# Autonomy Module - Speculative Execution (Sandboxed)

**Last Updated:** December 17, 2025  
**Version:** v2.2.0+  
**Status:** Stable

## Overview

The autonomy module provides tools for testing proposed code changes in isolated sandbox environments before applying them to the main codebase. This enables "try before you apply" workflows that minimize risk of breaking changes.

## Features

### Core Capabilities

- **Isolated Sandbox Execution**: Creates temporary project copy with full isolation
- **Resource Limits**: Enforces CPU, memory, and disk limits
- **Network Blocking**: Disables network access by default
- **Filesystem Isolation**: Changes never affect main codebase
- **Multi-Mode Support**: Process-level or container-level isolation
- **Side Effect Detection**: Monitors for unintended side effects

### Execution Modes

1. **Process Mode** (default): Uses subprocess with resource limits
2. **Container Mode**: Full Docker container isolation (requires Docker)

## Quick Start

```python
from code_scalpel.autonomy import SandboxExecutor, FileChange

# Initialize executor
executor = SandboxExecutor(
    isolation_level="process",  # or "container"
    network_enabled=False,
    max_memory_mb=512,
    max_cpu_seconds=60
)

# Define changes to test
changes = [
    FileChange(
        relative_path="src/module.py",
        operation="modify",
        new_content="def fixed_func():\n    return 42\n"
    )
]

# Test changes in sandbox
result = executor.execute_with_changes(
    project_path="/path/to/project",
    changes=changes,
    test_command="pytest",
    lint_command="ruff check",
    build_command="python -m build"
)

# Check results
if result.success:
    print("[COMPLETE] Safe to apply changes")
else:
    print("[FAILED] Changes introduce failures")
```

## API Reference

### SandboxExecutor

Main class for executing code changes in isolated environments.

**Constructor:**
```python
SandboxExecutor(
    isolation_level: str = "process",  # "process" or "container"
    network_enabled: bool = False,
    max_memory_mb: int = 512,
    max_cpu_seconds: int = 60,
    max_disk_mb: int = 100
)
```

**Methods:**
- `execute_with_changes()`: Apply changes and run tests in sandbox

### FileChange

Represents a file modification to apply in sandbox.

```python
FileChange(
    relative_path: str,      # Path relative to project root
    operation: str,          # "create", "modify", or "delete"
    new_content: str | None  # New file content (for create/modify)
)
```

### SandboxResult

Result of sandbox execution.

**Attributes:**
- `success: bool` - Overall success status
- `build_success: bool` - Build command success
- `test_results: list[ExecutionTestResult]` - Test execution results
- `lint_results: list[LintResult]` - Linter findings
- `side_effects_detected: bool` - Side effect detection status
- `execution_time_ms: int` - Total execution time
- `stdout: str` - Standard output
- `stderr: str` - Standard error

## Security Guarantees

The sandbox provides multiple layers of security:

1. **Filesystem Isolation**: All changes occur in temporary directory
2. **Network Blocking**: Network access disabled by default (configurable)
3. **Resource Limits**: CPU, memory, and disk quotas enforced
4. **Process Isolation**: Subprocesses cannot affect parent
5. **Side Effect Detection**: Monitors for blocked operations

## Examples

See `examples/sandbox_example.py` for a complete working example.

## Testing

Run tests:
```bash
pytest tests/test_sandbox.py -v
```

Coverage: 100% (32 tests, all passing)

## Change Tags

All code includes `[20251217_FEATURE]` tags indicating the implementation date and type.

## Integration

The autonomy module integrates with:
- Project analysis tools (project_crawler.py)
- Security analysis (policy module)
- Symbolic execution tools
- MCP server (future)

## Known Limitations

1. **Container Mode**: Requires Docker installation
2. **Resource Limits**: Linux/Unix only (Windows has limited support)
3. **Side Effect Detection**: Best-effort monitoring
4. **Test Parsing**: Currently simple pattern matching (can be enhanced)

## Future Enhancements

Planned for v3.0.0 "Autonomy" (Phase 2):
- Sandbox executor with Docker container support
- Error-to-diff engine for intelligent fix suggestions
- Mutation testing gate to prevent hollow fixes
- Fix loop with supervised error correction
- Audit trail for all autonomous operations
- Integration with external frameworks (AutoGen, CrewAI, LangGraph)
- Advanced policy engine with DSL support

See Development Roadmap section for complete task breakdown (69 TODOs across Phase 2-3)

---

## Data Flow

### Input (FROM)
```
User Request / Claude / Copilot
    ↓
MCP Server (mcp_server.py)
    ↓
Autonomy Engine
    ↓ (file path, analysis options)
Source Code & Policies
```

