docs: Reorganize and clean up documentation structure

[ryanwclark1]

Comprehensive documentation cleanup and reorganization:

Added:

• docs/README.md - Complete documentation index with:
  • Table of contents organized by category
  • Quick start guide for documentation
  • Finding information by topic and task
  • Documentation standards
  • Recent updates tracking

Reorganized:

• docs/guides/ - Core documentation (testing, troubleshooting, Docker, scripts)

  • testing-guide.md - Test framework and running tests
  • troubleshooting.md - Common issues and solutions
  • docker-testing.md - Docker testing modes and usage
  • script-reference.md - Complete script documentation

• docs/setup/ - Tool setup guides

  • serena-setup.md - Serena coding agent setup
  • context7-setup.md - Context7 documentation setup
  • qwen-setup.md - Qwen CLI with Ollama

• docs/mcp/ - MCP server documentation

  • mcp-server-status.md - Server status tracking
  • claude-to-gemini-mcp-migration.md - Gemini MCP usage
  • github-mcp-setup.md - GitHub integration
  • memorybank-mcp-setup.md - Memory persistence
  • MCP-MIGRATION-SUMMARY.md - Historical migration notes

Updated:

• MCP-MIGRATION-SUMMARY.md - Added note that migration is complete and scripts are archived
• README.md - Updated all doc references to new paths
• CONTRIBUTING.md - Updated doc path references

Benefits:

• Clear organization by purpose (guides/setup/mcp)
• Easier to find relevant documentation
• Comprehensive index for navigation
• Better maintainability
• Clearer separation of concerns

All internal links updated to reflect new structure.