feat: enhance search, ranking, reranker and CLI tooling across ccw and codex-lens

Major improvements to smart-search, chain-search cascade, ranking pipeline,
reranker factory, CLI history store, codex-lens integration, and uv-manager.
Simplify command-generator skill by inlining phases. Add comprehensive tests.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

codex-lens/tests/test_index_tree_ignore_dirs.py

@@ -5,7 +5,10 @@ from pathlib import Path
 from unittest.mock import MagicMock
 
 from codexlens.config import Config
-from codexlens.storage.index_tree import IndexTreeBuilder
+from codexlens.storage.dir_index import DirIndexStore
+from codexlens.storage.index_tree import DirBuildResult, IndexTreeBuilder
+from codexlens.storage.path_mapper import PathMapper
+from codexlens.storage.registry import RegistryStore
 
 
 def _relative_dirs(source_root: Path, dirs_by_depth: dict[int, list[Path]]) -> set[str]:
@@ -145,3 +148,148 @@ def test_builder_loads_saved_ignore_and_extension_filters_by_default(tmp_path: P
 
     assert [path.name for path in source_files] == ["app.ts"]
     assert "frontend/dist" not in discovered_dirs
+
+
+def test_prune_stale_project_dirs_removes_ignored_artifact_mappings(tmp_path: Path) -> None:
+    workspace = tmp_path / "workspace"
+    src_dir = workspace / "src"
+    dist_dir = workspace / "dist"
+    src_dir.mkdir(parents=True)
+    dist_dir.mkdir(parents=True)
+    (src_dir / "app.py").write_text("print('ok')\n", encoding="utf-8")
+    (dist_dir / "bundle.py").write_text("print('artifact')\n", encoding="utf-8")
+
+    mapper = PathMapper(index_root=tmp_path / "indexes")
+    registry = RegistryStore(db_path=tmp_path / "registry.db")
+    registry.initialize()
+    project = registry.register_project(workspace, mapper.source_to_index_dir(workspace))
+    registry.register_dir(project.id, workspace, mapper.source_to_index_db(workspace), depth=0)
+    registry.register_dir(project.id, src_dir, mapper.source_to_index_db(src_dir), depth=1)
+    registry.register_dir(project.id, dist_dir, mapper.source_to_index_db(dist_dir), depth=1)
+
+    builder = IndexTreeBuilder(
+        registry=registry,
+        mapper=mapper,
+        config=Config(data_dir=tmp_path / "data"),
+        incremental=False,
+    )
+
+    dirs_by_depth = builder._collect_dirs_by_depth(workspace)
+    pruned = builder._prune_stale_project_dirs(
+        project_id=project.id,
+        source_root=workspace,
+        dirs_by_depth=dirs_by_depth,
+    )
+
+    remaining = {mapping.source_path.resolve() for mapping in registry.get_project_dirs(project.id)}
+    registry.close()
+
+    assert dist_dir.resolve() in pruned
+    assert workspace.resolve() in remaining
+    assert src_dir.resolve() in remaining
+    assert dist_dir.resolve() not in remaining
+
+
+def test_force_full_build_prunes_stale_ignored_mappings(tmp_path: Path) -> None:
+    workspace = tmp_path / "workspace"
+    src_dir = workspace / "src"
+    dist_dir = workspace / "dist"
+    src_dir.mkdir(parents=True)
+    dist_dir.mkdir(parents=True)
+    (src_dir / "app.py").write_text("print('ok')\n", encoding="utf-8")
+    (dist_dir / "bundle.py").write_text("print('artifact')\n", encoding="utf-8")
+
+    mapper = PathMapper(index_root=tmp_path / "indexes")
+    registry = RegistryStore(db_path=tmp_path / "registry.db")
+    registry.initialize()
+    project = registry.register_project(workspace, mapper.source_to_index_dir(workspace))
+    registry.register_dir(project.id, workspace, mapper.source_to_index_db(workspace), depth=0)
+    registry.register_dir(project.id, dist_dir, mapper.source_to_index_db(dist_dir), depth=1)
+
+    builder = IndexTreeBuilder(
+        registry=registry,
+        mapper=mapper,
+        config=Config(
+            data_dir=tmp_path / "data",
+            global_symbol_index_enabled=False,
+        ),
+        incremental=False,
+    )
+
+    def fake_build_level_parallel(
+        dirs: list[Path],
+        languages,
+        workers,
+        *,
+        source_root: Path,
+        project_id: int,
+        global_index_db_path: Path,
+    ) -> list[DirBuildResult]:
+        return [
+            DirBuildResult(
+                source_path=dir_path,
+                index_path=mapper.source_to_index_db(dir_path),
+                files_count=1 if dir_path == src_dir else 0,
+                symbols_count=0,
+                subdirs=[],
+            )
+            for dir_path in dirs
+        ]
+
+    builder._build_level_parallel = fake_build_level_parallel  # type: ignore[method-assign]
+    builder._link_children_to_parent = MagicMock()
+
+    build_result = builder.build(workspace, force_full=True, workers=1)
+
+    remaining = {mapping.source_path.resolve() for mapping in registry.get_project_dirs(project.id)}
+    registry.close()
+
+    assert build_result.total_dirs == 2
+    assert workspace.resolve() in remaining
+    assert src_dir.resolve() in remaining
+    assert dist_dir.resolve() not in remaining
+
+
+def test_force_full_build_rewrites_directory_db_and_drops_stale_ignored_subdirs(
+    tmp_path: Path,
+) -> None:
+    project_root = tmp_path / "project"
+    src_dir = project_root / "src"
+    build_dir = project_root / "build"
+    src_dir.mkdir(parents=True)
+    build_dir.mkdir(parents=True)
+    (src_dir / "app.py").write_text("print('ok')\n", encoding="utf-8")
+    (build_dir / "generated.py").write_text("print('artifact')\n", encoding="utf-8")
+
+    mapper = PathMapper(index_root=tmp_path / "indexes")
+    registry = RegistryStore(db_path=tmp_path / "registry.db")
+    registry.initialize()
+    config = Config(
+        data_dir=tmp_path / "data",
+        global_symbol_index_enabled=False,
+    )
+
+    root_index_db = mapper.source_to_index_db(project_root)
+    with DirIndexStore(root_index_db, config=config) as store:
+        store.register_subdir(
+            name="build",
+            index_path=mapper.source_to_index_db(build_dir),
+            files_count=1,
+        )
+
+    builder = IndexTreeBuilder(
+        registry=registry,
+        mapper=mapper,
+        config=config,
+        incremental=False,
+    )
+
+    build_result = builder.build(project_root, force_full=True, workers=1)
+
+    with DirIndexStore(root_index_db, config=config) as store:
+        subdir_names = [link.name for link in store.get_subdirs()]
+
+    registry.close()
+
+    assert build_result.total_dirs == 2
+    assert subdir_names == ["src"]