Harden MetaInformAnt package and RNA release lane

[docxology]

Summary

Harden the MetaInformAnt integration lane around the published Amalgkit v0.16.33 contract, project-owned RNA execution state, reproducible documentation, package quality gates, and nested release boundaries. This PR remains draft and must not be merged as a scientific-completion claim.

Current commits

• Parent: 63ea3a1 (agent/publish-metainformant-full-20260802)
• BeeWAS: dd70e59 (agent/publish-apis-gwas-20260802)
• Hymenoptera Amalgkit: 2069381d (agent/publish-hymenoptera-amalgkit-20260802)
• Upstream: Amalgkit v0.16.33, source 8dfb4e005209ca24867431a8bfd116f441ebc54e

Changes

• Authoritative matrix --python setup with explicit recreation, test skipping, no implicit NCBI contact persistence, and read-only Amalgkit capability verification.
• Blocking CI quality/security gates; hosted Safety runs from a neutral directory with interpreter safe-path isolation. macOS fast jobs use the core/scientific setup path without the incompatible optional louvain/igraph source build; Ubuntu retains full Amalgkit validation.
• Hash-bound RNA resume, lock, SRA-environment, provenance, quantification, cleanup, and readiness contracts.
• Synchronized active docs, API anchors, generated references, Cursor skills, legacy import facades, and optional-dependency test guards.
• Published reachable nested gitlinks; no nested contents edited from the parent.

Validation

• Parent env -u VIRTUAL_ENV uv run pytest -q: 7683 passed, 8 skipped in 554.58s.
• 27 Hymenoptera configs/docs valid; 167 Cursor skills match; core docs 232/232 with 0 issues.
• 3270 links across 1312 Markdown files; 0 broken internal/external links.
• Black, isort, flake8, Bandit (0 medium/high), Safety (0 vulnerabilities), uv lock --check, and git diff --check pass.
• Python 3.11/3.12 disposable setup smoke passes. BeeWAS guarded validation and source-provenance verification pass; only the intentionally excluded parent tmp/ artifact is warned.
• Hosted PR checks: 18 successful, 0 failing, 0 pending.

Campaign boundary

The live RNA campaign was not interrupted or modified. It remains acquisition-bound and incomplete; no partial cohort is promoted as a complete scientific result or biological inference. The parent tmp/ runtime artifact remains intentionally untracked and excluded. No merge is requested.

[github-actions]

Test Results

31 tests  +31   31 ✅ +31   45s ⏱️ +45s
 1 suites + 1    0 💤 ± 0 
 1 files   + 1    0 ❌ ± 0 

Results for commit 63ea3a1. ± Comparison against base commit 311574f.

♻️ This comment has been updated with latest results.