@monoes/cli 1.0.0

package/.claude/commands/monitoring/README.md

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+# Monitoring Commands
+
+Commands for monitoring operations in Monobrain.
+
+## Available Commands
+
+- [swarm-monitor](./swarm-monitor.md)
+- [agent-metrics](./agent-metrics.md)
+- [real-time-view](./real-time-view.md)

package/.claude/commands/monitoring/agent-metrics.md

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+# agent-metrics
+
+View agent performance metrics.
+
+## Usage
+```bash
+npx monobrain agent metrics [options]
+```
+
+## Options
+- `--agent-id <id>` - Specific agent
+- `--period <time>` - Time period
+- `--format <type>` - Output format
+
+## Examples
+```bash
+# All agents metrics
+npx monobrain agent metrics
+
+# Specific agent
+npx monobrain agent metrics --agent-id agent-001
+
+# Last hour
+npx monobrain agent metrics --period 1h
+```

package/.claude/commands/monitoring/agents.md

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+# List Active Patterns
+
+## 🎯 Key Principle
+**This tool coordinates Claude Code's actions. It does NOT write code or create content.**
+
+## MCP Tool Usage in Claude Code
+
+**Tool:** `mcp__monobrain__agent_list`
+
+## Parameters
+```json
+{
+  "swarmId": "current"
+}
+```
+
+## Description
+View all active cognitive patterns and their current focus areas
+
+## Details
+Filters:
+- **all**: Show all defined patterns
+- **active**: Currently engaged patterns
+- **idle**: Available but unused patterns
+- **busy**: Patterns actively coordinating tasks
+
+## Example Usage
+
+**In Claude Code:**
+1. List all agents: Use tool `mcp__monobrain__agent_list`
+2. Get specific agent metrics: Use tool `mcp__monobrain__agent_metrics` with parameters `{"agentId": "coder-123"}`
+3. Monitor agent performance: Use tool `mcp__monobrain__swarm_monitor` with parameters `{"interval": 2000}`
+
+## Important Reminders
+- ✅ This tool provides coordination and structure
+- ✅ Claude Code performs all actual implementation
+- ❌ The tool does NOT write code
+- ❌ The tool does NOT access files directly
+- ❌ The tool does NOT execute commands
+
+## See Also
+- Main documentation: /CLAUDE.md
+- Other commands in this category
+- Workflow examples in /workflows/

package/.claude/commands/monitoring/real-time-view.md

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+# real-time-view
+
+Real-time view of swarm activity.
+
+## Usage
+```bash
+npx monobrain monitoring real-time-view [options]
+```
+
+## Options
+- `--filter <type>` - Filter view
+- `--highlight <pattern>` - Highlight pattern
+- `--tail <n>` - Show last N events
+
+## Examples
+```bash
+# Start real-time view
+npx monobrain monitoring real-time-view
+
+# Filter errors
+npx monobrain monitoring real-time-view --filter errors
+
+# Highlight pattern
+npx monobrain monitoring real-time-view --highlight "API"
+```

package/.claude/commands/monitoring/status.md

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+# Check Coordination Status
+
+## 🎯 Key Principle
+**This tool coordinates Claude Code's actions. It does NOT write code or create content.**
+
+## MCP Tool Usage in Claude Code
+
+**Tool:** `mcp__monobrain__swarm_status`
+
+## Parameters
+```json
+{
+  "swarmId": "current"
+}
+```
+
+## Description
+Monitor the effectiveness of current coordination patterns
+
+## Details
+Shows:
+- Active coordination topologies
+- Current cognitive patterns in use
+- Task breakdown and progress
+- Resource utilization for coordination
+- Overall system health
+
+## Example Usage
+
+**In Claude Code:**
+1. Check swarm status: Use tool `mcp__monobrain__swarm_status`
+2. Monitor in real-time: Use tool `mcp__monobrain__swarm_monitor` with parameters `{"interval": 1000}`
+3. Get agent metrics: Use tool `mcp__monobrain__agent_metrics` with parameters `{"agentId": "agent-123"}`
+4. Health check: Use tool `mcp__monobrain__health_check` with parameters `{"components": ["swarm", "memory", "neural"]}`
+
+## Important Reminders
+- ✅ This tool provides coordination and structure
+- ✅ Claude Code performs all actual implementation
+- ❌ The tool does NOT write code
+- ❌ The tool does NOT access files directly
+- ❌ The tool does NOT execute commands
+
+## See Also
+- Main documentation: /CLAUDE.md
+- Other commands in this category
+- Workflow examples in /workflows/

