Musubix MCP Server
MUSUBIX MCP Server - Model Context Protocol Server for AI Platforms
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MUSUBIX - Neuro-Symbolic AI Integration System
Next-generation AI Coding System powered by Git-Native Knowledge Integration
v3.8.1 - 25 packages, 107 MCP tools, 5,738+ tests
Overview
MUSUBIX is an innovative AI coding system that integrates Neural (LLM) and Symbolic (Knowledge Graph) reasoning. It combines MUSUBI SDD methodology with Git-native knowledge management to support high-quality software development.
๐ v3.8 Highlights
- 25 packages - Comprehensive neuro-symbolic AI development toolkit
- 107 MCP tools - SDD, Pattern, Knowledge, Policy, Decision, Synthesis, Workflow, Agent, Skill tools
- 5,738+ tests - All passing across 25 packages
- 13 Agent Skills - Claude Code integration for SDD workflow automation
- Monorepo optimizations - Unified
tsc -bbuilds, standardized dependencies, Prettier formatting - Deep Research - AI-driven iterative research system with 6 integration modules
- Git-Native Knowledge - File-based knowledge graph in
.knowledge/(zero dependencies) - Codegraph - Code structure analysis supporting 16 languages
Features
- ๐ง Neuro-Symbolic Integration - Fusion of LLM creativity and knowledge graph precision
- ๐ Git-Native Knowledge - File-based knowledge graph management (v3.0.0)
- ๐ DFG/CFG Analysis - Data flow and control flow graph extraction for TypeScript/JavaScript
- ๐งฎ Lean 4 Integration - Formal theorem proving with EARS-to-Lean conversion
- ๐ Library Learning - DreamCoder-style hierarchical abstraction and pattern compression
- ๐ Neural Search - Neural-guided program synthesis with beam search
- โ๏ธ Program Synthesis - DSL-based PBE synthesis with witness functions
- ๐ Symbolic Reasoning - Formal verification, hallucination detection, constitution enforcement
- ๐ EARS Requirements Analysis - Conversion and validation from natural language to formal requirements
- ๐จ Design Pattern Recommendations - Context-based C4 model and ADR generation
- โ Test-Driven Development - Quality assurance through Test-First principles
- ๐ Complete Traceability - Tracking from requirements to code
- ๐ก๏ธ Security Analysis - Vulnerability scanning, secret detection, taint analysis (v1.8.0)
- ๐ฌ Formal Verification - Z3 SMT solver integration, Hoare triple verification (v1.7.5)
- ๐ฅ๏ธ Interactive REPL - Command completion, history, session variables (v1.6.0)
- ๐ฎ Advanced Inference - OWL 2 RL reasoning and Datalog evaluation (v1.4.5)
Architecture
flowchart TB
subgraph MUSUBIX["MUSUBIX System v3.8"]
subgraph Core["Core"]
CLI["musubix CLI"]
CoreLib["@nahisaho/musubix-core"]
Knowledge["@musubix/knowledge"]
end
subgraph Agent["Agent Layer"]
MCP["@nahisaho/musubix-mcp-server\n107 tools"]
Orchestrator["Agent Orchestrator"]
Skills["Skill Manager"]
end
subgraph Learning["Learning"]
WakeSleep["Wake-Sleep"]
DeepResearch["Deep Research"]
end
subgraph Security["Verification"]
SecPkg["Security Analysis"]
FormalVerify["Formal Verification"]
end
CLI --> CoreLib
CoreLib <--> MCP
MCP <--> Orchestrator
Orchestrator <--> Skills
CoreLib --> Knowledge
CoreLib --> Learning
CoreLib --> Security
end
Project Structure
| Path | Description |
|---|---|
packages/core/ | Core library (249 modules) |
packages/core/auth/ | Authentication & Authorization |
packages/core/cli/ | CLI Interface |
packages/core/codegen/ | Code Generation & Analysis |
packages/core/design/ | Design Patterns & C4 Models |
packages/core/error/ | Error Handling |
packages/core/explanation/ | Explanation Generation & Visualization |
packages/core/learning/ | Self-Learning & Pattern Extraction |
packages/core/requirements/ | Requirements Analysis & Decomposition |
