docs: organize repository knowledge for agents

[ZimoLiao]

Summary

ScholarAIO's agent-facing docs now have a stable repository knowledge system instead of routing durable specs, plans, audits, and validation evidence through a broad development bucket. Agents can start at docs/DESIGN.md, follow plan and quality indexes, and land in explicit design, execution, reference, generated, product-spec, or validation areas.

• Added a repository knowledge map, plan map, quality scorecard, and per-section indexes for agent navigation.
• Relocated runtime layout specs, upgrade plans, audits, and validation reports into role-specific directories while updating entry docs, README files, MkDocs nav, and the agent reference.
• Updated documentation tests so the new knowledge system and current runtime-doc paths are protected instead of relying on the old docs/development/ layout.

Test Plan

• python -m pytest tests/test_agent_entry_docs.py tests/test_repository_layout.py -q -p no:cacheprovider (149 passed)
• python -m mkdocs build --strict (exit 0; Material for MkDocs prints its upstream MkDocs 2.0 notice, and the build completes)
• python -m ruff check tests/test_agent_entry_docs.py tests/test_repository_layout.py
• python -m ruff format --check tests/test_agent_entry_docs.py tests/test_repository_layout.py
• git diff --cached --check

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