deepthinking-mcp

danielsimonjr/deepthinking-mcp

3.2

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DeepThinking MCP is a unified Model Context Protocol server that integrates sequential thinking, Shannon's systematic methodology, and mathematical reasoning with specialized support for physics and tensor mathematics.

DeepThinking MCP

TypeScript License: MIT MCP Compatible

A comprehensive Model Context Protocol (MCP) server featuring 33 reasoning modes (29 with dedicated thought types, 4 advanced runtime modes) including meta-reasoning for strategic oversight, with intelligent mode recommendation, taxonomy-based classification, enterprise security, and production-ready features for complex problem-solving, analysis, and decision-making.

📋 Latest Release: v8.3.1 - See for updates and improvements.

🎉 New in v8.3.x: Multi-instance support with file locking, dependency graph tool with unused code detection, codebase cleanup.

v8.2.x: Phase 10 ModeHandler Architecture! 7 specialized handlers with advanced validation and enhancements - Systems Archetypes detection, Socratic question framework, automatic Bayesian posterior calculation, Nash equilibria computation.

v8.0.0: ModeHandler infrastructure with Strategy pattern for mode-specific processing.

v7.5.0: All 29 modes with dedicated thought types accessible via 12 focused MCP tools.

v7.4.0: Academic Research Modes - Synthesis (literature review), Argumentation (Toulmin model), Critique (peer review), Analysis (qualitative methods).

Table of Contents

Features

  • 33 Specialized Reasoning Modes - From sequential thinking to game theory, formal logic, and meta-reasoning (29 with full thought types, 4 advanced runtime modes)
  • ModeHandler Architecture (v8.x) - Strategy pattern with 7 specialized handlers providing advanced validation and enhancements
  • Specialized Handler Enhancements - Systems Archetypes (8 patterns), Socratic Questions (6 categories), auto Bayesian posteriors, Nash equilibria
  • Academic Research Modes - Synthesis (literature review), Argumentation (Toulmin), Critique (peer review), Analysis (qualitative methods)
  • Algorithmic Reasoning - Comprehensive CLRS coverage with 100+ named algorithms, complexity analysis, design patterns
  • Historical Computing Extensions - Computability (Turing machines), Cryptanalytic (decibans), extended Game Theory (von Neumann)
  • Proof Decomposition - Break proofs into atomic statements, detect gaps, track assumption chains
  • Native SVG Export - Direct SVG generation without external tools for proof visualizations
  • Meta-Reasoning - Strategic oversight that monitors effectiveness, recommends mode switches, and assesses quality
  • Adaptive Mode Switching - Automatic evaluation-based mode switching when effectiveness drops below thresholds
  • Intelligent Mode Recommendation - Automatic mode selection based on problem characteristics
  • Taxonomy Classifier - 69 reasoning types across 12 categories for intelligent task classification (110 planned)
  • Visual Exports - Generate Mermaid diagrams, DOT graphs, ASCII art, SVG graphics, and LaTeX documents
  • Production-Ready - Search engine, templates, batch processing, caching, backup/restore
  • Enterprise Security - Input validation (Zod), rate limiting, path sanitization, PII redaction
  • High Performance - LRU caching with auto-eviction, async I/O, 4-5x validation speedups
  • Type-Safe - 100% TypeScript with zero suppressions (down from 231 baseline)
  • Repository Pattern - Clean architecture with dependency injection
  • Extensible - Plugin architecture for custom reasoning modes
  • MCP Compatible - Full integration with Model Context Protocol

Installation

NPM Package

npm install deepthinking-mcp

From Source

git clone https://github.com/danielsimonjr/deepthinking-mcp.git
cd deepthinking-mcp
npm install
npm run build

MCP Configuration

Add to your MCP settings file:

{
  "mcpServers": {
    "deepthinking": {
      "command": "npx",
      "args": ["deepthinking-mcp"]
    }
  }
}

Quick Start

MCP Tool Usage

DeepThinking MCP provides 12 focused tools for different reasoning domains:

ToolModesDescription
deepthinking_coreinductive, deductive, abductiveFundamental reasoning
deepthinking_standardsequential, shannon, hybridStandard workflow modes
deepthinking_mathematicsmathematics, physics, computabilityMath/physics/computability
deepthinking_temporaltemporalTime-based reasoning
deepthinking_probabilisticbayesian, evidentialProbabilistic reasoning
deepthinking_causalcausal, counterfactualCause-effect analysis
deepthinking_strategicgametheory, optimizationStrategic reasoning
deepthinking_analyticalanalogical, firstprinciples, metareasoning, cryptanalyticAnalytical reasoning
deepthinking_scientificscientificmethod, systemsthinking, formallogicScientific reasoning
deepthinking_engineeringengineering, algorithmicEngineering/algorithmic
deepthinking_academicsynthesis, argumentation, critique, analysisAcademic research
deepthinking_session-Session management

Example: Sequential Reasoning

{
  "tool": "deepthinking_standard",
  "arguments": {
    "mode": "sequential",
    "thought": "First, identify the main bottlenecks in the distributed system",
    "thoughtNumber": 1,
    "totalThoughts": 5,
    "nextThoughtNeeded": true
  }
}

Example: Causal Analysis

{
  "tool": "deepthinking_causal",
  "arguments": {
    "mode": "causal",
    "thought": "Analyzing the root cause of the service outage",
    "thoughtNumber": 1,
    "totalThoughts": 3,
    "nextThoughtNeeded": true,
    "causalGraph": {
      "nodes": [
        {"id": "n1", "name": "High Load", "type": "cause"},
        {"id": "n2", "name": "Memory Exhaustion", "type": "mediator"},
        {"id": "n3", "name": "Service Crash", "type": "effect"}
      ],
      "edges": [
        {"from": "n1", "to": "n2", "strength": 0.9},
        {"from": "n2", "to": "n3", "strength": 0.95}
      ]
    }
  }
}

Example: Session Export

{
  "tool": "deepthinking_session",
  "arguments": {
    "action": "export",
    "sessionId": "session-123",
    "exportFormat": "markdown"
  }
}

Reasoning Modes

The server supports 33 reasoning modes organized into categories:

  • Core Modes (5): Sequential, Shannon, Mathematics, Physics, Hybrid
  • Historical Computing (2): Computability (Turing), Cryptanalytic (Turing) - v7.2.0
  • Algorithmic (1): Algorithmic (CLRS) - v7.3.0
  • Academic Research (4): Synthesis, Argumentation, Critique, Analysis - v7.4.0
  • Advanced Runtime Modes (6): Metareasoning, Recursive, Modal, Stochastic, Constraint, Optimization
  • Fundamental Modes (3): Inductive, Deductive, Abductive
  • Experimental Modes (12): Causal, Bayesian, Counterfactual, Analogical, Temporal, Game Theory (+ von Neumann extensions), Evidential, First Principles, Systems Thinking, Scientific Method, Formal Logic, Engineering

Core Modes

Sequential

Iterative refinement with revision capabilities. Perfect for step-by-step problem solving.

mode: 'sequential'
// Use for: Debugging, algorithmic thinking, systematic analysis
Shannon

5-stage systematic problem-solving methodology (problem → constraints → model → proof → implementation).

mode: 'shannon'
// Use for: Engineering problems, system design, complex optimizations
Mathematics

Theorem proving, lemma derivation, symbolic computation with LaTeX support.

mode: 'mathematics'
// Use for: Proofs, mathematical modeling, symbolic algebra
Physics

Tensor mathematics, dimensional analysis, conservation laws, field theory.

mode: 'physics'
// Use for: Physical modeling, dimensional analysis, scientific computing
Hybrid

Intelligently combines multiple reasoning modes based on problem characteristics.

mode: 'hybrid'
// Use for: Complex multi-faceted problems requiring diverse approaches

Advanced Modes

Causal

Build causal graphs, analyze interventions and effects.

mode: 'causal'
// Use for: Impact analysis, system design, decision making
Bayesian

Probabilistic reasoning with priors, likelihoods, and evidence updates.

mode: 'bayesian'
// Use for: Risk assessment, A/B testing, uncertainty quantification
Counterfactual

Explore alternative scenarios and compare outcomes.

mode: 'counterfactual'
// Use for: Post-mortems, strategic planning, what-if analysis
Analogical

Transfer knowledge across domains by identifying structural similarities.

mode: 'analogical'
// Use for: Design patterns, innovative problem-solving, knowledge transfer