packages/core/symbolic/ | Symbolic Reasoning |
packages/core/traceability/ | Traceability |
packages/core/types/ | Type Definitions |
packages/core/utils/ | Utilities |
packages/core/validators/ | EARS Validation |
packages/mcp-server/ | MCP Server (107 tools, 5 prompts) |
packages/security/ | Security Analysis |
packages/formal-verify/ | Formal Verification |
packages/pattern-mcp/ | Pattern Learning |
packages/ontology-mcp/ | Ontology Engine |
packages/wake-sleep/ | Wake-Sleep Learning |
packages/sdd-ontology/ | SDD Ontology |
packages/dfg/ | DFG/CFG Extraction - Data Flow Analysis |
packages/lean/ | Lean 4 Integration - Theorem Proving |
packages/library-learner/ | Library Learning - DreamCoder-style |
packages/neural-search/ | Neural Search - Guided Synthesis |
packages/synthesis/ | Program Synthesis - DSL/PBE |
packages/agent-orchestrator/ | Agent Orchestrator - Sub-agent Distribution |
packages/workflow-engine/ | Workflow Engine - 5-Phase Control |
packages/skill-manager/ | Skill Manager - Dynamic Skill Loading |
packages/codegraph/ | Codegraph - Code Structure Analysis (16 languages) |
packages/expert-delegation/ | Expert Delegation - 7 AI Expert Types |
packages/deep-research/ | Deep Research - AI-driven Iterative Research |
packages/assistant-axis/ | Assistant Axis - Multimodal Integration |
packages/musubi/ | Musubi - AI Summarization |
packages/knowledge/ | Knowledge Store - Git-friendly JSON Graph |
packages/policy/ | Policy Engine - 9 Constitutional Articles |
packages/decisions/ | Decision Records - ADR Management |
steering/ | Project Memory |
storage/ | Specifications & Artifacts |
templates/ | Templates |
docs/ | Documentation |
Requirements
- Node.js >= 20.0.0
- npm >= 10.0.0
- TypeScript >= 5.3
Installation
npm/npx (Recommended)
# Global installation
npm install -g musubix
# Run directly with npx
npx musubix init
npx musubix --help
# Start MCP Server
npx @nahisaho/musubix-mcp-server
npx musubix-mcp --transport stdio
Scoped Packages
# Install individual packages
npm install @nahisaho/musubix-core
npm install @nahisaho/musubix-mcp-server
npm install @nahisaho/musubix-security
npm install @nahisaho/musubix-formal-verify
npm install @musubix/knowledge
npm install @musubix/decisions
npm install @musubix/policy
Build from Source
git clone https://github.com/nahisaho/MUSUBIX.git
cd MUSUBIX
npm install
npm run build
Development
# Build
npm run build
# Run tests
npm test
# Lint
npm run lint
# Type check
npm run type-check
Key Features
Requirements Definition (Article II Compliant)
- EARS Validation: Easy Approach to Requirements Syntax pattern validation
- Interactive Q&A Hearing: Dialogue-based requirements gathering
- Requirements Decomposition: Breaking down large requirements into implementation units
- Related Requirements Search: Automatic detection of similar and dependent requirements
Design Generation (Article III Compliant)
- C4 Model Generation: Context/Container/Component/Code diagrams
- ADR Generation: Architecture Decision Records
- Pattern Detection: Automatic detection and recommendation of design patterns
- SOLID Validation: SOLID principle compliance checking
Code Generation & Verification
- Static Analysis: Quality metrics and complexity calculation
- Security Scanning: Vulnerability detection
- Test Generation: Unit and integration test generation
- Coverage Reporting: Test coverage measurement
MCP Server
Provides 107 tools and 5 prompts covering SDD, Pattern, Knowledge, Policy, Decision, Synthesis, Workflow, Agent, and Skill management:
# Start MCP Server
npx @nahisaho/musubix-mcp-server
Documentation
| Document | Description |
|---|---|
| Requirements Specification | EARS format functional/non-functional requirements |
