Refactor Codex Builder and Add Docstrings

[google-labs-jules]

This PR improves code quality and documentation in the HeadySystems_v13 directory.

Changes:

• codex_builder_v13.py:
  • Refactored main into _generate_registry, _generate_governance, _generate_gateway_config, _create_structure, and _generate_context.
  • Refactored AtomicWriter to use a private _write_to_temp_and_replace helper, reducing code duplication.
  • Added class and method docstrings.
• Iteration Scripts (Heady_itX_v_1_0_0.py):
  • Added docstrings to main functions.
• Helper Scripts (scripts/**/*.py):
  • Added module docstrings and function docstrings.

Verified by running codex_builder_v13.py to ensure deterministic generation is preserved (reverted generated file changes to keep commit clean).

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PR created automatically by Jules for task 5720851413129961019 started by @HeadyConnection

[google-labs-jules]

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