burhan-mop 0.1.0

package/.claude/commands/training/neural-patterns.md

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+# Neural Pattern Training
+
+## Purpose
+Continuously improve coordination through neural network learning with SONA (Self-Optimizing Neural Architecture).
+
+## Pattern Persistence
+
+Patterns are **automatically persisted** to disk:
+- **Patterns**: `.claude-flow/neural/patterns.json`
+- **Stats**: `.claude-flow/neural/stats.json`
+
+Patterns survive process restarts and are loaded automatically on next session.
+
+## How Training Works
+
+### 1. Automatic Learning
+Every successful operation trains the neural networks:
+- Edit patterns for different file types
+- Search strategies that find results faster
+- Task decomposition approaches
+- Agent coordination patterns
+
+### 2. Manual Training
+```bash
+# Train coordination patterns (50 epochs)
+npx claude-flow neural train -p coordination -e 50
+
+# Train optimization patterns with custom learning rate
+npx claude-flow neural train -p optimization -l 0.005
+
+# Quick training (10 epochs)
+npx claude-flow neural train -e 10
+```
+
+### 3. Pattern Types
+
+**Training Pattern Types:**
+- `coordination` - Task coordination strategies (default)
+- `optimization` - Performance optimization patterns
+- `prediction` - Predictive preloading patterns
+
+**Cognitive Patterns:**
+- Convergent: Focused problem-solving
+- Divergent: Creative exploration
+- Lateral: Alternative approaches
+- Systems: Holistic thinking
+- Critical: Analytical evaluation
+- Abstract: High-level design
+
+### 4. Improvement Tracking
+```bash
+# Check neural system status
+npx claude-flow neural status
+```
+
+## Pattern Management
+
+```bash
+# List all persisted patterns
+npx claude-flow neural patterns --action list
+
+# Search patterns by query
+npx claude-flow neural patterns --action list -q "error handling"
+
+# Analyze patterns
+npx claude-flow neural patterns --action analyze -q "coordination"
+```
+
+## Performance Targets
+
+| Metric | Target |
+|--------|--------|
+| SONA Adaptation | <0.05ms (achieved: ~2μs) |
+| Pattern Search | O(log n) with HNSW |
+| Memory Efficient | Circular buffers |
+
+## Benefits
+- 🧠 Learns your coding style
+- 📈 Improves with each use
+- 🎯 Better task predictions
+- ⚡ Faster coordination
+- 💾 Patterns persist across sessions
+
+## CLI Reference
+
+```bash
+# Train neural patterns
+npx claude-flow neural train -p coordination -e 50
+
+# Check neural status
+npx claude-flow neural status
+
+# List patterns
+npx claude-flow neural patterns --action list
+
+# Search patterns
+npx claude-flow neural patterns --action list -q "query"
+
+# Analyze patterns
+npx claude-flow neural patterns --action analyze -q "coordination"
+```
+
+## Related Commands
+
+- `neural train` - Train patterns with SONA
+- `neural status` - Check neural system status
+- `neural patterns` - List and search patterns
+- `neural predict` - Make predictions using trained models

