docs: update README and manifest for v2.16.0 two-tier tool system

- Version badge and tool count updated (259 tools: 66 core + 193 advanced)
- New tools table showing core vs advanced split per category
- Added v2.16.0 changelog entry explaining the two-tier architecture
- New troubleshooting entry for tool visibility issue in Claude/Cowork
- Manifest updated with complete core tool list + meta-tools
- Manifest description and long_description reflect two-tier system

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