Update documentation for monorepo structure

Update CONTRIBUTING.md, AGENTS.md, and CHANGES.md to reflect the new
monorepo organization with unified versioning across all packages.

- Update repository structure documentation
- Change commands to use monorepo-aware task runners
- Add information about database adapter packages
- Document unified versioning approach

[ci skip]

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