package/.claude/commands/training/neural-train.md

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+# neural-train
+
+Train neural patterns with SONA (Self-Optimizing Neural Architecture) for adaptive learning and pattern recognition.
+
+## Usage
+```bash
+npx claude-flow neural train [options]
+```
+
+## Options
+- `-p, --pattern <type>` - Pattern type: coordination, optimization, prediction (default: coordination)
+- `-e, --epochs <n>` - Number of training epochs (default: 50)
+- `-d, --data <file>` - Training data file (JSON)
+- `-m, --model <id>` - Model ID to train
+- `-l, --learning-rate <rate>` - Learning rate (default: 0.001)
+- `-b, --batch-size <n>` - Batch size (default: 32)
+
+## Pattern Persistence
+
+Trained patterns are **automatically persisted** to disk:
+- **Location**: `.claude-flow/neural/patterns.json`
+- **Stats**: `.claude-flow/neural/stats.json`
+
+Patterns survive process restarts and are loaded automatically on next session.
+
+## Examples
+
+```bash
+# Train coordination patterns (50 epochs)
+npx claude-flow neural train -p coordination -e 50
+
+# Train with custom learning rate
+npx claude-flow neural train -p optimization -l 0.005
+
+# Train from file
+npx claude-flow neural train -d ./training-data.json
+
+# Quick training (10 epochs)
+npx claude-flow neural train -e 10
+```
+
+## Output
+
+Training produces:
+- **Patterns Recorded**: Number of patterns stored in ReasoningBank
+- **Trajectories**: Complete learning sequences recorded
+- **SONA Adaptation**: Target is <0.05ms per operation
+- **Persistence Path**: Where patterns are saved
+
+## List Trained Patterns
+
+```bash
+# List all persisted patterns
+npx claude-flow neural patterns --action list
+
+# Search patterns by query
+npx claude-flow neural patterns --action list -q "error handling"
+
+# Analyze patterns
+npx claude-flow neural patterns --action analyze -q "coordination"
+```
+
+## Performance Targets
+
+| Metric | Target |
+|--------|--------|
+| SONA Adaptation | <0.05ms (achieved: ~2μs) |
+| Pattern Search | O(log n) with HNSW |
+| Memory Efficient | Circular buffers |
+
+## Related Commands
+
+- `neural patterns` - List and search patterns
+- `neural status` - Check neural system status
+- `neural predict` - Make predictions using trained models

package/.claude/commands/training/pattern-learn.md

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+# pattern-learn
+
+Learn patterns from successful operations.
+
+## Usage
+```bash
+npx claude-flow training pattern-learn [options]
+```
+
+## Options
+- `--source <type>` - Pattern source
+- `--threshold <score>` - Success threshold
+- `--save <name>` - Save pattern set
+
+## Examples
+```bash
+# Learn from all ops
+npx claude-flow training pattern-learn
+
+# High success only
+npx claude-flow training pattern-learn --threshold 0.9
+
+# Save patterns
+npx claude-flow training pattern-learn --save optimal-patterns
+```

package/.claude/commands/training/specialization.md

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+# Agent Specialization Training
+
+## Purpose
+Train agents to become experts in specific domains for better performance.
+
+## Specialization Areas
+
+### 1. By File Type
+Agents automatically specialize based on file extensions:
+- **.js/.ts**: Modern JavaScript patterns
+- **.py**: Pythonic idioms
+- **.go**: Go best practices
+- **.rs**: Rust safety patterns
+
+### 2. By Task Type
+```
+Tool: mcp__claude-flow__agent_spawn
+Parameters: {
+  "type": "coder",
+  "capabilities": ["react", "typescript", "testing"],
+  "name": "React Specialist"
+}
+```
+
+### 3. Training Process
+The system trains through:
+- Successful edit operations
+- Code review patterns
+- Error fix approaches
+- Performance optimizations
+
+### 4. Specialization Benefits
+```
+# Check agent specializations
+Tool: mcp__claude-flow__agent_list
+Parameters: {"swarmId": "current"}
+
+Result shows expertise levels:
+{
+  "agents": [
+    {
+      "id": "coder-123",
+      "specializations": {
+        "javascript": 0.95,
+        "react": 0.88,
+        "testing": 0.82
+      }
+    }
+  ]
+}
+```
+
+## Continuous Improvement
+Agents share learnings across sessions for cumulative expertise!
+
+## CLI Usage
+```bash
+# Train agent specialization via CLI
+npx claude-flow train agent --type coder --capabilities "react,typescript"
+
+# Check specializations
+npx claude-flow agent list --specializations
+```

