feat: Complete SWE agent system implementation and fixes

[TerminallyLazy]

Complete SWE Agent System Implementation

Summary

This PR completes the implementation of the SWE (Software Engineering) multi-agent system for Agent Zero, fixing critical bugs and adding
comprehensive workflow management capabilities.

What's New

🤖 Complete Multi-Agent Workflow

• swe-planner: Analyzes requirements, reads project rules, creates development plans
• swe-programmer: Implements code, runs tests, manages task execution
• swe-reviewer: Validates quality, runs security scans, ensures standards compliance
• swe-orchestrator: Coordinates the complete workflow with advanced management tools

🔧 Critical Bug Fixes

• Fixed infinite recursion in rules_parser.save_state() causing stack overflow
• Added missing ReviewIssue class to GraphState with proper serialization support
• Fixed AgentContext history calls in AGENTS.md generation API
• Enhanced state sharing between subordinate agents using dual-format persistence

🛠️ Enhanced Tool System

• Workflow Management: pause/resume, retry failed tasks, skip operations
• Status Monitoring: comprehensive progress tracking and reporting
• Diagnostic Tools: troubleshoot tool availability and state issues
• Proper Tool Registration: all agents have access to required tools

Key Features

🎯 Intelligent Planning

# Automatically analyzes requirements and creates actionable tasks
swe_orchestrator(user_request="Implement user authentication with JWT")

🔄 State Management

- Shared GraphState across all agents
- Dual-format serialization (object + dictionary)
- History tracking and iteration management
- Robust error handling and recovery

✅ Quality Assurance

- Automated testing and validation
- Security scanning and vulnerability detection
- Code quality checks and standards compliance
- Comprehensive review feedback with structured issues

Files Changed

Core System

- python/helpers/swe_graph_state.py - Added ReviewIssue class and enhanced serialization
- python/tools/swe_orchestrator.py - Enhanced workflow coordination and state management
- python/api/swe_generate_agents_md.py - Fixed agent history method calls

Agent Profiles

- agents/swe-orchestrator/ - Complete orchestrator agent with workflow tools
- agents/swe-planner/tools/ - Enhanced diagnostic and state management tools
- agents/swe-programmer/tools/ - File operations, grep, and task management
- agents/swe-reviewer/tools/ - Quality checking, security scanning, test running

Bug Fixes

- Fixed recursion bug in agents/swe-planner/tools/rules_parser.py
- Enhanced error handling in python/helpers/tool.py

Usage

Simple Workflow

# Request software engineering work - the system handles the rest
"Add user authentication with JWT tokens to this API"

Advanced Control

# Manual agent coordination
call_subordinate(profile="swe-planner", message="Plan user auth system")
call_subordinate(profile="swe-programmer", message="Implement task 1")
call_subordinate(profile="swe-reviewer", message="Review implementation")

Testing

- ✅ All critical recursion bugs resolved
- ✅ Tool registration system verified
- ✅ State management tested across agents
- ✅ AGENTS.md generation working without errors
- ✅ JSON formatting requirements enforced for all agents

Impact

This PR transforms Agent Zero into a comprehensive software engineering platform capable of:
- 📋 Intelligent Planning - Requirement analysis and task decomposition
- 💻 Quality Implementation - Test-driven development with error handling
- 🔍 Thorough Validation - Multi-layer quality checks and automated testing
- 🔄 Complete Traceability - Full audit trail of changes and decisions

The SWE system is now production-ready for complex software development tasks.