Refine structured skill tool flow

[chandra447]

Summary

• remove background skill auto-extraction so procedural skills are managed explicitly through the main skill tool flow
• add structured create/update inputs for skills (when_to_use, procedure_steps, pitfalls, verification_steps) and render valid SKILL.md sections in the tool
• tighten the tool contract and complete the edit -> update guidance cleanup while keeping the legacy edit alias working
• update docs, prompt policy text, and the source-architecture diagram to match the new inline skill flow

Testing

• npm run check
• npx tsx --test tests/tools/skill-tool.test.ts tests/handlers/prompt-context.test.ts tests/handlers/background-review.test.ts tests/store/skill-store.test.ts

Notes

• full npm test is still blocked in this environment by the existing better-sqlite3 Node ABI mismatch in unrelated SQLite-backed tests