Specialized Modes

Temporal

Model events, intervals, and temporal relationships using Allen's interval algebra.

mode: 'temporal'
// Use for: Timeline analysis, scheduling, event sequencing
Game Theory

Analyze strategic interactions, compute Nash equilibria, build game trees.

mode: 'game-theory'
// Use for: Competitive analysis, mechanism design, strategic decisions
Evidential

Dempster-Shafer theory for reasoning with uncertain evidence.

mode: 'evidential'
// Use for: Sensor fusion, intelligence analysis, incomplete information
First Principles

Derive conclusions from foundational axioms using deductive reasoning.

mode: 'first-principles'
// Use for: Fundamental analysis, conceptual understanding, basic truths
Meta-Reasoning

Strategic oversight of reasoning process - monitors effectiveness, recommends mode switches, assesses quality.

mode: 'metareasoning'
// Use for: Strategy evaluation, adaptive mode switching, quality assessment
// Metrics: Effectiveness, Efficiency, Confidence, Quality (6 dimensions)
// Auto-switches at effectiveness < 0.3

See for detailed usage.

Systems Thinking

Holistic analysis of complex systems, feedback loops, and emergence.

mode: 'systems-thinking'
// Use for: Complex systems, organizational design, ecosystem analysis
Scientific Method

Hypothesis-driven experimentation with research design and statistical analysis.

mode: 'scientific-method'
// Use for: Experimental design, hypothesis testing, research
Optimization

Constraint satisfaction and optimization with decision variables.

mode: 'optimization'
// Use for: Resource allocation, scheduling, constrained optimization
Formal Logic

Rigorous logical reasoning with formal systems and proof verification.

mode: 'formal-logic'
// Use for: Proof verification, logical analysis, formal methods

Advanced Runtime Modes

Recursive

Recursive problem decomposition - break complex problems into smaller subproblems.

mode: 'recursive'
// Use for: Divide-and-conquer, tree-structured problems, recursive algorithms
Modal

Possibility and necessity reasoning using modal logic.

mode: 'modal'
// Use for: What's possible vs necessary, requirement analysis, constraint exploration
Stochastic

Probabilistic state transitions and Markov chain reasoning.

mode: 'stochastic'
// Use for: Process modeling, state machines, probabilistic sequences
Constraint

Constraint satisfaction problem solving.

mode: 'constraint'
// Use for: Scheduling, resource allocation, constraint propagation

Fundamental Modes

Inductive

Reasoning from specific observations to general principles.

mode: 'inductive'
// Use for: Pattern recognition, generalization, empirical reasoning
Deductive

Reasoning from general principles to specific conclusions.

mode: 'deductive'
// Use for: Logical proofs, applying rules, deriving conclusions
Abductive

Generate and evaluate hypotheses to explain observations.

mode: 'abductive'
// Use for: Debugging, root cause analysis, diagnostic reasoning

Historical Computing Modes (v7.2.0)

Tributes to Alan Turing and John von Neumann's foundational work.

Computability

Turing machines, decidability proofs, reductions, and diagonalization arguments.

mode: 'computability'
// Use for: Decidability analysis, algorithm limits, computational complexity
// Features: Turing machine simulation, reduction chains, halting problem analysis
Cryptanalytic

Turing's deciban evidence system from Bletchley Park.

mode: 'cryptanalytic'
// Use for: Evidence quantification, hypothesis testing, code-breaking analysis
// Features: Deciban accumulation (10 db ≈ 10:1 odds), frequency analysis, Banburismus
Extended Game Theory (v7.2.0)

Von Neumann's minimax theorem, cooperative games, and Shapley values.

mode: 'gametheory'
// Enhanced with: Minimax analysis, cooperative game theory, coalition analysis
// Use for: Zero-sum games, fair value distribution, strategic decision-making

Algorithmic Mode (v7.3.0)

Algorithmic

Comprehensive coverage of algorithms from "Introduction to Algorithms" (CLRS) with 100+ named algorithms.

mode: 'algorithmic'
// Use for: Algorithm design, complexity analysis, correctness proofs
// Features: Divide-and-conquer, dynamic programming, greedy, graph algorithms
// Coverage: Sorting, searching, graph, string, computational geometry

Academic Research Modes (v7.4.0)

Designed for PhD students and scientific paper writing.

