refactor(wiki): retire legacy JSON cache

[fishmingyu]

Summary

Retire the one-release AgentWiki JSON compatibility path after the v0.2.3 migration window. WikiStore is now the only persistence boundary; an AgentWiki without an injected store is memory-only.

Closes #749.

Changes

• Remove legacy agentwiki_*.json discovery, parsing, adoption, writing, file locks, and provenance markers.
• Make Wiki cache quality and coverage audits store-only; bump the coverage report to schema v2 with database-only storage accounting.
• Preserve SQLite entry identities, schema, existing rows, the WikiStore protocol, and the exact eight-symbol codenib.storage facade.
• Update Web, CLI, prewarm, benchmark, tests, operating docs, and durable roadmaps for the retired path.

Type of Change

• Bug fix
• New feature
• Breaking change
• Documentation update
• Refactoring
• Performance improvement
• Tests

Testing

• Tests pass locally

• Added new tests for the changes

• pytest -q test/wiki/test_agent_wiki.py test/wiki/test_cache_audit.py test/wiki/test_quality.py test/web/test_app_runtime.py --tb=short (251 passed)

• pytest -q test/wiki/test_store_contract.py test/wiki/test_sqlite_store.py test/test_storage_api.py test/wiki/test_prewarm.py --tb=short (68 passed)

• pytest -q test/scripts/test_benchmark_demo_wiki.py test/test_cli.py --tb=short (90 passed)

• Full local unit tier excluding test/sandbox/test_docker.py (6876 passed, 35 skipped, 190 deselected); the unfiltered run reached 3395 passed before the environment-only /usr/bin/docker absence stopped it.

• Black, isort (--profile black), flake8, compileall, and git diff --check pass for the changed surface.

Checklist

• My code follows the project's style guidelines
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• My changes generate no new warnings
• Any dependent changes have been merged and published

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-05T20:11:01.123198Z	be0b86f	PR opened

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