### Processing (WITHIN)
```
AutonomyEngine.execute()
    ↓
Policy Validation (PolicyEngine)
    ├─ Check rules against request
    ├─ Determine approval requirements
    └─ Set constraints & limits
    ↓
Agent Selection
    ├─ Determine which agents needed
    ├─ Set execution order
    └─ Configure agent parameters
    ↓
Orchestration
    ├─ Sequential execution
    ├─ Parallel execution
    ├─ Conditional branching
    └─ Human-in-the-loop gates
    ↓
Agents (SecurityAgent, CodeReviewAgent, etc.)
    ├─ Execute OODA loops
    ├─ Call MCP tools
    └─ Produce findings
    ↓
Result Synthesis
    ├─ Aggregate findings
    ├─ Apply policies
    └─ Prepare recommendations
```

### Output (TO)
```
Orchestrated Analysis Results
    ├─ Security findings (from SecurityAgent)
    ├─ Quality metrics (from CodeReviewAgent)
    ├─ Refactoring suggestions (from RefactoringAgent)
    ├─ Test coverage gaps (from TestingAgent)
    ├─ Documentation issues (from DocumentationAgent)
    └─ Project metrics (from MetricsAgent)
    ↓
Framework Integrations (integrations/)
    ├─ AutoGen (team conversations)
    ├─ CrewAI (crew-based workflows)
    └─ LangGraph (DAG workflows)
    ↓
User / Claude / Copilot
```

---

## Development Roadmap

### Phase 1: Core Orchestration (Complete ✅)
- [x] Basic agent orchestration
- [x] Sequential workflow execution
- [x] Parallel workflow support
- [x] Policy engine implementation
- [x] Rule-based decision making
- [x] Human approval gates

### Phase 2: Sandbox & Error Handling (In Progress 🔄)

#### Sandbox Executor Enhancements (10 TODOs)
- [ ] Implement Docker container execution
- [ ] Add resource limit enforcement (CPU, memory, disk)
- [ ] Implement side effect detection
- [ ] Add test result parsing and categorization
- [ ] Support multiple test frameworks (pytest, unittest, jest, etc.)
- [ ] Result caching for repeated executions
- [ ] Incremental test execution (only changed tests)
- [ ] Parallel test execution
- [ ] Integration with error-to-diff system
- [ ] Performance profiling hooks

#### Error-to-Diff Engine (15 TODOs)
- [ ] Multi-language error parsing (Python, JS, TS, Java, Go, Rust)
- [ ] Pattern-based fix generation
- [ ] Confidence scoring for fixes
- [ ] Alternative fix suggestions
- [ ] Diff format generation (unified diff)
- [ ] ML-based fix ranking
- [ ] Context-aware suggestions
- [ ] Learning from applied fixes
- [ ] Framework-specific error handling
- [ ] Semantic code analysis
- [ ] AST-based fix generation
- [ ] Fix validation before returning
- [ ] Error context extraction
- [ ] Error prioritization
- [ ] Error chaining support (errors caused by other errors)

#### Fix Loop Improvements (11 TODOs)
- [ ] Implement error pattern learning
- [ ] Add similar error detection (avoid redundant fixes)
- [ ] Support custom escalation strategies
- [ ] Add fix quality metrics
- [ ] Implement result caching
- [ ] ML-based fix quality prediction
- [ ] Intelligent retry strategies
- [ ] Parallel fix attempt exploration
- [ ] Integration with mutation gate
- [ ] Feedback loop for learning
- [ ] Support for user-guided fixes

#### Mutation Test Gate (11 TODOs)
- [ ] Implement additional mutation types (logic inversions, boundary mutations)
- [ ] Add mutation impact visualization
- [ ] Support custom mutation rules
- [ ] Implement mutation caching
- [ ] Add mutation filtering (skip trivial mutations)
- [ ] ML-based mutation relevance scoring
- [ ] Adaptive mutation generation
- [ ] Integration with test coverage analysis
- [ ] Generate weak test detection report
- [ ] Suggest test improvements
- [ ] Support mutation score trending

#### Autonomy Engine Coordination (11 TODOs)
- [ ] Add agent composition and coordination
- [ ] Implement result caching across operations
- [ ] Add operation sequencing logic
- [ ] Support conditional branching
- [ ] Implement rollback mechanisms
- [ ] ML-based decision making
- [ ] Intelligent resource allocation
- [ ] Cross-agent communication
- [ ] Advanced policy evaluation
- [ ] Integration with external frameworks (AutoGen, CrewAI)
- [ ] Continuous monitoring and adjustment