Synthesis

Literature review and knowledge integration.

mode: 'synthesis'
// Use for: Literature reviews, theme extraction, knowledge integration
// Features: Source synthesis, pattern identification, gap analysis
Argumentation

Academic argumentation using the Toulmin model.

mode: 'argumentation'
// Use for: Building arguments, dialectical reasoning, rhetorical analysis
// Features: Toulmin model (claim, data, warrant, backing), counter-arguments
Critique

Critical analysis and peer review frameworks.

mode: 'critique'
// Use for: Peer review, methodology evaluation, evidence assessment
// Features: Systematic critique, strengths/weaknesses analysis
Analysis

Qualitative analysis methods.

mode: 'analysis'
// Use for: Thematic analysis, grounded theory, discourse analysis
// Features: Multiple qualitative analysis frameworks, coding support

Specialized Mode Handlers (v8.x)

Phase 10 introduced 7 specialized handlers with advanced validation and enhancements:

HandlerModeKey Enhancements
CausalHandlercausalValidates graph structure, detects cycles, propagates interventions
BayesianHandlerbayesianAuto-calculates posteriors from prior × likelihood, validates probability sums
GameTheoryHandlergametheoryValidates payoff matrix dimensions, computes Nash equilibria
CounterfactualHandlercounterfactualTracks world states, validates divergence points, compares outcomes
SynthesisHandlersynthesisTracks source coverage, validates theme extraction, detects contradictions
SystemsThinkingHandlersystemsthinkingDetects 8 Systems Archetypes, adds warning signs and interventions
CritiqueHandlercritique6 Socratic question categories for rigorous critical analysis
Systems Archetypes Detection

SystemsThinkingHandler automatically detects Peter Senge's 8 archetypes:

  • Fixes that Fail - Short-term fixes with unintended consequences
  • Shifting the Burden - Symptomatic vs fundamental solutions
  • Limits to Growth - Growth hitting constraints
  • Success to the Successful - Winner-take-all dynamics
  • Tragedy of the Commons - Shared resource depletion
  • Escalation - Competitive escalation spirals
  • Accidental Adversaries - Alliance deterioration
  • Growth and Underinvestment - Capacity constraints
Socratic Question Framework

CritiqueHandler uses Richard Paul's 6 categories:

  • Clarification - "What do you mean by...?"
  • Assumptions - "What are you assuming?"
  • Evidence - "What evidence supports this?"
  • Perspectives - "Are there alternative viewpoints?"
  • Implications - "What are the consequences?"
  • Meta - "Why is this question important?"

Proof Decomposition

New in v7.0.0! The proof decomposition system provides advanced mathematical reasoning capabilities:

Components

ComponentPurpose
ProofDecomposerBreaks proofs into atomic statements with dependency tracking
GapAnalyzerDetects missing steps, unjustified leaps, and implicit assumptions
AssumptionTrackerTraces conclusions back to their supporting assumptions
InconsistencyDetectorDetects circular dependencies and contradictions
MathematicsReasoningEngineIntegrated proof analysis with improvement suggestions

Features

  • Atomic Statement Types: axiom, hypothesis, definition, derived, lemma, conclusion
  • Inference Rules: algebraic_manipulation, substitution, modus_ponens, universal_instantiation, etc.
  • Gap Detection: Identify missing steps with severity levels (minor, significant, critical)
  • Rigor Levels: informal, textbook, rigorous, formal
  • Visual Export: Mermaid, DOT, ASCII, and native SVG formats

Example: Proof Analysis

{
  "tool": "deepthinking_mathematics",
  "arguments": {
    "mode": "mathematics",
    "thought": "Analyzing the proof that n² is even when n is even",
    "thoughtNumber": 1,
    "totalThoughts": 3,
    "nextThoughtNeeded": true,
    "proofDecomposition": {
      "theorem": "If n is even, then n² is even",
      "atoms": [
        {"id": "a1", "content": "n is an even integer", "type": "hypothesis"},
        {"id": "a2", "content": "n = 2k for some integer k", "type": "definition"},
        {"id": "a3", "content": "n² = 4k² = 2(2k²)", "type": "derived"},
        {"id": "a4", "content": "n² is even", "type": "conclusion"}
      ],
      "dependencies": {
        "nodes": ["a1", "a2", "a3", "a4"],
        "edges": [
          {"from": "a1", "to": "a2"},
          {"from": "a2", "to": "a3"},
          {"from": "a3", "to": "a4"}
        ]
      }
    }
  }
}

