Update README and bootstrap script

- Enhanced README with comprehensive governance documentation
  - Added emphasis on security governance and credentials/secrets handling
  - Expanded documentation governance section explaining AI agent instructions
  - Added complete structure with all required sections from CONTEXT.md
  - Included architecture overview, installation, usage, and troubleshooting
- Updated bootstrap-template-structure.sh to reflect current repository structure
  - Added missing scripts/ directory
  - Added LICENSE, .gitignore, .pymarkdown.json files
  - Fixed CI workflow filename to use .yaml extension
  - Added docs/ci-and-precommit.md and scripts/run-precommit.sh

Author: christopherpaquin