docs: add architecture audit with scored assessment and refactoring roadmap

[SatoryKono]

Motivation

• Provide a reproducible baseline architecture audit covering src/bioetl, tests/architecture and active documentation, so future changes can be measured against a concrete scorecard.
• Surface high‑risk areas and an actionable, prioritized refactoring roadmap to reduce technical debt and improve maintainability.

Description

• Add a new audit document docs/99-archive/reports/architecture-audit-2026-03-03/00-audit-baseline.md containing an executive summary, verification log, a 10‑category weighted scorecard and an integrated project score.
• Documented findings using RFC‑2119 severity levels (Critical/Moderate/Informational) and provided concrete recommendations (RF-001..RF-006) with module‑level actions, risks, mitigations and done‑criteria.
• Included suggested KPIs and tests to monitor architecture drift and an expected score uplift model after implementing key refactors.

Testing

• Ran the full architecture suite with uv run python -m pytest tests/architecture/ -q, which is mostly green but reports 1 failing test tests/architecture/test_documentation_sync.py::test_no_legacy_kebab_pipeline_ids_in_active_docs due to docs/exports/full-documentation-no-plans-reports-skills.merged.md.
• Ran focused suites uv run python -m pytest tests/architecture/test_layer_dependencies.py tests/architecture/test_di_compliance.py tests/architecture/test_naming_conventions.py tests/architecture/test_medallion_invariants.py -q and uv run python -m pytest tests/architecture/test_code_metrics.py -q, all of which passed.
• Pre-commit checks surfaced unrelated baseline issues (missing pip-audit executable, markdown formatting adjustment and VCR filename policy violations) which do not block the audit content but should be addressed separately.

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Codex Task