@monoes/cli 1.0.0

package/.claude/commands/agents/agent-capabilities.md

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+---
+name: agent-capabilities
+description: Capability matrix for all agent types
+type: reference
+---
+
+# Agent Capabilities Reference
+
+Matrix of agent capabilities and their specializations for Monobrain v1.
+
+## Capability Matrix
+
+### Core Development
+
+| Agent      | Code  | Test  | Review | Design | Research |
+| ---------- | :---: | :---: | :----: | :----: | :------: |
+| coder      | **5** |   3   |   2    |   2    |    2     |
+| reviewer   |   3   |   2   | **5**  |   3    |    2     |
+| tester     |   2   | **5** |   2    |   1    |    2     |
+| planner    |   2   |   1   |   2    | **5**  |    4     |
+| researcher |   2   |   1   |   2    |   3    |  **5**   |
+
+### Specialized
+
+| Agent                | Security | Memory | Performance | Architecture |
+| -------------------- | :------: | :----: | :---------: | :----------: |
+| security-architect   |  **5**   |   2    |      3      |    **5**     |
+| security-auditor     |  **5**   |   2    |      2      |      3       |
+| memory-specialist    |    3     | **5**  |      4      |      3       |
+| performance-engineer |    2     |   3    |    **5**    |      4       |
+| core-architect       |    3     |   3    |      3      |    **5**     |
+
+### Swarm Coordination
+
+| Agent                               | Coordination | Consensus | Scaling | Fault Tolerance |
+| ----------------------------------- | :----------: | :-------: | :-----: | :-------------: |
+| hierarchical-coordinator            |    **5**     |     4     |    4    |        4        |
+| mesh-coordinator                    |      4       |     4     |  **5**  |        4        |
+| adaptive-coordinator                |    **5**     |     4     |  **5**  |        4        |
+| collective-intelligence-coordinator |      4       |   **5**   |    4    |        4        |
+
+### GitHub Integration
+
+| Agent               |  PR   | Issues | CI/CD | Release | Review |
+| ------------------- | :---: | :----: | :---: | :-----: | :----: |
+| pr-manager          | **5** |   3    |   2   |    3    |   4    |
+| code-review-swarm   |   4   |   2    |   2   |    2    | **5**  |
+| issue-tracker       |   2   | **5**  |   2   |    2    |   2    |
+| release-manager     |   3   |   3    |   4   |  **5**  |   2    |
+| workflow-automation |   2   |   3    | **5** |    4    |   2    |
+
+## Capability Levels
+
+| Level | Description                     |
+| ----- | ------------------------------- |
+| **5** | Expert - Primary specialization |
+| 4     | Advanced - Strong capability    |
+| 3     | Intermediate - Good capability  |
+| 2     | Basic - Limited capability      |
+| 1     | Minimal - Not a focus           |
+
+## Performance Capabilities
+
+| Capability      | Agents                                  | Performance Gain |
+| --------------- | --------------------------------------- | ---------------- |
+| Flash Attention | memory-specialist, performance-engineer | 2.49x-7.47x      |
+| HNSW Search     | memory-specialist                       | 150x-12,500x     |
+| Quantization    | performance-engineer                    | 50-75% memory    |
+| SONA Adaptation | sona-learning-optimizer                 | <0.05ms          |
+
+## Consensus Capabilities
+
+| Agent                 |  BFT  | Raft  | Gossip | CRDT  |
+| --------------------- | :---: | :---: | :----: | :---: |
+| byzantine-coordinator | **5** |   2   |   2    |   2   |
+| raft-manager          |   2   | **5** |   2    |   2   |
+| gossip-coordinator    |   2   |   2   | **5**  |   3   |
+| crdt-synchronizer     |   2   |   2   |   3    | **5** |
+| quorum-manager        |   4   |   4   |   3    |   3   |
+
+## Tool Access by Agent Type
+
+### Code Tools
+
+```
+coder: Read, Write, Edit, MultiEdit, Glob, Grep, Bash
+reviewer: Read, Glob, Grep
+tester: Read, Write, Bash, Glob
+```
+
+### Swarm Tools
+
+```
+hierarchical-coordinator: mcp__monobrain__swarm_*, mcp__monobrain__agent_*
+mesh-coordinator: mcp__monobrain__swarm_*, mcp__monobrain__coordination_*
+adaptive-coordinator: mcp__monobrain__topology_*, mcp__monobrain__swarm_*
+```
+
+### GitHub Tools
+
+```
+pr-manager: mcp__github__*, Bash (gh CLI)
+code-review-swarm: mcp__github__*, mcp__monobrain__swarm_*
+release-manager: mcp__github__*, mcp__monobrain__workflow_*
+```
+
+## Querying Capabilities
+
+```bash
+# List all capabilities for an agent type
+npx monobrain agent spawn -t coder --help
+
+# View agent definition
+cat .claude/agents/core/coder.md
+```
+
+## Capability-Based Selection
+
+### For Security Tasks
+
+1. `security-architect` - Design and threat modeling
+2. `security-auditor` - Vulnerability assessment
+3. `security-manager` - Consensus security
+
+### For Performance Tasks
+
+1. `performance-engineer` - Optimization
+2. `memory-specialist` - Memory/search optimization
+3. `performance-analyzer` - Bottleneck analysis
+
+### For Multi-Agent Coordination
+
+1. `hierarchical-coordinator` - Complex hierarchical tasks
+2. `mesh-coordinator` - Research and exploration
+3. `adaptive-coordinator` - Dynamic requirements
+
+### For GitHub Workflows
+
+1. `pr-manager` - PR lifecycle
+2. `code-review-swarm` - Comprehensive reviews
+3. `workflow-automation` - CI/CD automation
+
+## See Also
+
+- [agent-types](./agent-types.md) - All 87 agent types
+- [agent-coordination](./agent-coordination.md) - Coordination patterns
+- [spawn](./spawn.md) - Spawn command

