[codex] Clean staging on init install race

[yibeichan]

Summary

• add a shared final install helper for completed init staging trees
• clean up staging if the final target rmdir/rename fails
• apply the helper to standalone, spoke, and hub init flows
• add regression coverage for target-populated-after-precheck races in all three flows

Root cause

The init flows cleaned staging during build failures, but the final rmdir/rename install step was outside that error handling. If the target became non-empty after the early empty-directory guard, target.rmdir() raised and left the completed staging directory behind.

Validation

• cd cli && uv run --with pytest --with . python -m pytest tests/test_init_standalone.py tests/test_sync.py tests/test_hub.py
• cd cli && uv run --with pytest --with . python -m pytest tests/

Closes #52