package/.claude/commands/monitoring/swarm-monitor.md

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+# swarm-monitor
+
+Real-time swarm monitoring.
+
+## Usage
+```bash
+npx monobrain swarm monitor [options]
+```
+
+## Options
+- `--interval <ms>` - Update interval
+- `--metrics` - Show detailed metrics
+- `--export` - Export monitoring data
+
+## Examples
+```bash
+# Start monitoring
+npx monobrain swarm monitor
+
+# Custom interval
+npx monobrain swarm monitor --interval 5000
+
+# With metrics
+npx monobrain swarm monitor --metrics
+```

package/.claude/commands/monobrain-help.md

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+---
+name: monobrain-help
+description: Show Monobrain commands and usage
+---
+
+# Monobrain Commands
+
+## 🌊 Monobrain: Agent Orchestration Platform
+
+Monobrain is the ultimate multi-terminal orchestration platform that revolutionizes how you work with Claude Code.
+
+## Core Commands
+
+### 🚀 System Management
+- `./monobrain start` - Start orchestration system
+- `./monobrain start --ui` - Start with interactive process management UI
+- `./monobrain status` - Check system status
+- `./monobrain monitor` - Real-time monitoring
+- `./monobrain stop` - Stop orchestration
+
+### 🤖 Agent Management
+- `./monobrain agent spawn <type>` - Create new agent
+- `./monobrain agent list` - List active agents
+- `./monobrain agent info <id>` - Agent details
+- `./monobrain agent terminate <id>` - Stop agent
+
+### 📋 Task Management
+- `./monobrain task create <type> "description"` - Create task
+- `./monobrain task list` - List all tasks
+- `./monobrain task status <id>` - Task status
+- `./monobrain task cancel <id>` - Cancel task
+- `./monobrain task workflow <file>` - Execute workflow
+
+### 🧠 Memory Operations
+- `./monobrain memory store "key" "value"` - Store data
+- `./monobrain memory query "search"` - Search memory
+- `./monobrain memory stats` - Memory statistics
+- `./monobrain memory export <file>` - Export memory
+- `./monobrain memory import <file>` - Import memory
+
+### ⚡ SPARC Development
+- `./monobrain sparc "task"` - Run SPARC orchestrator
+- `./monobrain sparc modes` - List all 17+ SPARC modes
+- `./monobrain sparc run <mode> "task"` - Run specific mode
+- `./monobrain sparc tdd "feature"` - TDD workflow
+- `./monobrain sparc info <mode>` - Mode details
+
+### 🐝 Swarm Coordination
+- `./monobrain swarm "task" --strategy <type>` - Start swarm
+- `./monobrain swarm "task" --background` - Long-running swarm
+- `./monobrain swarm "task" --monitor` - With monitoring
+- `./monobrain swarm "task" --ui` - Interactive UI
+- `./monobrain swarm "task" --distributed` - Distributed coordination
+
+### 🌍 MCP Integration
+- `./monobrain mcp status` - MCP server status
+- `./monobrain mcp tools` - List available tools
+- `./monobrain mcp config` - Show configuration
+- `./monobrain mcp logs` - View MCP logs
+
+### 🤖 Claude Integration
+- `./monobrain claude spawn "task"` - Spawn Claude with enhanced guidance
+- `./monobrain claude batch <file>` - Execute workflow configuration
+
+## 🌟 Quick Examples
+
+### Initialize with SPARC:
+```bash
+npx -y monobrain@latest init --sparc
+```
+
+### Start a development swarm:
+```bash
+./monobrain swarm "Build REST API" --strategy development --monitor --review
+```
+
+### Run TDD workflow:
+```bash
+./monobrain sparc tdd "user authentication"
+```
+
+### Store project context:
+```bash
+./monobrain memory store "project_requirements" "e-commerce platform specs" --namespace project
+```
+
+### Spawn specialized agents:
+```bash
+./monobrain agent spawn researcher --name "Senior Researcher" --priority 8
+./monobrain agent spawn developer --name "Lead Developer" --priority 9
+```
+
+## 🎯 Best Practices
+- Use `./monobrain` instead of `npx monobrain` after initialization
+- Store important context in memory for cross-session persistence
+- Use swarm mode for complex tasks requiring multiple agents
+- Enable monitoring for real-time progress tracking
+- Use background mode for tasks > 30 minutes
+
+## 📚 Resources
+- Documentation: https://github.com/nokhodian/claude-code-flow/docs
+- Examples: https://github.com/nokhodian/claude-code-flow/examples
+- Issues: https://github.com/nokhodian/claude-code-flow/issues

