SIM-ONE

Phase 22: Paper2Agent Integration - TODO List

Status: In Progress Started: 2025-01-10 Target Completion: 2025-01-13

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Priority 1: Naming & Documentation (Foundation)

Naming Clarification

• TODO-001: Add mcp_server naming clarification notice to root README.md
  • Insert warning after badges, before “Core Philosophy” section
  • Use standard warning template from implementation plan
• TODO-002: Add mcp_server naming clarification notice to code/README.md
  • Insert warning after title, before “Project Overview”
  • Use standard warning template
• TODO-003: Create code/mcp_server/README.md with detailed naming explanation
  • Full explanation of historic naming
  • Clarify NOT Model Context Protocol
  • Link to migration plan

Migration Planning

• TODO-004: Create MIGRATION_PLAN.md with future renaming strategy
  • Document mcp_server → agent_core transition roadmap
  • Symlink strategy for backward compatibility
  • URL preservation approach
  • Timeline (6-12 month window)
• TODO-005: Create code/mcp_server/FUTURE_NAMING.md for internal transition plan
  • Internal reference for new naming conventions
  • Docstring update strategy
  • Gradual transition milestones

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Priority 2: Five Laws Governance Tools (Core Functionality)

Five Laws Validator (HIGHEST PRIORITY)

• TODO-006: Create code/tools/lib/ directory for shared libraries

• TODO-007: Create code/tools/lib/five_laws_evaluator.py - unified evaluation logic
  • Import all 5 law validators from governance/five_laws_validator/
  • Create unified interface for evaluating any text
  • Aggregate scores from all laws
  • Generate compliance report with recommendations
  • Export evaluate_text() function
• TODO-008: Create code/tools/run_five_laws_validator.py (HIGHEST PRIORITY)
  • CLI wrapper for Five Laws evaluation
  • Support –text, –file, and stdin input modes
  • JSON output with compliance scores
  • Include MCP_TOOL_ENTRYPOINT marker
  • Comprehensive docstring with usage examples

Governance Orchestration Tools

• TODO-009: Create code/tools/run_governed_response.py - governed response generator
  • Accept user prompt via CLI
  • Execute through protocol stack (REP, ESL, VVP)
  • Apply Five Laws validation automatically
  • Return governed response + compliance report
  • Support –protocols flag to select which protocols to use
  • Support –min-compliance threshold
• TODO-010: Create code/tools/run_cognitive_workflow.py - multi-step orchestrator
  • Support predefined workflows: reason_validate_govern, analyze_govern, full_governance
  • Accept –workflow flag to select workflow type
  • Accept –input for text/file input
  • Chain multiple protocols in sequence
  • Generate comprehensive execution trace
  • Output final result + Five Laws compliance

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Priority 3: Individual Protocol Wrappers

Core Protocols (Priority 3A)

• TODO-011: Create code/tools/run_rep_tool.py - Reasoning & Explanation Protocol wrapper
  • CLI wrapper for REP protocol
  • Support multiple reasoning types (deductive, inductive, abductive, etc.)
  • Accept –facts, –rules, –reasoning-type flags
  • JSON output with reasoning chain
• TODO-012: Create code/tools/run_esl_tool.py - Emotional State Layer Protocol wrapper
  • CLI wrapper for ESL protocol
  • Accept –user-input flag or stdin
  • Output emotional analysis with detected emotions
  • Include valence, intensity, confidence scores
• TODO-013: Create code/tools/run_vvp_tool.py - Validation & Verification Protocol wrapper
  • CLI wrapper for VVP protocol
  • Accept –rules flag for validation rules
  • Output validation status and reason
  • Support JSON input/output
• TODO-014: Create code/tools/run_ccp_tool.py - Cognitive Control Protocol wrapper
  • CLI wrapper for CCP protocol
  • Accept workflow definition via JSON
  • Output coordination results and metrics
  • Support async execution
• TODO-015: Create code/tools/run_sep_tool.py - Semantic Encoding Protocol wrapper
  • CLI wrapper for SEP protocol (if exists, check first)
  • Accept text for semantic encoding
  • Output encoded representation
• TODO-016: Create code/tools/run_mtp_tool.py - Memory Tagging Protocol wrapper
  • CLI wrapper for MTP protocol
  • Accept entity extraction input
  • Output tagged entities and patterns

Additional Protocols (Priority 3B)

• TODO-017: Create code/tools/run_eep_tool.py - Energy Efficiency Protocol wrapper
  • CLI wrapper for EEP protocol (check if exists)
  • Measure energy/resource usage
  • Output efficiency metrics
• TODO-018: Create code/tools/run_hip_tool.py - Human Interaction Protocol wrapper
  • CLI wrapper for HIP protocol
  • Handle human interaction patterns
  • Output interaction analysis
• TODO-019: Create code/tools/run_sp_tool.py - Security Protocol wrapper
  • CLI wrapper for SP protocol (check if exists)
  • Security validation and checks
  • Output security assessment
• TODO-020: Create code/tools/run_pocp_tool.py - Protocol Orchestration wrapper
  • CLI wrapper for POCP (check if exists)
  • Orchestrate multiple protocols
  • Output orchestration results

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Priority 4: Workflow Wrappers

• TODO-021: Create code/tools/run_writing_team_workflow.py - multi-agent writing workflow
  • Execute Ideator → Drafter → Critic → Revisor → Summarizer workflow
  • Accept writing prompt/topic
  • Output final document + workflow trace
  • Apply Five Laws validation to final output
• TODO-022: Create code/tools/run_reasoning_workflow.py - reasoning pipeline workflow
  • Execute full reasoning pipeline
  • REP → VVP → Five Laws validation
  • Output reasoning chain + compliance report
• TODO-023: Create code/tools/run_analysis_workflow.py - analysis workflow
  • Execute analysis-focused workflow
  • ESL + REP → VVP → Five Laws
  • Output comprehensive analysis + governance report

