Re-scope transformation plan to protocol-only focus

- Clarify repository scope: protocols vs implementations
- Create TRANSFORMATION_PLAN_V2.md focused on protocol definitions
- Create TECHNICAL_RECOMMENDATIONS_V2.md with protocol design examples
- Update IMPLEMENTATION_CHECKLIST.md with clear Part A/B separation
- Update EVALUATION_SUMMARY.md with architecture clarification
- Archive original mixed-scope documents as backups

Co-authored-by: hotlong <50353452+hotlong@users.noreply.github.com>

Author: Copilot