feat: close tree review remediation

[FuqingZh]

Summary

• align README, architecture, and testing contracts with metadata v2 and current noun-terminal APIs
• replace repository-written versions with SCM-derived release identity and separate nightly, tag-build, and GitHub Release publication boundaries
• make UniProt pipe normalization mandatory only on declared caller-owned UniProt-capable boundaries
• harden GO endpoint validation, KEGG publication identity, snapshot capability errors, and tidy resource identity

Verification

• BIOEXTRACT_TEST_THREADS=1 pdm run check — 956 passed
• clean throwaway tagged checkout: build, strict identity verification, and twine check
• sdist-to-wheel rebuild without Git metadata
• exact-wheel fresh install and publication metadata readback
• independent final review found no P0/P1 issue

Release boundary

This PR prepares final 0.8.0. Tag creation, GitHub Release publication, protected-environment approval, and PyPI readback occur only after exact-head CI and merge. It does not publish database snapshots, write CephFS, activate catalogs, or delete artifacts.

[chatgpt-codex-connector]

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