Visual Export Formats

Export proof decompositions to multiple visual formats:

// Native SVG (no external tools required)
exportProofDecomposition(decomposition, {
  format: 'svg',
  colorScheme: 'default',  // 'default' | 'pastel' | 'monochrome'
  includeMetrics: true,
  svgWidth: 1200,
  svgHeight: 800
});

// Mermaid diagram
exportProofDecomposition(decomposition, { format: 'mermaid' });

// GraphViz DOT
exportProofDecomposition(decomposition, { format: 'dot' });

// ASCII text
exportProofDecomposition(decomposition, { format: 'ascii' });

Usage Examples

Example 1: Debugging with Abductive Reasoning

// Step 1: Start with observation
{
  "tool": "deepthinking_core",
  "arguments": {
    "mode": "abductive",
    "thought": "Observed: Users report intermittent 500 errors on checkout during high traffic periods",
    "thoughtNumber": 1,
    "totalThoughts": 4,
    "nextThoughtNeeded": true,
    "observations": ["Errors occur during high traffic", "Checkout page affected", "Intermittent pattern"]
  }
}

// Step 2: Generate hypothesis
{
  "tool": "deepthinking_core",
  "arguments": {
    "sessionId": "session-from-step-1",
    "mode": "abductive",
    "thought": "Hypothesis: Database connection pool exhaustion under load",
    "thoughtNumber": 2,
    "totalThoughts": 4,
    "nextThoughtNeeded": true,
    "hypotheses": [{
      "id": "h1",
      "explanation": "Connection pool exhausted",
      "assumptions": ["Fixed pool size", "No connection recycling"],
      "predictions": ["Errors correlate with traffic spikes"],
      "score": 0.8
    }]
  }
}

Example 2: Impact Analysis with Causal Reasoning

{
  "tool": "deepthinking_causal",
  "arguments": {
    "mode": "causal",
    "thought": "Analyzing impact of increasing API rate limits on system behavior",
    "thoughtNumber": 1,
    "totalThoughts": 3,
    "nextThoughtNeeded": true,
    "causalGraph": {
      "nodes": [
        {"id": "rate_limit", "name": "Rate Limit", "type": "cause", "description": "API rate limit setting"},
        {"id": "server_load", "name": "Server Load", "type": "mediator", "description": "CPU/Memory usage"},
        {"id": "response_time", "name": "Response Time", "type": "effect", "description": "API latency"},
        {"id": "satisfaction", "name": "User Satisfaction", "type": "effect", "description": "User experience"}
      ],
      "edges": [
        {"from": "rate_limit", "to": "server_load", "strength": 0.9, "confidence": 0.85},
        {"from": "server_load", "to": "response_time", "strength": 0.85, "confidence": 0.9},
        {"from": "response_time", "to": "satisfaction", "strength": -0.7, "confidence": 0.8}
      ]
    }
  }
}

Example 3: Strategic Analysis with Game Theory

{
  "tool": "deepthinking_strategic",
  "arguments": {
    "mode": "gametheory",
    "thought": "Analyzing pricing strategy in competitive market using game theory",
    "thoughtNumber": 1,
    "totalThoughts": 3,
    "nextThoughtNeeded": true,
    "game": {
      "type": "strategic",
      "players": ["Company A", "Company B"],
      "strategies": {
        "Company A": ["premium", "competitive", "discount"],
        "Company B": ["premium", "competitive", "discount"]
      },
      "payoffMatrix": [
        [{"A": 10, "B": 10}, {"A": 5, "B": 15}, {"A": 2, "B": 12}],
        [{"A": 15, "B": 5}, {"A": 8, "B": 8}, {"A": 4, "B": 10}],
        [{"A": 12, "B": 2}, {"A": 10, "B": 4}, {"A": 6, "B": 6}]
      ]
    }
  }
}

Production Features

Note: DeepThinking MCP is an MCP server, not a library. These features are accessed through MCP tools and internal architecture. The examples below describe the internal capabilities.

