# PAIML MCP Agent Toolkit - Feature Summary

## Overview

This document provides a comprehensive summary of all features implemented in PMAT, including those not yet documented in the main README.

## Core Features

### 1. **Multi-Protocol Support**
- **CLI**: Traditional command-line interface
- **MCP**: Model Context Protocol for AI agents
- **HTTP**: RESTful API for integrations
- **TUI**: Terminal UI for interactive use [planned]

### 2. **Language Support**
- **Rust**: Full AST analysis, borrow checker integration
- **TypeScript/JavaScript**: Complete parsing via SWC
- **Python**: AST analysis via RustPython parser
- **C/C++**: Tree-sitter based parsing with goto tracking
- **Kotlin**: Tree-sitter based parsing with coroutine support
- **Cython**: Hybrid Python/C analysis

## Analysis Features

### Code Quality Analysis

#### **Complexity Analysis** (`analyze complexity`)
- Cyclomatic complexity calculation
- Cognitive complexity metrics
- Halstead metrics
- Maintainability index
- Function-level and file-level analysis
- Top files ranking by complexity

#### **Technical Debt Gradient** (`analyze tdg`)
- Quantitative debt measurement
- Time-decay modeling
- Multi-factor analysis (complexity, design, test, docs, deps)
- Predictive modeling for future debt
- Risk level classification

#### **Dead Code Detection** (`analyze dead-code`)
- Unused function detection with AST-based reachability analysis
- Entry point detection (main functions, public APIs)
- Function call tracing and dependency graph analysis
- Unreachable code identification
- File-level aggregation with scoring
- Exit status support for CI/CD integration (`--fail-on-violation`)
- Comprehensive property testing (9 tests) and full integration (CLI, MCP, Quality Gates)

#### **SATD Detection** (`analyze satd`)
- Self-admitted technical debt identification
- Severity classification (Critical/High/Medium/Low)
- Evolution tracking over time
- Category analysis (Design/Implementation/Testing/Documentation/Performance)
- Author and team analytics

### Code Intelligence

#### **Deep Context Analysis** (`analyze deep-context`)
- Comprehensive codebase understanding
- Multi-dimensional analysis (AST, complexity, churn, dependencies)
- AI-optimized output formats
- Incremental analysis support
- Intelligent caching

#### **Dependency Analysis** (`analyze dag`)
- Dependency graph generation
- Circular dependency detection
- Module coupling analysis
- Mermaid diagram output
- GraphML export

#### **Git Churn Analysis** (`analyze churn`)
- File modification frequency
- Author contribution patterns
- Coupled file detection
- Stability indicators
- Customizable time windows

### Advanced Analysis

#### **Provability Analysis** (`analyze provability`)
- Lightweight formal verification
- Property domain analysis
- Nullability checking
- Alias analysis
- Confidence scoring

#### **Defect Prediction** (`analyze defect-prediction`)
- ML-based bug prediction
- Risk scoring by file
- Feature importance analysis
- Historical pattern recognition

#### **Name Similarity Analysis** (`analyze name-similarity`)
- Semantic naming consistency
- Identifier clustering
- Naming convention violations
- Refactoring suggestions

## Build & Quality Tools

### **Makefile Linter** (`lint-makefile`)
- 50+ built-in rules
- Syntax validation
- Portability checks
- Performance analysis
- Best practice enforcement
- SARIF output for CI/CD

### **Excellence Tracker** (`excellence-tracker`)
- Comprehensive quality metrics
- Test coverage tracking
- Type safety analysis
- Documentation coverage
- Performance metrics
- Dependency health
- Trend analysis and alerts

## Refactoring Tools

### **Emit-Refactor Engine** (`refactor`)

#### Server Mode (`refactor serve`)
- Real-time defect emission
- <5ms latency guarantee
- Lock-free ring buffer
- Continuous monitoring
- Auto-emit on threshold

#### Interactive Mode (`refactor interactive`)
- JSON-based protocol
- State machine visibility
- Checkpoint/resume support
- Agent-friendly interface
- Detailed explanations