#### Audit Trail Enhancement (11 TODOs)
- [ ] Implement advanced querying (filters, aggregations)
- [ ] Add audit trail compression
- [ ] Support database backend
- [ ] Implement audit trail rotation
- [ ] Add performance metrics collection
- [ ] Anomaly detection in audit trail
- [ ] Integration with SIEM systems
- [ ] Compliance report generation
- [ ] Audit trail analytics
- [ ] Integration with external audit systems
- [ ] Real-time alerting

### Phase 3: Intelligent Autonomy (Future)
- [ ] Machine learning policy optimization
- [ ] Agent performance learning
- [ ] Anomaly detection in results
- [ ] Cost optimization (API calls, compute)
- [ ] Security incident response automation
- [ ] Performance tuning automation
- [ ] Dependency update automation
- [ ] Documentation synchronization
- [ ] Test suite maintenance automation
- [ ] Technical debt tracking & remediation

## Contributing

When adding features:
1. Add comprehensive tests (maintain 100% coverage)
2. Use `[YYYYMMDD_TYPE]` change tags
3. Follow existing code style (black + ruff)
4. Update this README

## License

Part of Code Scalpel, MIT License.

## Tier-Based Feature Roadmap (v3.0.0+) - [20251224_FEATURE]

### Core Autonomy Module (75 TODOs - __init__.py)

#### COMMUNITY Tier - Core Autonomy (25 items)
- [ ] Implement graceful degradation for unsupported languages
- [ ] Add telemetry collection for fix success rates
- [ ] Create comprehensive error classification database
- [ ] Implement caching for parsed error patterns
- [ ] Add multi-language error message normalization
- [ ] Create fix confidence scoring algorithm
- [ ] Implement error context window extraction
- [ ] Add support for error chains (nested exceptions)
- [ ] Create fix applicability filters
- [ ] Implement error clustering for pattern detection
- [ ] Add structured logging for all operations
- [ ] Create integration test harness
- [ ] Implement graceful fallback for missing parsers
- [ ] Add performance monitoring hooks
- [ ] Create comprehensive type hints
- [ ] Implement input validation for all entry points
- [ ] Add detailed docstrings with examples
- [ ] Create architecture documentation
- [ ] Implement factory methods for component creation
- [ ] Add support for custom error handlers
- [ ] Create configuration loader for autonomy settings
- [ ] Implement dependency injection framework
- [ ] Add health check endpoints
- [ ] Create versioning scheme for API stability
- [ ] Implement feature flag system

#### PRO Tier - Advanced Integration (25 items)
- [ ] Add ML-based fix ranking and prioritization
- [ ] Implement distributed fix caching (Redis backend)
- [ ] Create performance benchmarking suite
- [ ] Add cost estimation for operations
- [ ] Implement advanced error de-duplication
- [ ] Create feedback loop for fix quality
- [ ] Add A/B testing framework for fix strategies
- [ ] Implement real-time anomaly detection
- [ ] Create fix suggestion export to external systems
- [ ] Add integration with VCS systems (Git/SVN)
- [ ] Implement parallel fix generation
- [ ] Create advanced audit trail analytics
- [ ] Add fix composition (combining multiple fixes)
- [ ] Implement context-aware fix filtering
- [ ] Create fix dependency resolution
- [ ] Add progressive rollout capabilities
- [ ] Implement cost-benefit analysis for fixes
- [ ] Create performance profiling tools
- [ ] Add advanced error correlation
- [ ] Implement fix templates and patterns
- [ ] Create custom error handler registration
- [ ] Add support for domain-specific languages
- [ ] Implement fix impact prediction
- [ ] Create advanced logging and debugging
- [ ] Add automatic test generation for fixes

#### ENTERPRISE Tier - Enterprise Features (25 items)
- [ ] Implement federated fix caching (multi-region)
- [ ] Create enterprise audit compliance reporting
- [ ] Add encryption for sensitive error data
- [ ] Implement role-based access control (RBAC)
- [ ] Create centralized fix policy management
- [ ] Add organization-wide fix templates
- [ ] Implement multi-tenant support with isolation
- [ ] Create enterprise SLA tracking and reporting
- [ ] Add integration with enterprise SIEM systems
- [ ] Implement advanced fraud detection
- [ ] Create regulatory compliance frameworks (SOC2/HIPAA)
- [ ] Add encryption-at-rest for audit logs
- [ ] Implement disaster recovery procedures
- [ ] Create high-availability deployments
- [ ] Add geographic data residency support
- [ ] Implement advanced access controls
- [ ] Create comprehensive enterprise documentation
- [ ] Add enterprise support tooling
- [ ] Implement advanced security scanning
- [ ] Create billing and usage tracking
- [ ] Add organization hierarchy support
- [ ] Implement cross-organization analytics
- [ ] Create enterprise API with rate limiting
- [ ] Add comprehensive security certification
- [ ] Implement advanced compliance automation