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Priority 5: Discovery & Manifest System

• TODO-024: Create code/tools/tools_manifest.json - complete tool discovery manifest
  • JSON structure with all tools categorized
  • Include governance_tools, orchestration_tools, protocol_tools, workflow_tools
  • Specify input/output for each tool
  • Mark composable tools
  • Include version and framework info
• TODO-025: Create PAPER2AGENT_INTEGRATION.md - comprehensive integration guide
  • Overview of Paper2Agent + SIM-ONE integration
  • Quick Start section with one-line examples
  • Five Laws Governance section with detailed examples
  • Protocol Composition patterns
  • Example Scenarios (5+ scenarios)
  • Tool Discovery guide
  • API Reference for all tools
• TODO-026: Create code/tools/README.md - tool catalog and usage documentation
  • Complete catalog of all available tools
  • Usage examples for each wrapper
  • Protocol composition patterns
  • Input/output specifications for each tool
  • Error handling guide
  • Troubleshooting section

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Priority 6: Main Documentation Updates

• TODO-027: Update root README.md with Tool Entrypoints section
  • Add section after Case Studies: “🛠️ Tool Entrypoints for AI Agent Integration”
  • Include Five Laws Governance subsection
  • Include Available Tools list
  • Link to PAPER2AGENT_INTEGRATION.md, tools/README.md, tools_manifest.json
• TODO-028: Update code/README.md with standalone tools usage section
  • Add section after Quick Start: “Using SIM-ONE Protocols as Standalone Tools”
  • Include Individual Protocol Tools subsection
  • Include Governance Tools subsection
  • Include Example Usage with code blocks
  • Link to tools/README.md

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Priority 7: Examples & Use Cases

• TODO-029: Create examples/paper2agent_usage_examples.sh - example scripts
  • Example 1: Validate external AI response
  • Example 2: Generate governed response
  • Example 3: Multi-step workflow
  • Example 4: Protocol composition/chaining
  • Make executable (chmod +x)
• TODO-030: Create examples/USE_CASES.md - use case scenarios documentation
  • Scenario 1: Paper2Agent Self-Governance
  • Scenario 2: Multi-Agent Validation
  • Scenario 3: Governed Content Generation
  • Scenario 4: Reasoning Chain Validation
  • Scenario 5: Emotional Intelligence Analysis
  • Include code examples for each scenario

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Priority 8: Testing & Validation

• TODO-031: Create code/tests/test_tool_wrappers.py - wrapper testing suite
  • Test each wrapper executes successfully
  • Test CLI argument parsing
  • Test JSON output validity
  • Test error handling
  • Test stdin/file input modes
  • Test protocol integration correctness
• TODO-032: Create code/tests/test_five_laws_tools.py - Five Laws validator tests
  • Test validate compliant response (expect high scores)
  • Test validate non-compliant response (expect low scores)
  • Test detect truth violations
  • Test detect governance failures
  • Test recommendations are actionable
  • Test edge cases (empty input, invalid JSON, etc.)
• TODO-033: Create code/tests/test_paper2agent_integration.py - integration tests
  • Test manifest file is valid JSON
  • Test all listed tools exist in filesystem
  • Test all tools are executable
  • Test tool discovery mechanism
  • Test protocol composition
  • Test end-to-end workflow
• TODO-034: Create code/tests/test_backward_compatibility.py - compatibility tests
  • Test existing API endpoints still work
  • Test FastAPI server functions unchanged
  • Test all original workflows execute correctly
  • Test no breaking changes in core protocols
  • Regression test suite

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Priority 9: Contributing Guidelines

• TODO-035: Update CONTRIBUTING.md with tool wrapper creation guidelines
  • Add “Creating Tool Wrappers” section
  • Document wrapper conventions and standards
  • Provide step-by-step guide for new wrappers
  • Include code template
  • Reference implementation plan

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Priority 10: Final Validation & Deployment

• TODO-036: Run all tests and validate backward compatibility
  • Execute pytest on all test files
  • Verify all tests pass
  • Check code coverage
  • Validate no regressions
• TODO-037: Final validation: Paper2Agent tool discovery and Five Laws validator
  • Manually test Paper2Agent can discover tools via manifest
  • Test Five Laws validator with multiple sample responses
  • Validate all tool wrappers work standalone
  • Test protocol composition chains
  • Verify documentation is complete and accurate
• TODO-038: Create release notes and update changelog
  • Document all new features
  • List all new tool wrappers
  • Explain naming clarification strategy
  • Note backward compatibility maintained

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Completion Checklist

Documentation Complete

• All 8 documentation files created/updated
• Naming clarifications in all READMEs
• Migration plan documented
• Integration guide complete

Tools Complete

• Five Laws validator working
• All core protocol wrappers functional
• Workflow orchestrators operational
• Manifest file accurate and complete

Testing Complete

• All unit tests passing
• Integration tests passing
• Backward compatibility verified
• Zero regressions detected

Quality Assurance

• All tools follow standard template
• JSON output validated
• Error handling robust
• Documentation accurate
• Examples tested and working

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Total Tasks: 38 Estimated Effort: 20-25 hours Target Completion: 2025-01-13

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Notes & Observations

Use this section to track progress notes, blockers, or observations during implementation

• Note: Check which protocols actually exist before creating wrappers (SEP, EEP, SP may need verification)
• Note: Ensure async handling is correct in all wrappers that use async protocols
• Note: Validate Five Laws validator modules exist and are importable
• Note: Consider adding –verbose flag to all wrappers for debugging

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Document Version: 1.0 Created: 2025-01-10 Status: Active - In Progress

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