refactor(guide): restructure guide/ into thematic subdirectories

Reorganize 22 guide files from a flat directory into 5 thematic subdirs:
- core/ (architecture, methodologies, known-issues, claude-code-releases, visual-reference)
- security/ (security-hardening, sandbox-isolation, sandbox-native, production-safety, data-privacy)
- ecosystem/ (ai-ecosystem, mcp-servers-ecosystem, third-party-tools, remarkable-ai)
- roles/ (ai-roles, adoption-approaches, learning-with-ai, agent-evaluation)
- ops/ (devops-sre, observability, ai-traceability)

All internal links updated across ~50 files (ultimate-guide.md, workflows/,
diagrams/, README.md, docs/, tools/, examples/, machine-readable/).

Also: merge search-tools-cheatsheet.md into cheatsheet.md, rewrite guide/README.md
with H2 grouped sections, update CLAUDE.md repository structure.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

guide/workflows/iterative-refinement.md

@@ -635,4 +635,4 @@ Being honest about what doesn't work yet, so you don't waste time reinventing so
 - [exploration-workflow.md](./exploration-workflow.md) — Explore alternatives before iterating
 - [tdd-with-claude.md](./tdd-with-claude.md) — TDD is iterative refinement with tests
 - [plan-driven.md](./plan-driven.md) — Plan before iterating
-- [../methodologies.md](../methodologies.md) — Iterative Loops methodology
+- [../core/methodologies.md](../core/methodologies.md) — Iterative Loops methodology