New-CI: Update Documentation

[andrew-m-leonard]

Title: Document Phase 2 implementation

Description:
Update all documentation to reflect the complete pipeline with all stages.

Tasks:

• Update CI_AGNOSTIC_ARCHITECTURE.md
  • Add all 7 new stages
  • Update stage flow diagrams
• Update stage-specific documentation
  • Document each new stage
  • Add usage examples
  • Include troubleshooting
• Update ARTIFACT_DIRECTORY_PATTERN.md
  • Add examples for new stages
• Create Phase 2 completion report
  • Summary of work completed
  • Lessons learned
  • Known issues
• Update README files
  • Add complete stage list
  • Update examples

Acceptance Criteria:

• All documentation updated
• Examples provided for all stages
• Phase 2 report complete
• Team reviewed
• [ ]