package/.claude/commands/monobrain-memory.md

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+---
+name: monobrain-memory
+description: Interact with Monobrain memory system
+---
+
+# 🧠 Monobrain Memory System
+
+The memory system provides persistent storage for cross-session and cross-agent collaboration with CRDT-based conflict resolution.
+
+## Store Information
+```bash
+# Store with default namespace
+./monobrain memory store "key" "value"
+
+# Store with specific namespace
+./monobrain memory store "architecture_decisions" "microservices with API gateway" --namespace arch
+```
+
+## Query Memory
+```bash
+# Search across all namespaces
+./monobrain memory query "authentication"
+
+# Search with filters
+./monobrain memory query "API design" --namespace arch --limit 10
+```
+
+## Memory Statistics
+```bash
+# Show overall statistics
+./monobrain memory stats
+
+# Show namespace-specific stats
+./monobrain memory stats --namespace project
+```
+
+## Export/Import
+```bash
+# Export all memory
+./monobrain memory export full-backup.json
+
+# Export specific namespace
+./monobrain memory export project-backup.json --namespace project
+
+# Import memory
+./monobrain memory import backup.json
+```
+
+## Cleanup Operations
+```bash
+# Clean entries older than 30 days
+./monobrain memory cleanup --days 30
+
+# Clean specific namespace
+./monobrain memory cleanup --namespace temp --days 7
+```
+
+## 🗂️ Namespaces
+- **default** - General storage
+- **agents** - Agent-specific data and state
+- **tasks** - Task information and results
+- **sessions** - Session history and context
+- **swarm** - Swarm coordination and objectives
+- **project** - Project-specific context
+- **spec** - Requirements and specifications
+- **arch** - Architecture decisions
+- **impl** - Implementation notes
+- **test** - Test results and coverage
+- **debug** - Debug logs and fixes
+
+## 🎯 Best Practices
+
+### Naming Conventions
+- Use descriptive, searchable keys
+- Include timestamp for time-sensitive data
+- Prefix with component name for clarity
+
+### Organization
+- Use namespaces to categorize data
+- Store related data together
+- Keep values concise but complete
+
+### Maintenance
+- Regular backups with export
+- Clean old data periodically
+- Monitor storage statistics
+- Compress large values
+
+## Examples
+
+### Store SPARC context:
+```bash
+./monobrain memory store "spec_auth_requirements" "OAuth2 + JWT with refresh tokens" --namespace spec
+./monobrain memory store "arch_api_design" "RESTful microservices with GraphQL gateway" --namespace arch
+./monobrain memory store "test_coverage_auth" "95% coverage, all tests passing" --namespace test
+```
+
+### Query project decisions:
+```bash
+./monobrain memory query "authentication" --namespace arch --limit 5
+./monobrain memory query "test results" --namespace test
+```
+
+### Backup project memory:
+```bash
+./monobrain memory export project-$(date +%Y%m%d).json --namespace project
+```