package/.claude/commands/agents/agent-coordination.md

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+# agent-coordination
+
+Coordination patterns for multi-agent collaboration.
+
+## Coordination Patterns
+
+### Hierarchical
+Queen-led with worker specialization
+```bash
+npx monobrain swarm init --topology hierarchical
+```
+
+### Mesh
+Peer-to-peer collaboration
+```bash
+npx monobrain swarm init --topology mesh
+```
+
+### Adaptive
+Dynamic topology based on workload
+```bash
+npx monobrain swarm init --topology adaptive
+```
+
+## Best Practices
+- Use hierarchical for complex projects
+- Use mesh for research tasks
+- Use adaptive for unknown workloads

package/.claude/commands/agents/agent-spawning.md

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+# agent-spawning
+
+Guide to spawning agents with Claude Code's Task tool.
+
+## Using Claude Code's Task Tool
+
+**CRITICAL**: Always use Claude Code's Task tool for actual agent execution:
+
+```javascript
+// Spawn ALL agents in ONE message
+Task("Researcher", "Analyze requirements...", "researcher")
+Task("Coder", "Implement features...", "coder")
+Task("Tester", "Create tests...", "tester")
+```
+
+## MCP Coordination Setup (Optional)
+
+MCP tools are ONLY for coordination:
+```javascript
+mcp__monobrain__swarm_init { topology: "mesh" }
+mcp__monobrain__agent_spawn { type: "researcher" }
+```
+
+## Best Practices
+1. Always spawn agents concurrently
+2. Use Task tool for execution
+3. MCP only for coordination
+4. Batch all operations

