docs(phase3): complete WP6.5 - COMMANDS.md comprehensive reference

- Add complete documentation for all 8 slash commands
- /blueprint-init: Interactive setup wizard (5-step guided process)
- /plan-to-issues: Convert Claude plans to GitHub issues (max 10 tasks)
- /commit-smart: Smart commit with quality checks + secret scanning
- /create-pr: PR creation with auto-linking and validation
- /review-pr: Comprehensive Claude-powered code review
- /release: Production release management with changelog generation
- /sync-status: Manual status synchronization for issues/board
- /kill-switch: Emergency workflow disable mechanism

Each command includes:
- Purpose and when to use
- Usage examples (basic and advanced scenarios)
- Step-by-step workflow explanation
- Configuration options
- Comprehensive troubleshooting section
- Best practices (DO/DON'T format)
- Integration with workflows

Additional sections:
- Command system overview
- Quick reference table
- Command integration with workflows
- Common patterns (4 real-world scenarios)
- General troubleshooting
- Best practices for all commands

3,078 lines, 65KB comprehensive reference
Follows same structure as WORKFLOWS.md

Phase 3 Progress: 40% complete (6/15 deliverables)
- ✅ README.md, QUICK_START.md, COMPLETE_SETUP.md, TROUBLESHOOTING.md, WORKFLOWS.md, COMMANDS.md
- ⏳ CUSTOMIZATION.md (next), ARCHITECTURE.md
- ⏳ Setup automation (3 scripts)
- ⏳ Testing & examples (4 deliverables)

Total Phase 3 documented: ~8,600 lines

🤖 Generated with Claude Code (https://claude.com/claude-code)

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

Author: alirezarezvani