Audit current codebase before cleanup

[OrF8]

Summary

• documents the current project pipeline and execution order
• inventories tracked scripts, notebooks, configuration, results, and intermediate files
• identifies possible unused code and files without removing them
• records duplicated logic, hard-coded configuration, and generated artifacts
• proposes a safe order for later cleanup

Scope

This PR is intentionally non-destructive. It does not delete, move, rename, or refactor source code, and it does not rerun expensive notebooks.

Validation

• python -m compileall -q .
• git diff --check
• repository-wide static searches
• no full notebook reruns