package/.claude/commands/agents/agent-types.md

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+---
+name: agent-types
+description: Complete guide to all 87 available agent types in Monobrain v1
+type: reference
+---
+
+# Agent Types Reference
+
+Complete guide to all 87 available agent types in Monobrain v1.
+
+## Core Development (5)
+
+| Agent        | Description                              | Best For                       |
+| ------------ | ---------------------------------------- | ------------------------------ |
+| `coder`      | Code implementation with neural patterns | Feature development, bug fixes |
+| `reviewer`   | Code quality assurance                   | PR reviews, security checks    |
+| `tester`     | Testing with automation                  | Unit tests, integration tests  |
+| `planner`    | Strategic task planning                  | Project planning, roadmaps     |
+| `researcher` | Information gathering                    | Requirements, documentation    |
+
+## Specialized (12)
+
+| Agent                      | Description            | Best For                |
+| -------------------------- | ---------------------- | ----------------------- |
+| `security-architect`       | Security architecture  | Threat modeling, design |
+| `security-auditor`         | CVE remediation        | Vulnerability scanning  |
+| `memory-specialist`        | AgentDB unification    | 150x-12,500x search     |
+| `performance-engineer`     | Optimization targets   | 2.49x-7.47x speedup     |
+| `core-architect`           | DDD restructure        | Domain modeling         |
+| `adr-architect`            | Architecture decisions | ADR documentation       |
+| `claims-authorizer`        | Access control         | Claims-based auth       |
+| `ddd-domain-expert`        | Domain design          | Bounded contexts        |
+| `reasoningbank-learner`    | Pattern learning       | Self-improvement        |
+| `sona-learning-optimizer`  | Neural optimization    | SONA adaptation         |
+| `sparc-orchestrator`       | SPARC methodology      | Development workflow    |
+| `v1-integration-architect` | v1 integration         | System integration      |
+
+## Swarm Coordination (6)
+
+| Agent                                 | Description            | Best For          |
+| ------------------------------------- | ---------------------- | ----------------- |
+| `hierarchical-coordinator`            | Queen-led coordination | Complex projects  |
+| `mesh-coordinator`                    | P2P peer networks      | Research tasks    |
+| `adaptive-coordinator`                | Dynamic topology       | Unknown workloads |
+| `collective-intelligence-coordinator` | Consensus decisions    | Group decisions   |
+| `swarm-memory-manager`                | Distributed memory     | Data sharing      |
+| `coordinator-swarm-init`              | Swarm initialization   | Setup             |
+
+## Consensus Agents (7)
+
+| Agent                   | Description            | Best For            |
+| ----------------------- | ---------------------- | ------------------- |
+| `byzantine-coordinator` | BFT consensus          | Fault tolerance     |
+| `raft-manager`          | Leader-based consensus | Consistent state    |
+| `gossip-coordinator`    | Eventual consistency   | Scalability         |
+| `crdt-synchronizer`     | CRDT replication       | Conflict-free sync  |
+| `quorum-manager`        | Quorum consensus       | Voting systems      |
+| `security-manager`      | Consensus security     | Secure coordination |
+| `consensus-coordinator` | General consensus      | Distributed systems |
+
+## GitHub Integration (14)
+
+| Agent                 | Description            | Best For              |
+| --------------------- | ---------------------- | --------------------- |
+| `pr-manager`          | PR lifecycle           | Pull requests         |
+| `code-review-swarm`   | Multi-agent review     | Comprehensive reviews |
+| `issue-tracker`       | Issue management       | Bug tracking          |
+| `release-manager`     | Release coordination   | Versioning            |
+| `workflow-automation` | CI/CD automation       | GitHub Actions        |
+| `github-modes`        | GitHub operations      | Multi-mode GitHub     |
+| `multi-repo-swarm`    | Cross-repo sync        | Monorepo management   |
+| `project-board-sync`  | Project boards         | Kanban/Projects       |
+| `release-swarm`       | Release automation     | Deployments           |
+| `repo-architect`      | Repository structure   | Architecture          |
+| `swarm-issue`         | Issue-based swarms     | Task decomposition    |
+| `swarm-pr`            | PR-based swarms        | Review workflows      |
+| `sync-coordinator`    | Multi-repo sync        | Version alignment     |
+| `github-pr-manager`   | PR management template | PR workflows          |
+
+## SPARC Methodology (5)
+
+| Agent               | Description         | Best For         |
+| ------------------- | ------------------- | ---------------- |
+| `sparc-coordinator` | SPARC orchestration | Full SPARC cycle |
+| `specification`     | Requirements phase  | Specs writing    |
+| `pseudocode`        | Algorithm design    | Logic design     |
+| `architecture`      | System design       | Architecture     |
+| `refinement`        | Iteration phase     | Improvements     |
+
+## Optimization (6)
