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Documentation Index

Last Updated: 2026-02-10 Total Files: 693+ markdown files Purpose: Comprehensive index of all documentation in the repository

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Active Documentation

Core Documentation

Document Purpose Last Updated Status
README.md Project overview 2026-02-10 ✅ Active
AGENTS.md Agent operations playbook 2025-12-10 ✅ Active
CONTRIBUTING.md Contribution guidelines 2026-02-10 ✅ Active
SECURITY.md Security policy 2026-02-10 ✅ Active
CODE_OF_CONDUCT.md Community standards 2026-02-10 ✅ Active
GOVERNANCE.md Governance model 2026-02-10 ✅ Active

Recent Additions (2025-12-11)

Document Size Purpose
COMPREHENSIVE_GAP_ANALYSIS.md 15.3KB Gap analysis with priority matrix
PR_FINAL_SUMMARY.md 10.6KB PR summary with metrics
CONTRIBUTOR_ONBOARDING.md 12.3KB Onboarding guide
ARCHITECTURE_BLUEPRINT.md 32KB Comprehensive architecture reference

Agent Infrastructure (64KB+)

Document Size Category
agents/prompts/debugging/test-failure-debugging.md 4.8KB Debugging
agents/prompts/debugging/resolve-merge-conflicts.md 6.3KB Debugging
agents/prompts/debugging/performance-optimization.md 7.0KB Debugging
agents/prompts/debugging/security-remediation.md 8.6KB Debugging
agents/prompts/audit/run-full-audit.md - Audit
agents/prompts/audit/check-regressions.md - Audit
agents/prompts/deployment/pre-release-deployment.md - Deployment
agents/prompts/documentation/generate-wiki.md - Documentation
agents/prompts/organization/repository-cleanup.md - Organization
agents/prompts/self-healing/feedback-loop.md - Self-Healing

Archived Documentation

Historical Documents (archive/historical_docs_20251210/)

Status: Archived as of 2025-12-10 Reason: Information preserved in more recent documents or no longer relevant Count: 50+ documents

Category Count Examples
Status Updates 15+ STATUS_UPDATE_AUDIT_REPORT.md, WORK_SUMMARY.md
Implementation Reports 10+ IMPLEMENTATION_COMPLETE.md, MSP_IMPLEMENTATION_SUMMARY.md
Phase Completions 8+ PHASE_6_INTEGRATION_COMPLETE.md, PHASE_C_SUMMARY.md
Gap Analyses 5+ GAP_REMEDIATION_STATUS.md, MLOPS_GAP_ANALYSIS_AND_ROADMAP.md
Achievement Reports 5+ ACHIEVEMENT_99_PERCENT.md, FINAL_STATUS_100_PERCENT.md

Full Index: See workbench/INDEX.md

Removed Documents (archive/removed/)

Status: Removed from active use Count: 10+ documents Examples: - Codex_Questions.md - STATUS_UPDATE (various dates) - CODEBASE_AUDIT (historical versions)

Technical Documentation

Architecture

Document Purpose Diagrams
ARCHITECTURE_BLUEPRINT.md Comprehensive architecture reference Yes (Mermaid)
agents/prompts/ARCHITECTURE.md System architecture diagrams Yes (Mermaid)
agents/ORCHESTRATION.md Physics-inspired orchestration Yes

API Documentation

Document Purpose
agents/prompts/API_MODEL.md API model documentation
agents/codex_client/README.md Codex client API

Configuration

Document Purpose
.codex/docs/README.md Codex environment setup
training/config.py Training configuration (code)
pyproject.toml Project configuration

Guides and Tutorials

User Guides

Guide Audience Updated
CONTRIBUTOR_ONBOARDING.md New contributors 2025-12-11
MCP_DEVELOPER_GUIDE.md MCP developers 2026-02-10
USAGE_GUIDE.md End users 2026-02-10

Agent Guides

Guide Purpose Updated
AGENTS.md Comprehensive agent guide 2025-12-10
agents/TOKENIZED_WORKFLOWS.md Workflow tokens 2026-02-10
agents/prompts/README.md Prompts library 2025-12-11

Integration Guides

Guide Focus
HAR_INTEGRATION_PLAN.md HAR file integration
COPILOT_PROMPT_100_PERCENT.md Copilot integration
MCP_100_PERCENT_ROADMAP.md MCP integration roadmap

Status Reports

Active Reports

Report Purpose Date
COMPREHENSIVE_GAP_ANALYSIS.md Current gaps and priorities 2025-12-11
PR_FINAL_SUMMARY.md Latest PR summary 2025-12-11
codex_gap_registry.yaml Gap tracking (YAML) 2025-12-11