package/.claude/commands/monobrain-swarm.md

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+---
+name: monobrain-swarm
+description: Coordinate multi-agent swarms for complex tasks
+---
+
+# 🐝 Monobrain Swarm Coordination
+
+Advanced multi-agent coordination system with timeout-free execution, distributed memory sharing, and intelligent load balancing.
+
+## Basic Usage
+```bash
+./monobrain swarm "your complex task" --strategy <type> [options]
+```
+
+## 🎯 Swarm Strategies
+- **auto** - Automatic strategy selection based on task analysis
+- **development** - Code implementation with review and testing
+- **research** - Information gathering and synthesis
+- **analysis** - Data processing and pattern identification
+- **testing** - Comprehensive quality assurance
+- **optimization** - Performance tuning and refactoring
+- **maintenance** - System updates and bug fixes
+
+## 🤖 Agent Types
+- **coordinator** - Plans and delegates tasks to other agents
+- **developer** - Writes code and implements solutions
+- **researcher** - Gathers and analyzes information
+- **analyzer** - Identifies patterns and generates insights
+- **tester** - Creates and runs tests for quality assurance
+- **reviewer** - Performs code and design reviews
+- **documenter** - Creates documentation and guides
+- **monitor** - Tracks performance and system health
+- **specialist** - Domain-specific expert agents
+
+## 🔄 Coordination Modes
+- **centralized** - Single coordinator manages all agents (default)
+- **distributed** - Multiple coordinators share management
+- **hierarchical** - Tree structure with nested coordination
+- **mesh** - Peer-to-peer agent collaboration
+- **hybrid** - Mixed coordination strategies
+
+## ⚙️ Common Options
+- `--strategy <type>` - Execution strategy
+- `--mode <type>` - Coordination mode
+- `--max-agents <n>` - Maximum concurrent agents (default: 5)
+- `--timeout <minutes>` - Timeout in minutes (default: 60)
+- `--background` - Run in background for tasks > 30 minutes
+- `--monitor` - Enable real-time monitoring
+- `--ui` - Launch terminal UI interface
+- `--parallel` - Enable parallel execution
+- `--distributed` - Enable distributed coordination
+- `--review` - Enable peer review process
+- `--testing` - Include automated testing
+- `--encryption` - Enable data encryption
+- `--verbose` - Detailed logging output
+- `--dry-run` - Show configuration without executing
+
+## 🌟 Examples
+
+### Development Swarm with Review
+```bash
+./monobrain swarm "Build e-commerce REST API" \
+  --strategy development \
+  --monitor \
+  --review \
+  --testing
+```
+
+### Long-Running Research Swarm
+```bash
+./monobrain swarm "Analyze AI market trends 2024-2025" \
+  --strategy research \
+  --background \
+  --distributed \
+  --max-agents 8
+```
+
+### Performance Optimization Swarm
+```bash
+./monobrain swarm "Optimize database queries and API performance" \
+  --strategy optimization \
+  --testing \
+  --parallel \
+  --monitor
+```
+
+### Enterprise Development Swarm
+```bash
+./monobrain swarm "Implement secure payment processing system" \
+  --strategy development \
+  --mode distributed \
+  --max-agents 10 \
+  --parallel \
+  --monitor \
+  --review \
+  --testing \
+  --encryption \
+  --verbose
+```
+
+### Testing and QA Swarm
+```bash
+./monobrain swarm "Comprehensive security audit and testing" \
+  --strategy testing \
+  --review \
+  --verbose \
+  --max-agents 6
+```
+
+## 📊 Monitoring and Control
+
+### Real-time monitoring:
+```bash
+# Monitor swarm activity
+./monobrain monitor
+
+# Monitor specific component
+./monobrain monitor --focus swarm
+```
+
+### Check swarm status:
+```bash
+# Overall system status
+./monobrain status
+
+# Detailed swarm status
+./monobrain status --verbose
+```
+
+### View agent activity:
+```bash
+# List all agents
+./monobrain agent list
+
+# Agent details
+./monobrain agent info <agent-id>
+```
+
+## 💾 Memory Integration
+
+Swarms automatically use distributed memory for collaboration:
+
+```bash
+# Store swarm objectives
+./monobrain memory store "swarm_objective" "Build scalable API" --namespace swarm
+
+# Query swarm progress
+./monobrain memory query "swarm_progress" --namespace swarm
+
+# Export swarm memory
+./monobrain memory export swarm-results.json --namespace swarm
+```
+
+## 🎯 Key Features
+
+### Timeout-Free Execution
+- Background mode for long-running tasks
+- State persistence across sessions
+- Automatic checkpoint recovery
+
+### Work Stealing & Load Balancing
+- Dynamic task redistribution
+- Automatic agent scaling
+- Resource-aware scheduling
+
+### Circuit Breakers & Fault Tolerance
+- Automatic retry with exponential backoff
+- Graceful degradation
+- Health monitoring and recovery
+
+### Real-Time Collaboration
+- Cross-agent communication
+- Shared memory access
+- Event-driven coordination
+
+### Enterprise Security
+- Role-based access control
+- Audit logging
+- Data encryption
+- Input validation
+
+## 🔧 Advanced Configuration
+
+### Dry run to preview:
+```bash
+./monobrain swarm "Test task" --dry-run --strategy development
+```
+
+### Custom quality thresholds:
+```bash
+./monobrain swarm "High quality API" \
+  --strategy development \
+  --quality-threshold 0.95
+```
+
+### Scheduling algorithms:
+- FIFO (First In, First Out)
+- Priority-based
+- Deadline-driven
+- Shortest Job First
+- Critical Path
+- Resource-aware
+- Adaptive
+
+For detailed documentation, see: https://github.com/nokhodian/claude-code-flow/docs/swarm-system.md

