Update Python tooling to 3.13 and parse scripts at boundaries

[acgetchell]

Summary

Update Python support tooling to Python 3.13 and run a parse-don't-validate cleanup pass over the Python scripts.

Current State

The repository currently supports Python 3.12+ for development scripts. The scripts are typed and checked, but follow-up cleanup should make boundary parsing and validated domain objects more explicit.

Proposed Changes

• Require Python 3.13 for the Python development/tooling environment.
• Update Python version metadata, CI setup, lockfile/tooling configuration, and docs.
• Review CLI args, TOML/JSON/CSV parsing, subprocess output, filesystem paths, and report-generation inputs.
• Parse raw inputs at boundaries into typed, validated objects before computation.
• Prefer stdlib typing tools such as TypedDict, dataclass(frozen=True, slots=True), Enum, Literal, NewType, and TypeIs where they clarify invariants.
• Avoid adding heavier validation dependencies unless they are already justified.

Benefits

• Gives all Python tooling a modern 3.13 typing baseline.
• Reduces raw dict[str, Any], string-mode, and optional-field drift.
• Makes Python scripts easier to share or adapt across related crates.

Implementation Notes

• Keep repository-specific script entrypoints local.
• Extract only genuinely reusable helpers after the cleanup proves stable.
• Validate with the repository's Python checks and full CI.