Flatten over-nested single-file packages and __init__.py-only implementations under amber/src/main/python/core/util/

[Yicong-Huang]

Task Summary

Several core/util/<X>/<X>.py directories under amber/src/main/python/ exist only to host a single file, transplanting the Java/Scala "one class per directory" convention into Python where it adds noise without value:

• core/util/runnable/runnable.py → should be core/util/runnable.py
• core/util/stoppable/stoppable.py → should be core/util/stoppable.py
• core/util/thread/atomic.py → should be core/util/atomic.py (or thread.py)
• core/util/protocol/base_protocols.py → should be core/util/base_protocols.py
• core/util/operator/__init__.py is 16 lines (license header only) — appears to be dead code

A related pattern: implementations written directly inside __init__.py rather than a named module:

• core/util/expression_evaluator/__init__.py is 211 lines of evaluator implementation
• core/util/virtual_identity/__init__.py is 99 lines of virtual-identity logic

__init__.py should re-export from a sibling module, not host the implementation.

Task Type

• Refactor / Cleanup