Cover the four paths introduced by the wake split:
- default manifests (recursive_sources=False) skip subdirs entirely,
- opt-in manifests walk non-subpackage subdirs with /-joined paths,
- subdirs containing __init__.py are skipped to avoid double-counting
existing component subpackages, and __pycache__ is always skipped,
- FILTER_SOURCE_FILES entries accept /-joined subpaths.