package/.claude/commands/optimization/README.md

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+# Optimization Commands
+
+Commands for optimization operations in Monobrain.
+
+## Available Commands
+
+- [topology-optimize](./topology-optimize.md)
+- [parallel-execute](./parallel-execute.md)
+- [cache-manage](./cache-manage.md)

package/.claude/commands/optimization/auto-topology.md

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+# Automatic Topology Selection
+
+## Purpose
+Automatically select the optimal swarm topology based on task complexity analysis.
+
+## How It Works
+
+### 1. Task Analysis
+The system analyzes your task description to determine:
+- Complexity level (simple/medium/complex)
+- Required agent types
+- Estimated duration
+- Resource requirements
+
+### 2. Topology Selection
+Based on analysis, it selects:
+- **Star**: For simple, centralized tasks
+- **Mesh**: For medium complexity with flexibility needs
+- **Hierarchical**: For complex tasks requiring structure
+- **Ring**: For sequential processing workflows
+
+### 3. Example Usage
+
+**Simple Task:**
+```
+Tool: mcp__monobrain__task_orchestrate
+Parameters: {"task": "Fix typo in README.md"}
+Result: Automatically uses star topology with single agent
+```
+
+**Complex Task:**
+```
+Tool: mcp__monobrain__task_orchestrate
+Parameters: {"task": "Refactor authentication system with JWT, add tests, update documentation"}
+Result: Automatically uses hierarchical topology with architect, coder, and tester agents
+```
+
+## Benefits
+- 🎯 Optimal performance for each task type
+- 🤖 Automatic agent assignment
+- ⚡ Reduced setup time
+- 📊 Better resource utilization
+
+## Hook Configuration
+The pre-task hook automatically handles topology selection:
+```json
+{
+  "command": "npx monobrain hook pre-task --optimize-topology"
+}
+```
+
+## Direct Optimization
+```
+Tool: mcp__monobrain__topology_optimize
+Parameters: {"swarmId": "current"}
+```
+
+## CLI Usage
+```bash
+# Auto-optimize topology via CLI
+npx monobrain optimize topology
+```

package/.claude/commands/optimization/cache-manage.md

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+# cache-manage
+
+Manage operation cache for performance.
+
+## Usage
+```bash
+npx monobrain optimization cache-manage [options]
+```
+
+## Options
+- `--action <type>` - Action (view, clear, optimize)
+- `--max-size <mb>` - Maximum cache size
+- `--ttl <seconds>` - Time to live
+
+## Examples
+```bash
+# View cache stats
+npx monobrain optimization cache-manage --action view
+
+# Clear cache
+npx monobrain optimization cache-manage --action clear
+
+# Set limits
+npx monobrain optimization cache-manage --max-size 100 --ttl 3600
+```