chore: comprehensive repository cleanup and documentation consolidation

- Remove 40+ obsolete files (Sprint 2 coordination, old versions, agent prompts)
- Archive completion reports to archive/completion-reports/
- Archive technical debt reports to archive/reports/
- Move development guides to docs/development/
- Delete 43 merged/stale git branches (keep only main)
- Clean up 18 old worktrees
- Remove build artifacts (github.com/, coverage.out, test outputs)
- 77% reduction in root directory clutter (48 → 11 markdown files)

New documentation:
- PROJECT-STATUS.md: Single source of truth for implementation status
- CODEBASE-ANALYSIS-2025-10-13.md: Deep repository analysis (563 lines)
- CLEANUP-SUMMARY-2025-10-13.md: Complete cleanup record

Updated documentation:
- README.md: Accurate Phase 3 status (60% complete) with status indicators
- STATUS.md: Honest implementation status and feature tracking
- STRATEGIC-PLAN.md: Current phase progress and remaining work
- .gitignore: Prevent future build artifact commits

Code formatting:
- internal/sandbox/command_validator.go: Align inline comments consistently

Key discoveries:
- Phase 3 is 60% complete (not 100% as previously claimed)
- Kubernetes support and 9 advanced agents implemented
- Real-time events and complete REST API not yet implemented
- OpenAPI specification missing

See CLEANUP-SUMMARY-2025-10-13.md for full details.