| Design Document | C4 model and ADR-based design |
| Task Definition | 56 tasks sprint plan |
| API Reference | Public API specification |
| Symbolic Integration | Neuro-Symbolic requirements (27 requirements) |
Symbolic Reasoning Module (v1.2.0)
The new symbolic reasoning module provides:
Phase 1: Foundation
- SemanticCodeFilterPipeline - LLM output semantic validation
- HallucinationDetector - Undefined symbol/invalid import detection
- ConstitutionRuleRegistry - 9 Constitution articles enforcement
- ConfidenceEstimator - AST complexity, requirement coverage scoring
- ConfidenceBasedRouter - Confidence-based routing decisions
- ErrorHandler - Graceful degradation
Phase 2: Formal Verification
- EarsToFormalSpecConverter - EARS โ SMT-LIB conversion
- VerificationConditionGenerator - Verification condition (VC) generation
- Z3Adapter - Z3 SMT solver integration
- SecurityScanner - OWASP patterns, secret detection
Phase 3: Advanced Features
- CandidateRanker - Multi-criteria candidate scoring
- ResultBlender - Neural/Symbolic result integration (3 strategies)
- ExtensibleRuleConfig - YAML/JSON rule configuration
- AuditLogger - SHA-256 hash-chain tamper detection
- PerformanceBudget - Step-level budgets, SLO metrics
- QualityGateValidator - Automated quality gate validation
Wake-Sleep Learning Cycle (v1.3.0)
Continuous learning system based on the Wake-Sleep algorithm:
| Phase | Processing |
|---|---|
| Wake | Code observation โ Pattern extraction โ Knowledge graph update |
| Sleep | Pattern consolidation โ Similar pattern compression โ Memory optimization |
Key Components
- WakeSleepCycle - Learning cycle orchestration
- PatternLibrary - Persistent pattern storage management
- PatternOntologyBridge - Pattern โ Ontology bidirectional conversion
- N3Store - RDF/OWL-based knowledge graph storage
New MCP Tools (7 tools)
pattern_extract- Extract patterns from codepattern_compress- Abstraction and compression of patternspattern_store- Save to pattern librarypattern_query- Search and retrieve patternspattern_consolidate- Consolidate similar patternsontology_query- Query ontology graphontology_infer- Execute ontology-based inference
Advanced Inference (v1.4.5)
OWL 2 RL profile reasoning and Datalog evaluation engine:
Inference Components
- OWL2RLReasoner - OWL 2 RL profile compliant inference (20+ built-in rules)
- DatalogEngine - Stratified Datalog evaluation with negation support
- InferenceExplainer - Human-readable inference explanation generator
- ProgressReporter - Real-time progress feedback (500ms interval)
OWL 2 RL Built-in Rules
| Category | Rules | Description |
|---|---|---|
| Class Axioms | cax-sco, cax-eqc | Subclass, Equivalent class inference |
| Property | prp-dom, prp-rng | Domain, Range inference |
| Property Characteristics | prp-symp, prp-trp, prp-inv | Symmetric, Transitive, Inverse |
| Equality | eq-ref, eq-sym, eq-trans | sameAs inference |
Explanation Formats
text- Plain text explanationmarkdown- Markdown formathtml- HTML format with escaping
Constitutional Articles (9 Articles)
MUSUBIX adheres to the following 9 constitutional articles:
- Specification First - Requirements before implementation
- Design Before Code - Design before coding
- Single Source of Truth - Project memory is authoritative
- Traceability - Tracking from requirements to code
- Incremental Progress - Small, frequent deliveries
- Decision Documentation - Decisions recorded as ADRs
- Quality Gates - Phase validation required
- User-Centric - Document user value
- Continuous Learning - Retrospectives and improvements
License
MIT License - See LICENSE for details
Author
nahisaho
Changelog
See CHANGELOG.md
Document ID: README Version: 3.8.1 Last Updated: 2026-02-08
