fix: scope stale cleanup to indexed directories

[zc277584121]

Summary

• restrict stale source cleanup to explicitly indexed directory roots
• treat explicit file paths as partial updates that do not prune unrelated sources
• document the scoped cleanup behavior for CLI and Python API users

Testing

• uv run python -m pytest tests/test_index_cleanup.py tests/test_core_encoding.py tests/test_embed_batching.py tests/test_scanner.py -q
• uv run python -m pytest -q
• uv run ruff check src tests
• uv run ruff format --check src tests