Audit Reports

Report Focus Location
Audit Artifacts Capability tracking audit_artifacts/
Reports Generated reports reports/
Stub Analysis Code stubs reports/stub_analysis.md

Architecture and Design

Design Documents

Document Focus Diagrams
ARCHITECTURE_BLUEPRINT.md System architecture Yes
LEVEL_4_MLOPS_ASSESSMENT.md MLOps maturity No
T1_SOLUTION.md T1 solution design No

Implementation Plans

Plan Status Location
HAR Integration Planned HAR_INTEGRATION_PLAN.md
MCP Roadmap Complete MCP_100_PERCENT_ROADMAP.md
Gap Remediation Complete COMPREHENSIVE_GAP_ANALYSIS.md

Documentation by Topic

MLOps and Training

  • LEVEL_4_MLOPS_ASSESSMENT.md - MLOps maturity assessment
  • training/ - Training documentation
  • audit_artifacts/ - Audit results
  • MATURITY_REMAINING_WORK.md - Maturity improvements

Testing and Quality

  • tests/ - Test documentation
  • reports/stub_analysis.md - Stub analysis
  • .codex/ - Quality checks
  • COMPREHENSIVE_GAP_ANALYSIS.md - Gap analysis

Security and Compliance

  • SECURITY.md - Security policy
  • security_allowlist.json - Approved exceptions
  • agents/prompts/debugging/security-remediation.md - Security guide
  • .bandit.yaml - Bandit configuration

Deployment and Operations

  • deploy/ - Deployment manifests
  • Dockerfile* - Container images
  • docker-compose.yml - Local orchestration
  • .github/workflows/ - CI/CD (gated)

AI Agent Integration

  • agents/ - Agent infrastructure
  • agents/prompts/ - Prompt library
  • AGENTS.md - Agent operations
  • agents/TOKENIZED_WORKFLOWS.md - Workflow tokens

Documentation Statistics

By Category

Category Count Percentage
Active Documentation ~100 14%
Archived Documentation ~50 7%
Agent Prompts ~10 1%
Test Documentation ~500 72%
Other ~33 5%

By Status

Status Count Notes
✅ Active ~600 Current and maintained
📦 Archived ~50 Preserved for reference
❌ Removed ~10 Obsolete, in archive/removed/
🆕 Recent (< 1 phase) ~10 Added in recent PRs

By Size

Size Range Count Examples
< 1KB ~300 Small test docs, stubs
1-10KB ~300 Standard documentation
10-50KB ~80 Comprehensive guides
> 50KB ~13 Major reference documents

Finding Documentation

By Task

I want to...

By Audience

I am a...

Maintenance Guidelines

For Contributors

Adding New Documentation: 1. Create file in appropriate directory 2. Add entry to this index 3. Follow naming conventions (lowercase-with-hyphens or UPPERCASE_WITH_UNDERSCORES) 4. Include metadata (date, author, purpose) 5. Link from related documents

Updating Documentation: 1. Update the document 2. Update "Last Updated" metadata 3. Update this index if location/status changes 4. Notify relevant stakeholders

Archiving Documentation: 1. Move to appropriate archive/ subdirectory 2. Update this index with archived status 3. Add redirect in original location if applicable 4. Update dependent documents

For AI Agents

Finding Documentation: 

from pathlib import Path

# List all markdown files
docs = list(Path('.').rglob('*.md'))

# Filter by category
active_docs = [d for d in docs if 'archive' not in str(d)]
archived_docs = [d for d in docs if 'archive' in str(d)]

# Search by topic
def find_docs(topic):
    return [d for d in docs if topic.lower() in d.name.lower()]

Using Index Programmatically: - Parse this markdown file - Extract links and metadata - Build documentation graph - Identify gaps or inconsistencies

  • Repository: https://github.com/Aries-Serpent/codex
  • Issues: https://github.com/Aries-Serpent/codex/issues
  • Pull Requests: https://github.com/Aries-Serpent/codex/pulls
  • Wiki: (Generate via agents/prompts/documentation/generate-wiki.md)

Internal Tools

  • Workflow Navigator: agents/workflow_navigator.py
  • Audit Runner: scripts/space_traversal/audit_runner.py
  • Documentation Generator: agents/prompts/documentation/

Changelog

Date Change Impact
2025-12-11 Created comprehensive index Initial version
2025-12-11 Added architecture blueprint 32KB new doc
2025-12-11 Added debugging guides 26KB new docs
2025-12-11 Added contributor onboarding 12KB new doc
2025-12-10 Archived historical documents 50+ files moved

Index Version: 1.0.0 Maintainer: Repository owners Last Full Audit: 2025-12-11 Next Review: 2026-01-11 (quarterly)