### Error-to-Diff Engine & Fix Loop (150 TODOs - error_to_diff.py, fix_loop.py)

See comprehensive tier-based TODOs in module docstrings (75 per file):
- Error-to-Diff (75): Python/JS/Java/Go/Rust parsing, fix generation, ML ranking, enterprise compliance
- Fix Loop (75): Core loop termination, advanced ML strategies, enterprise reliability features

### Mutation Gate & Sandbox (150 TODOs - mutation_gate.py, sandbox.py)

See comprehensive tier-based TODOs in module docstrings (75 per file):
- Mutation Gate (75): Core mutations, advanced analysis, enterprise QA features
- Sandbox Executor (75): Core isolation, advanced container/K8s, enterprise security

### Audit Trail & Engine (150 TODOs - audit.py, engine.py)

See comprehensive tier-based TODOs in module docstrings (75 per file):
- Audit Trail (75): Core hashing/storage, analytics/SIEM, enterprise compliance
- Autonomy Engine (75): Core orchestration, distributed execution, enterprise scale

### Framework Integrations (100 TODOs - integrations/)

See comprehensive tier-based TODOs in integration module docstrings:
- Core Integrations __init__ (75): Factory functions, LangGraph, AutoGen, CrewAI bridges
- Advanced Integrations (75+): Multi-agent coordination, streaming, distributed execution
- Enterprise Integrations (75+): Multi-region, high availability, compliance enforcement

**Total Autonomy Module TODOs: 575+ items across all files**
- COMMUNITY: 200+ (core features, multi-language support, basic frameworks)
- PRO: 200+ (ML/caching/distribution, advanced analysis, performance)
- ENTERPRISE: 175+ (multi-region/high-availability, compliance/audit, cost tracking)


---

## Feature Roadmap (Comprehensive Tier-Based TODOs)

### [20251224_TODO] Phase 1 - COMMUNITY Tier (Comprehensive Feature Set)

**Core Autonomy Engine:**
- [ ] Error analysis pipeline with multi-language support
- [ ] Fix suggestion ranking with confidence scoring
- [ ] Sandbox execution with process isolation
- [ ] Fix loop termination with attempt limits
- [ ] Mutation gate for hollow fix detection
- [ ] Audit trail with cryptographic hashing
- [ ] Error-to-Diff conversion engine
- [ ] Test execution framework integration
- [ ] Lint execution framework integration
- [ ] Build execution framework integration

**Multi-Language Support:**
- [ ] Python error parsing (SyntaxError, NameError, TypeError, etc.)
- [ ] TypeScript/JavaScript error parsing
- [ ] Java error parsing
- [ ] Error classification system
- [ ] Error normalization
- [ ] Error context extraction

**Fix Suggestion System:**
- [ ] AST-based fix generation
- [ ] Fix validation (AST correctness)
- [ ] Diff formatting (unified diff format)
- [ ] Alternative fix suggestions
- [ ] Import suggestion system
- [ ] Symbol lookup and namespace resolution

**Test Execution:**
- [ ] pytest integration
- [ ] unittest integration
- [ ] jest integration for JavaScript
- [ ] Test result parsing
- [ ] Test filtering by pattern
- [ ] Parallel test execution

**Sandbox Execution:**
- [ ] Temporary directory creation and cleanup
- [ ] Process-level isolation
- [ ] File copy and restoration
- [ ] Test execution monitoring
- [ ] Output capture (stdout/stderr)
- [ ] Resource limit enforcement
- [ ] Timeout mechanisms
- [ ] Test framework detection
- [ ] Filesystem change tracking
- [ ] Side effect monitoring

**Audit Trail:**
- [ ] SHA-256 hashing for all entries
- [ ] Parent-child relationship tracking
- [ ] Session-based audit grouping
- [ ] Timestamp normalization (UTC)
- [ ] Audit entry serialization to JSON
- [ ] Audit storage with file locking
- [ ] Audit entry validation on load
- [ ] Query by time range
- [ ] Entry deduplication

**Framework Integrations:**
- [ ] LangGraph StateGraph creation
- [ ] CrewAI Crew integration
- [ ] AutoGen AssistantAgent support
- [ ] Tool registration with frameworks
- [ ] Message format conversion
- [ ] State persistence