+
+| Agent                  | Description         | Best For             |
+| ---------------------- | ------------------- | -------------------- |
+| `topology-optimizer`   | Swarm topology      | Network optimization |
+| `load-balancer`        | Task distribution   | Workload balancing   |
+| `resource-allocator`   | Resource management | Capacity planning    |
+| `performance-monitor`  | Metrics tracking    | Observability        |
+| `benchmark-suite`      | Performance testing | Benchmarks           |
+| `performance-analyzer` | Analysis            | Bottleneck detection |
+
+## Sublinear Algorithms (5)
+
+| Agent                   | Description         | Best For                 |
+| ----------------------- | ------------------- | ------------------------ |
+| `matrix-optimizer`      | Matrix analysis     | Linear systems           |
+| `pagerank-analyzer`     | Graph analysis      | Network influence        |
+| `performance-optimizer` | System optimization | Resource efficiency      |
+| `trading-predictor`     | Market analysis     | Financial predictions    |
+| `consensus-coordinator` | Fast consensus      | Distributed coordination |
+
+## Analysis (2)
+
+| Agent                  | Description   | Best For          |
+| ---------------------- | ------------- | ----------------- |
+| `analyze-code-quality` | Code quality  | Static analysis   |
+| `code-analyzer`        | Code analysis | Pattern detection |
+
+## Architecture (1)
+
+| Agent                | Description   | Best For                |
+| -------------------- | ------------- | ----------------------- |
+| `arch-system-design` | System design | High-level architecture |
+
+## Data & ML (1)
+
+| Agent           | Description | Best For         |
+| --------------- | ----------- | ---------------- |
+| `data-ml-model` | ML models   | Machine learning |
+
+## Development (1)
+
+| Agent             | Description  | Best For     |
+| ----------------- | ------------ | ------------ |
+| `dev-backend-api` | Backend APIs | REST/GraphQL |
+
+## DevOps (1)
+
+| Agent             | Description     | Best For       |
+| ----------------- | --------------- | -------------- |
+| `ops-cicd-github` | CI/CD pipelines | GitHub Actions |
+
+## Documentation (1)
+
+| Agent              | Description       | Best For      |
+| ------------------ | ----------------- | ------------- |
+| `docs-api-openapi` | API documentation | OpenAPI specs |
+
+## Flow Nexus (9)
+
+| Agent            | Description         | Best For           |
+| ---------------- | ------------------- | ------------------ |
+| `app-store`      | App marketplace     | App publishing     |
+| `authentication` | User auth           | Login/registration |
+| `challenges`     | Coding challenges   | Gamification       |
+| `neural-network` | Neural training     | ML deployment      |
+| `payments`       | Payment processing  | Credits/billing    |
+| `sandbox`        | E2B sandboxes       | Isolated execution |
+| `swarm`          | Cloud swarms        | Cloud coordination |
+| `user-tools`     | User management     | Profile/storage    |
+| `workflow`       | Workflow automation | Event-driven       |
+
+## Goal Planning (2)
+
+| Agent          | Description        | Best For         |
+| -------------- | ------------------ | ---------------- |
+| `goal-planner` | GOAP planning      | Goal achievement |
+| `agent`        | General goal agent | Multi-purpose    |
+
+## Payments (1)
+
+| Agent              | Description | Best For            |
+| ------------------ | ----------- | ------------------- |
+| `agentic-payments` | AI commerce | Autonomous payments |
+
+## Specialized (1)
+
+| Agent                      | Description  | Best For           |
+| -------------------------- | ------------ | ------------------ |
+| `spec-mobile-react-native` | React Native | Mobile development |
+
+## Templates (8)
+
+| Agent                     | Description        | Best For            |
+| ------------------------- | ------------------ | ------------------- |
+| `automation-smart-agent`  | Smart automation   | Auto-spawning       |
+| `coordinator-swarm-init`  | Swarm setup        | Initialization      |
+| `github-pr-manager`       | PR workflows       | GitHub PRs          |
+| `implementer-sparc-coder` | SPARC coding       | Implementation      |
+| `memory-coordinator`      | Memory management  | State coordination  |
+| `orchestrator-task`       | Task orchestration | Workflow management |
+| `performance-analyzer`    | Performance        | Analysis            |
+| `sparc-coordinator`       | SPARC              | Methodology         |
+
+## Testing (3)
+
+| Agent                  | Description           | Best For            |
+| ---------------------- | --------------------- | ------------------- |
+| `tdd-london-swarm`     | TDD London School     | Mock-first TDD      |
+| `production-validator` | Deployment validation | Pre-deploy checks   |
+| `test-long-runner`     | Long-running tests    | Complex test suites |
+
+## Quick Reference
+
+```bash
+# List all agent types
+npx monobrain agent spawn --help
+
+# Spawn any agent
+npx monobrain agent spawn -t <agent-type>
+```
+
+## See Also
+
+- [agent-capabilities](./agent-capabilities.md) - Capability matrix
+- [agent-coordination](./agent-coordination.md) - Coordination patterns
+- [spawn](./spawn.md) - Spawn command details

