docs: update TOOLS.md to reflect unified project/workspace tools

- Updated overview to show 61 tools in 12 workflow groups
- Added Key Changes section highlighting v1.11+ consolidation
- Reorganized tool listings by actual workflow directories
- Added clear XOR parameter patterns documentation
- Included common workflows with updated tool names
- Added version history section
- Removed obsolete separate project/workspace tool listings
- Aligned with actual runtime tool counts from tools-cli.js

Author: cameroncooke