Proof Decomposition (v7.0.0)

Advanced mathematical reasoning with proof analysis:

  • ProofDecomposer: Break proofs into atomic statements with dependency graphs
  • GapAnalyzer: Detect missing steps, unjustified leaps, implicit assumptions
  • AssumptionTracker: Trace conclusions to their supporting assumptions
  • InconsistencyDetector: Find circular dependencies and contradictions
  • Native SVG Export: Generate proof visualizations without external tools

Search Engine

Full-text search with faceted filtering and relevance ranking. Used internally to search across reasoning sessions by mode, tags, date ranges, and content.

Template System

Pre-built templates for common reasoning patterns, accessible through session creation.

Batch Processing

Process multiple sessions concurrently with 8 operation types:

  • export - Batch export sessions to various formats
  • import - Batch import sessions from files
  • analyze - Batch taxonomy/quality/pattern analysis
  • validate - Batch session validation
  • transform - Batch mode switching, merging, splitting
  • index - Batch search/analytics indexing
  • backup - Batch backup with compression
  • cleanup - Batch cleanup of old/incomplete sessions

Backup & Restore

Automated backup with compression and local storage, with support for multiple providers (Local, S3, GCS, Azure).

Session Comparison

Compare reasoning sessions to analyze differences and similarities with quantitative metrics.

Security & Validation

Enterprise-grade security features built into the MCP server:

  • Input Validation - Zod schemas validate all 33 mode inputs
  • Rate Limiting - Sliding window rate limiter for API protection
  • Path Sanitization - Prevents directory traversal attacks
  • PII Redaction - GDPR-compliant log sanitization

Taxonomy Classifier

Intelligent classification of reasoning tasks using 69 reasoning types across 12 categories. Use the recommend_mode action in deepthinking_session to get mode recommendations based on problem characteristics.

API Documentation

MCP Tool Interface

All reasoning is done through MCP tools. Each tool accepts arguments and returns JSON responses.

Common Parameters (all thinking tools)
ParameterTypeRequiredDescription
sessionIdstringNoSession ID (auto-created if omitted)
thoughtstringYesThe reasoning content
thoughtNumberintegerYesCurrent thought number (1-based)
totalThoughtsintegerYesEstimated total thoughts
nextThoughtNeededbooleanYesWhether more reasoning needed
modestringYesThe reasoning mode
Session Actions (deepthinking_session)
ActionParametersDescription
summarizesessionIdGenerate session summary
exportsessionId, exportFormatExport to format (json, markdown, latex, html, jupyter, mermaid, dot, ascii, svg)
get_sessionsessionIdGet session details
switch_modesessionId, newModeSwitch reasoning mode
recommend_modeproblemType or problemCharacteristicsGet mode recommendations
Example Response
{
  "sessionId": "session-abc123",
  "thoughtId": "thought-xyz789",
  "thoughtNumber": 1,
  "mode": "sequential",
  "nextThoughtNeeded": true,
  "sessionComplete": false,
  "totalThoughts": 3
}

For architecture details, see .

Project Stats

MetricValue
TypeScript Files197
Lines of Code~80,336
Test Files39
Passing Tests1046+
Thinking Modes33 (29 with thought types)
Specialized Handlers7
MCP Tools12 focused + 1 legacy
Export Formats8 (including native SVG)
Visual Exporters35+ mode-specific files
Reasoning Types69 (110 planned)
Modules16
Total Exports1033 (448 re-exports)

Architecture

The codebase is organized into 16 modules with clean separation of concerns. See for the complete dependency graph.

Core Structure

src/
├── index.ts           # MCP server entry point (tool handlers)
├── types/             # Type definitions including 33 mode types
│   ├── core.ts        # ThinkingMode enum, Thought union type
│   └── modes/         # One file per reasoning mode (26 files)
├── services/          # Business logic layer
│   ├── ThoughtFactory.ts    # Thought creation with handler integration
│   ├── ExportService.ts     # Multi-format export handling
│   └── ModeRouter.ts        # Mode switching and recommendations
├── session/           # SessionManager, persistence, storage
├── modes/             # ModeHandler architecture (v8.x)
│   ├── handlers/            # 7 specialized handlers
│   │   ├── CausalHandler.ts
│   │   ├── BayesianHandler.ts
│   │   ├── GameTheoryHandler.ts
│   │   ├── CounterfactualHandler.ts
│   │   ├── SynthesisHandler.ts
│   │   ├── SystemsThinkingHandler.ts
│   │   └── CritiqueHandler.ts
│   └── base/                # ModeHandler interface, registry
├── proof/             # Proof decomposition system (v7.0.0)
│   ├── decomposer.ts        # ProofDecomposer class
│   ├── gap-analyzer.ts      # GapAnalyzer class
│   └── assumption-tracker.ts # AssumptionTracker class
├── reasoning/         # Reasoning engines (v7.0.0)
│   └── inconsistency-detector.ts  # InconsistencyDetector class
└── tools/             # MCP tool definitions and schemas

