Clean up repository root: move visualizations and summaries to docs/

[Copilot]

Repository root contained 13 non-essential files (7 PNG visualizations, 6 markdown summaries). Moved to logical subdirectories under docs/.

Changes

Directory structure:

• Created docs/figures/ for PNG outputs (7 files)
• Created docs/summaries/ for analysis documents (5 files)
• Moved CI_SETUP_COMPLETE.md to docs/

Updated references:

• Example scripts now output to docs/figures/ instead of root
• README repository structure section rewritten to reflect actual layout
• Internal file references updated in READING_GUIDE.md and IMPLEMENTATION_SUMMARY.md
• CONTRIBUTING.md structure section updated

Result

Before: root/ (13 non-essential files)
After:  root/ (essential files only)
        docs/
        ├── figures/       # visualizations
        ├── summaries/     # analysis docs
        └── ...

All example scripts verified working with new paths.

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