Integrate refactor milestones into master + stabilize CI type checks

[donglaiw]

Summary

• lands milestones 1-5 from the refactor stack into master
• keeps CLI/config behavior intact while improving module boundaries and maintainability
• narrows CI style/type checks to changed connectomics/**/*.py files
• adds .github/mypy_changed.ini so changed-file mypy uses stable settings (python_version=3.11, follow_imports=skip)
• adds type-annotation-only fixes in refactored files (runtime.py, data_factory.py, data_dicts.py)

Validation (in pytc env)

• conda run -n pytc python scripts/main.py --demo
• conda run -n pytc pytest tests/unit/test_main_cli_contract.py tests/unit/test_run_directory_contract.py tests/unit/test_lit_utils.py tests/integration/test_config_integration.py
• conda run -n pytc black --check <changed .py files>
• conda run -n pytc isort --check-only <changed .py files>
• conda run -n pytc flake8 --max-line-length=100 <changed .py files>
• conda run -n pytc mypy --config-file .github/mypy_changed.ini <changed .py files>

Notes

• this branch also includes intentional tutorial/cellmap removals that were already staged locally at commit time