package/.claude/commands/agents/health.md

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+---
+name: health
+description: Show agent health and metrics
+type: command
+---
+
+# Agent Health Command
+
+Monitor agent health status, resource usage, and detect issues.
+
+## Usage
+
+```bash
+npx monobrain agent health [agent-id] [options]
+```
+
+## Options
+
+| Option | Short | Description | Default |
+|--------|-------|-------------|---------|
+| `--watch` | `-w` | Continuous monitoring | false |
+| `--interval` | `-i` | Watch interval in seconds | 5 |
+| `--format` | | Output format (table, json) | table |
+
+## Examples
+
+```bash
+# Overall health check
+npx monobrain agent health
+
+# Specific agent health
+npx monobrain agent health coder-lx7m9k2
+
+# Continuous monitoring
+npx monobrain agent health --watch
+
+# Custom interval
+npx monobrain agent health -w -i 10
+
+# JSON output
+npx monobrain agent health --format json
+```
+
+## Output
+
+```
+Agent Health Status
+
+Overall: HEALTHY
+
++--------------------+---------+--------+--------+---------+
+| Agent              | Status  | Memory | CPU    | Tasks   |
++--------------------+---------+--------+--------+---------+
+| coder-lx7m9k2      | healthy | 45MB   | 2.3%   | 5/5     |
+| researcher-abc123  | healthy | 38MB   | 1.8%   | 3/3     |
+| tester-def456      | warning | 120MB  | 8.5%   | 12/14   |
++--------------------+---------+--------+--------+---------+
+
+Alerts
+  - tester-def456: High memory usage (120MB > 100MB threshold)
+  - tester-def456: Task failure rate above threshold (14.3%)
+
+Recommendations
+  - Consider restarting tester-def456
+  - Review failed tasks for error patterns
+```
+
+## Health Status Values
+
+| Status | Description |
+|--------|-------------|
+| `healthy` | All metrics within normal range |
+| `warning` | Some metrics approaching thresholds |
+| `critical` | Metrics exceeded critical thresholds |
+| `unknown` | Unable to determine health |
+
+## Health Checks
+
+### Resource Checks
+- Memory usage vs threshold
+- CPU utilization
+- Active connections
+- Queue depth
+
+### Performance Checks
+- Response time
+- Task success rate
+- Error frequency
+- Throughput
+
+### Connectivity Checks
+- MCP server connection
+- Memory backend
+- Neural services
+- Swarm coordination
+
+## Watch Mode
+
+Continuous monitoring with real-time updates:
+
+```bash
+npx monobrain agent health --watch
+
+# Output updates every 5 seconds:
+# [10:30:15] Agent Health: 3 healthy, 0 warning, 0 critical
+# [10:30:20] Agent Health: 3 healthy, 0 warning, 0 critical
+# [10:30:25] Agent Health: 2 healthy, 1 warning, 0 critical
+#   - tester-def456: Memory usage increased to 115MB
+```
+
+Press `Ctrl+C` to stop watching.
+
+## JSON Output
+
+```json
+{
+  "overall": "healthy",
+  "agents": [
+    {
+      "id": "coder-lx7m9k2",
+      "status": "healthy",
+      "metrics": {
+        "memoryMB": 45,
+        "cpuPercent": 2.3,
+        "tasksCompleted": 5,
+        "tasksTotal": 5
+      }
+    }
+  ],
+  "alerts": [],
+  "recommendations": []
+}
+```
+
+## Related Commands
+
+- `npx monobrain agent status` - Detailed agent info
+- `npx monobrain agent metrics` - Performance metrics
+- `npx monobrain doctor` - System-wide health

