docs: add architecture audit report and prioritized refactoring roadmap

[SatoryKono]

Motivation

• Stabilize and document the current architectural baseline for BioETL by producing an evidence-backed audit covering layering, hexagonal contracts, Medallion invariants and maintainability risks.
• Surface concrete, reproducible findings (including failing architecture test) to unblock CI quality gates and to prioritize refactor work.
• Provide a prioritized, low-risk refactoring roadmap and measurable metrics to guide incremental improvements and to raise the project quality score.

Description

• Added a new architecture audit report at docs/99-archive/reports/architecture-audit-2026-03-03.md containing a 10-category weighted scoring model, an overall score (7.87/10), and interpretation.
• Documented evidence-backed findings (layer boundaries, large orchestration modules, high Any usage, and a failing doc-sync test caused by legacy kebab-case pipeline IDs in a generated export).
• Delivered a prioritized refactoring plan RF-001..RF-007 with concrete module-level actions, goals, risks, mitigations and clear "Definition of Done" criteria.
• Proposed a set of architecture-quality metrics and mapped expected improvements to the integral score after key refactoring steps.

Testing

• Ran architecture test suite with uv run python -m pytest tests/architecture/ -q, which surfaced one failing test test_no_legacy_kebab_pipeline_ids_in_active_docs caused by legacy pipeline IDs in docs/exports/full-documentation-no-plans-reports-skills.merged.md.
• Ran static typing check with uv run python -m mypy --strict src/bioetl/, which completed successfully with no issues.
• Collected supporting static inspections (file size, import scans, occurrence counts) referenced in the report and included the verification command list for re-running the checks.

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Codex Task