### [20251224_TODO] Phase 2 - PRO Tier (Advanced Capabilities)

**Machine Learning & Analytics:**
- [ ] ML-based fix ranking
- [ ] Ensemble methods for suggestions
- [ ] Cross-project fix pattern detection
- [ ] Learning from applied fixes
- [ ] Feedback loop integration
- [ ] Anomaly detection in error patterns
- [ ] Advanced trend analysis

**Performance & Distribution:**
- [ ] Distributed fix execution
- [ ] Load balancing across workers
- [ ] Parallel fix attempt execution
- [ ] Async operations
- [ ] Streaming result updates
- [ ] Performance monitoring and profiling
- [ ] Cost-based optimization
- [ ] Adaptive scheduling and resource allocation

**Advanced Sandbox Features:**
- [ ] Docker container isolation
- [ ] Container networking
- [ ] Volume management
- [ ] Environment variable isolation
- [ ] Credential injection
- [ ] Build artifact caching
- [ ] Incremental testing
- [ ] Dependency caching
- [ ] Performance optimization

**Caching & Optimization:**
- [ ] Caching layer for fix suggestions
- [ ] Incremental analysis
- [ ] Fast-path detection
- [ ] Memoization
- [ ] Result caching
- [ ] Cache warming
- [ ] Smart prefetching
- [ ] Request coalescing
- [ ] Cache sharding

**Advanced Fix Features:**
- [ ] Fix composition engine
- [ ] Multi-fix coordination
- [ ] Fix interaction detection
- [ ] Cross-file fix tracking
- [ ] Version-aware suggestions
- [ ] Security vulnerability detection
- [ ] Performance optimization suggestions
- [ ] Architectural fix suggestions

### [20251224_TODO] Phase 3 - ENTERPRISE Tier (Scale, Compliance, Advanced Features)

**Multi-Region & High Availability:**
- [ ] Multi-region deployment
- [ ] Disaster recovery planning
- [ ] Backup and restoration
- [ ] Failover mechanisms
- [ ] Cross-region replication
- [ ] Geo-redundancy
- [ ] Circuit breaking
- [ ] Graceful degradation
- [ ] Auto-scaling based on demand

**Compliance & Governance:**
- [ ] Encryption-at-rest for logs
- [ ] GxP/FDA compliance mode
- [ ] SOC2 compliance tracking
- [ ] HIPAA privacy controls
- [ ] PCI-DSS compliance support
- [ ] GDPR compliance automation
- [ ] Immutable audit log storage
- [ ] Tamper detection mechanisms
- [ ] Regulatory compliance automation
- [ ] Compliance certification support

**Access Control & Security:**
- [ ] Role-based access control (RBAC)
- [ ] Fine-grained permissions
- [ ] Approval workflows
- [ ] Change advisory board (CAB) integration
- [ ] Encryption for sensitive operations
- [ ] Encryption in transit
- [ ] Key rotation
- [ ] Advanced threat detection
- [ ] Anomaly detection systems

**Cost Management & Billing:**
- [ ] Cost allocation by organization
- [ ] Billing integration
- [ ] Usage reporting and tracking
- [ ] Chargeback models
- [ ] Budget enforcement
- [ ] Rate limiting and quotas
- [ ] SLA tracking and monitoring
- [ ] Incident management
- [ ] Executive dashboards

**Organization Features:**
- [ ] Organization-wide fix templates
- [ ] Federated fix sharing
- [ ] Cross-org collaboration
- [ ] Centralized management
- [ ] Team management
- [ ] Peer review workflows
- [ ] Approval gates
- [ ] Cross-organization coordination

**Advanced Analytics:**
- [ ] Predictive error forecasting
- [ ] Machine learning insights
- [ ] Advanced data mining
- [ ] Statistical analysis
- [ ] Performance benchmarking
- [ ] Cost optimization recommendations
- [ ] Capacity planning
- [ ] Demand forecasting
- [ ] Risk assessment and mitigation

---

## Implementation Priority Matrix

| Tier | Focus Area | Count | Priority | Timeline |
|------|-----------|-------|----------|----------|
| COMMUNITY | Core features, multi-language | 100+ | P0 | v3.1.0 |
| PRO | Distribution, ML, performance | 100+ | P1 | v3.2.0 |
| ENTERPRISE | Compliance, multi-region, billing | 100+ | P2 | v3.3.0+ |

**Total TODOs:** 300+ (100 per tier)
**Status:** All items documented and tracked
**Next Phase:** LangGraph state graph implementation (P0 - COMMUNITY tier)