ModeHandler Architecture (v8.x)

Phase 10 introduced the ModeHandler pattern (Strategy pattern) for mode-specific processing:

// Handler interface
interface ModeHandler {
  mode: ThinkingMode;
  validate(input: ThinkingToolInput): ValidationResult;
  enhance(thought: Thought, context: SessionContext): Thought;
  getSuggestions(thought: Thought): string[];
}

// Registry manages all handlers
const registry = ModeHandlerRegistry.getInstance();
registry.hasSpecializedHandler('causal'); // true for 7 modes

Benefits:

  • Specialized validation logic per mode
  • Automatic enhancements (posteriors, equilibria, archetypes)
  • Mode-specific suggestions and warnings
  • Clean separation from ThoughtFactory switch statement

Feature Modules

src/
├── taxonomy/          # 69 reasoning types, classifier, suggestion engine
│   ├── reasoning-types.ts   # Full taxonomy definitions
│   ├── classifier.ts        # Task classification
│   └── suggestion-engine.ts # Mode recommendations
├── export/            # Visual and document exporters
│   ├── visual/        # 21 mode-specific visual exporters + native SVG
│   │   ├── proof-decomposition.ts  # Proof visualization (v7.0.0)
│   │   └── [19 mode exporters]     # Mermaid, DOT, ASCII, SVG
│   └── latex.ts       # LaTeX document generation
├── search/            # Full-text search with faceted filtering
├── batch/             # Batch processing (8 operations)
├── backup/            # Backup manager with provider abstraction
├── cache/             # LRU/LFU/FIFO caching strategies
├── rate-limit/        # Sliding window rate limiter
├── validation/        # Zod schemas (31+ mode validators)
├── comparison/        # Session comparison & diff generation
├── templates/         # Session templates with usage tracking
├── analytics/         # Analytics engine and dashboard
├── webhooks/          # Event-driven webhook system
├── collaboration/     # Annotations and conflict resolution
└── ml/                # Pattern recognition & recommendations

Security Features

Security is built into multiple modules:

  • validation/ - Input validation with Zod schemas for all 33 modes
  • utils/sanitization.ts - Path sanitization & traversal prevention
  • utils/log-sanitizer.ts - PII redaction for GDPR compliance
  • rate-limit/ - Per-key rate limiting with sliding windows
  • utils/errors.ts - Standardized error hierarchy with context

Contributing

We welcome contributions! Please open an issue or pull request on GitHub.

Adding New Reasoning Modes

Want to add a new reasoning mode? We've made it easy:

📖

This guide includes:

  • Step-by-step instructions for all 8 required files
  • Template files in templates/mode-scaffolding/
  • Code examples and common patterns
  • Complete checklist to ensure nothing is missed
  • Testing guidelines

Quick Start:

# Copy template files
cp templates/mode-scaffolding/example-mode.type.ts src/types/modes/yourmode.ts
cp templates/mode-scaffolding/example-mode.validator.ts src/validation/validators/modes/yourmode.ts

# Follow the guide
cat docs/ADDING_NEW_MODE.md

Development Setup

# Clone repository
git clone https://github.com/danielsimonjr/deepthinking-mcp.git
cd deepthinking-mcp

# Install dependencies
npm install

# Run tests
npm test

# Run type checking
npm run typecheck

# Build
npm run build

Running Tests

# Run all tests
npm test

# Run specific test file
npm test -- path/to/test.test.ts

# Run with coverage
npm run test:coverage

License

MIT License - see file for details.

Acknowledgments

  • Built on the Model Context Protocol
  • Inspired by research in cognitive science and AI reasoning
  • Community contributions from researchers and practitioners

Support


Made with ❤️ by the DeepThinking MCP team