Refactor repository structure: remove outdated documentation and reorganize files

- Deleted REORGANIZATION_INDEX.md, REORGANIZATION_PROPOSAL.md, REORGANIZATION_QUICKREF.md, REORGANIZATION_SUMMARY.md, REORGANIZATION_VISUAL.md as part of the reorganization effort.
- Removed toolkit/README.md as it is no longer needed in the new structure.
- The changes aim to improve discoverability and reduce cognitive load by clearly separating concerns within the repository.

Author: Coderrob