package/.claude/commands/agents/list.md

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+---
+name: list
+description: List all active agents
+aliases: [ls]
+type: command
+---
+
+# Agent List Command
+
+List all active agents in the Monobrain system with filtering options.
+
+## Usage
+
+```bash
+npx monobrain agent list [options]
+npx monobrain agent ls [options]  # Alias
+```
+
+## Options
+
+| Option     | Short | Description                                 | Default |
+| ---------- | ----- | ------------------------------------------- | ------- |
+| `--all`    | `-a`  | Include inactive/terminated agents          | false   |
+| `--type`   | `-t`  | Filter by agent type                        | All     |
+| `--status` | `-s`  | Filter by status (active, idle, terminated) | active  |
+| `--format` |       | Output format (table, json)                 | table   |
+
+## Examples
+
+```bash
+# List all active agents
+npx monobrain agent list
+
+# List all agents including inactive
+npx monobrain agent list --all
+
+# Filter by type
+npx monobrain agent list -t coder
+
+# Filter by status
+npx monobrain agent list -s idle
+
+# JSON output for scripting
+npx monobrain agent list --format json
+
+# Combined filters
+npx monobrain agent list -t researcher -s active
+```
+
+## Output
+
+```
+Active Agents
+
++--------------------+-----------+--------+----------+---------------+
+| ID                 | Type      | Status | Created  | Last Activity |
++--------------------+-----------+--------+----------+---------------+
+| coder-lx7m9k2      | coder     | active | 10:30:15 | 10:45:23      |
+| researcher-abc123  | researcher| idle   | 09:15:00 | 10:20:45      |
+| tester-def456      | tester    | active | 11:00:00 | 11:12:30      |
++--------------------+-----------+--------+----------+---------------+
+
+Total: 3 agents
+```
+
+## JSON Output
+
+```json
+{
+  "agents": [
+    {
+      "id": "coder-lx7m9k2",
+      "agentType": "coder",
+      "status": "active",
+      "createdAt": "2026-01-08T10:30:15.000Z",
+      "lastActivityAt": "2026-01-08T10:45:23.000Z"
+    }
+  ],
+  "total": 3
+}
+```
+
+## Status Values
+
+| Status       | Description                        |
+| ------------ | ---------------------------------- |
+| `active`     | Agent is currently executing tasks |
+| `idle`       | Agent is waiting for tasks         |
+| `terminated` | Agent has been stopped             |
+
+## Agent Type Categories
+
+Use `--type` with any of the 87 agent types:
+
+- Core: `coder`, `reviewer`, `tester`, `planner`, `researcher`
+- v1: `security-architect`, `memory-specialist`, `performance-engineer`
+- Swarm: `hierarchical-coordinator`, `mesh-coordinator`, `adaptive-coordinator`
+- Consensus: `byzantine-coordinator`, `raft-manager`, `gossip-coordinator`
+- GitHub: `pr-manager`, `code-review-swarm`, `release-manager`
+- SPARC: `sparc-coordinator`, `specification`, `architecture`