file.write_text("# child config")
+
+        deep = subdir / "deep"
+        deep.mkdir()
+        result = discover_project_root(deep)
+        # Config at subdir is closer and wins
+        assert result == subdir
+
+    def test_discover_project_root_both_markers_same_level(self, tmp_path):
+        """When both config and index dir exist at same dir, both resolve correctly."""
+        # Both markers in the same directory
+        config_file = tmp_path / YAML_CONFIG_FILENAMES[0]
+        config_file.write_text("# config")
+        idx = tmp_path / ".java-codebase-rag"
+        idx.mkdir()
+        (idx / "code_graph.kuzu").write_bytes(b"\x00" * 16)
+
+        result = discover_project_root(tmp_path)
+        assert result == tmp_path
+
 
 class TestSourceRootFromYaml:
     """Tests for source_root YAML field parsing and resolution."""