#### Refactoring Operations
- Extract Function
- Flatten Nesting
- Replace HashMap (performance)
- Remove SATD
- Simplify Expressions

## Project Management

### **Scaffolding** (`scaffold`)
- Multi-language templates
- Project structure generation
- Best practice defaults
- Customizable templates
- Batch generation

### **Template Generation** (`generate`)
- Individual file generation
- Parameter substitution
- Template listing
- Custom template support

## Visualization & Reporting

### **Demo Mode** (`demo`)
- CLI table output
- Web interface with D3.js
- GitHub repository analysis
- Real-time visualization
- Export capabilities

### **Mermaid Generation**
- Automatic diagram creation
- Multiple diagram types
- Complexity-based filtering
- Custom styling
- SVG/PNG export

## Integration Features

### **MCP Protocol**
- Full JSON-RPC 2.0 compliance
- Tool discovery
- Resource management
- Streaming support
- Error handling

### **HTTP API**
- RESTful endpoints
- CORS support
- Health checks
- Batch operations
- WebSocket support [planned]

### **CI/CD Integration**
- GitHub Actions support
- GitLab CI templates
- Jenkins plugins [planned]
- Pre-commit hooks
- SARIF output

## Performance Features

### **Caching System**
- Three-tier cache (L1/L2/L3)
- Content-based invalidation
- Configurable TTL
- LRU eviction
- Persistent cache

### **Parallel Processing**
- Multi-core utilization
- Rayon for CPU-bound tasks
- Tokio for I/O-bound tasks
- Work-stealing scheduler

### **Incremental Analysis**
- Change detection
- Partial re-analysis
- Delta computation
- Baseline comparison

## Configuration

### **Global Configuration**
- TOML-based config files
- Environment variables
- Command-line overrides
- Per-project settings

### **Tool-Specific Configuration**
- Linter rules
- Analysis thresholds
- Cache settings
- Output formats

## Output Formats

### **Structured Formats**
- JSON (machine-readable)
- SARIF (security/CI tools)
- CSV (spreadsheets)
- XML (legacy tools)

### **Human-Readable Formats**
- Markdown (documentation)
- Plain text (terminals)
- HTML (web viewing)
- PDF (reports) [planned]

## Security Features

### **Input Validation**
- Path traversal prevention
- Command injection protection
- Resource limits
- Sandboxed execution

### **Access Control**
- Directory restrictions
- Read-only analysis
- No network access
- Audit logging

## Future Features (Roadmap)

### **In Development**
- TUI (Terminal UI) mode
- Real-time monitoring daemon
- IDE plugins (VSCode, IntelliJ)
- Cloud integration

### **Planned**
- Custom analyzer API
- Distributed analysis
- AI-powered suggestions
- Auto-fix capabilities
- Team dashboards

## Usage Examples

### Quick Start
```bash
# Install
cargo install pmat

# Basic analysis
pmat context                          # Auto-detect and analyze
pmat analyze complexity --top-files 5 # Find complex files
pmat lint-makefile Makefile          # Lint build files
pmat refactor interactive            # Start refactoring session

# Advanced usage
pmat analyze deep-context --format json --output context.json
pmat excellence-tracker --baseline baseline.json
pmat refactor serve --emit-threshold 15
```

### Integration Example
```yaml
# .github/workflows/code-quality.yml
name: Code Quality
on: [push, pull_request]

jobs:
  analyze:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Install PMAT
        run: cargo install pmat
      - name: Run Analysis
        run: |
          pmat analyze complexity --format sarif > complexity.sarif
          pmat tdg . --format json > tdg.json
          pmat lint-makefile Makefile > makefile-lint.txt
      - name: Upload Results
        uses: github/codeql-action/upload-sarif@v2
        with:
          sarif_file: complexity.sarif
```

## Support

- **Documentation**: See `/docs/features/` for detailed guides
- **Issues**: https://github.com/paiml/paiml-mcp-agent-toolkit/issues
- **Discussions**: https://github.com/paiml/paiml-mcp-agent-toolkit/issues
- **Email**: support@paiml.com