package/.claude/commands/truth/start.md

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+# 📊 Truth Command
+
+View truth scores and reliability metrics for your codebase and agent tasks.
+
+## Overview
+
+The `truth` command provides comprehensive insights into code quality, agent performance, and verification metrics.
+
+## Usage
+
+```bash
+claude-flow truth [options]
+```
+
+## Options
+
+- `--format <type>` - Output format: table (default), json, csv, html
+- `--period <time>` - Time period: 1h, 24h, 7d, 30d
+- `--agent <name>` - Filter by specific agent
+- `--threshold <0-1>` - Show only scores below threshold
+- `--export <file>` - Export metrics to file
+- `--watch` - Real-time monitoring mode
+
+## Metrics Displayed
+
+### Truth Scores
+- **Overall Score**: Aggregate truth score (0.0-1.0)
+- **File Scores**: Individual file truth ratings
+- **Agent Scores**: Per-agent reliability metrics
+- **Task Scores**: Task completion quality
+
+### Trends
+- **Improvement Rate**: Quality trend over time
+- **Regression Detection**: Identifies declining scores
+- **Agent Learning**: Shows agent improvement curves
+
+### Statistics
+- **Mean Score**: Average truth score
+- **Median Score**: Middle value of scores
+- **Standard Deviation**: Score consistency
+- **Confidence Interval**: Statistical reliability
+
+## Examples
+
+### Basic Usage
+```bash
+# View current truth scores
+claude-flow truth
+
+# View scores for last 7 days
+claude-flow truth --period 7d
+
+# Export to HTML report
+claude-flow truth --export report.html --format html
+```
+
+### Advanced Analysis
+```bash
+# Monitor real-time scores
+claude-flow truth --watch
+
+# Find problematic files
+claude-flow truth --threshold 0.8
+
+# Agent-specific metrics
+claude-flow truth --agent coder --period 24h
+
+# JSON for processing
+claude-flow truth --format json | jq '.overall_score'
+```
+
+## Dashboard View
+
+```
+📊 Truth Metrics Dashboard
+━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+
+Overall Truth Score: 0.947 ✅
+Trend: ↗️ +2.3% (7d)
+
+Top Performers:
+  verification-agent   0.982 ⭐
+  code-analyzer       0.971 ⭐
+  test-generator      0.958 ✅
+
+Needs Attention:
+  refactor-agent      0.821 ⚠️
+  docs-generator      0.794 ⚠️
+
+Recent Tasks:
+  task-456  0.991 ✅  "Implement auth"
+  task-455  0.967 ✅  "Add tests"
+  task-454  0.743 ❌  "Refactor API"
+```
+
+## Integration
+
+### With CI/CD
+```yaml
+# GitHub Actions example
+- name: Check Truth Scores
+  run: |
+    claude-flow truth --format json > truth.json
+    score=$(jq '.overall_score' truth.json)
+    if (( $(echo "$score < 0.95" | bc -l) )); then
+      echo "Truth score too low: $score"
+      exit 1
+    fi
+```
+
+### With Monitoring
+```bash
+# Send to monitoring system
+claude-flow truth --format json | \
+  curl -X POST https://metrics.example.com/api/truth \
+  -H "Content-Type: application/json" \
+  -d @-
+```
+
+## Configuration
+
+Set truth display preferences in `.claude-flow/config.json`:
+
+```json
+{
+  "truth": {
+    "defaultFormat": "table",
+    "defaultPeriod": "24h",
+    "warningThreshold": 0.85,
+    "criticalThreshold": 0.75,
+    "autoExport": {
+      "enabled": true,
+      "path": ".claude-flow/metrics/truth-daily.json"
+    }
+  }
+}
+```
+
+## Related Commands
+
+- `verify` - Run verification checks
+- `pair` - Collaborative development with truth tracking
+- `report` - Generate detailed reports

package/.claude/commands/verify/check.md

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+# verify check
+
+Run verification checks on code, tasks, or agent outputs.
+
+## Usage
+
+```bash
+claude-flow verify check [options]
+```
+
+## Options
+
+- `--file <path>` - Verify specific file
+- `--task <id>` - Verify task output
+- `--directory <path>` - Verify entire directory
+- `--threshold <0-1>` - Override default threshold (0.95)
+- `--auto-fix` - Attempt automatic fixes
+- `--json` - Output results as JSON
+- `--verbose` - Show detailed verification steps
+
+## Examples
+
+```bash
+# Basic file verification
+claude-flow verify check --file src/app.js
+
+# Verify with higher threshold
+claude-flow verify check --file src/critical.js --threshold 0.99
+
+# Verify and auto-fix issues
+claude-flow verify check --directory src/ --auto-fix
+
+# Get JSON output for CI/CD
+claude-flow verify check --json > verification.json
+```
+
+## Truth Scoring
+
+The check command evaluates:
+- Code correctness
+- Best practices adherence
+- Security vulnerabilities
+- Performance implications
+- Documentation completeness
+
+## Exit Codes
+
+- `0` - Verification passed
+- `1` - Verification failed
+- `2` - Error during verification

package/.claude/commands/verify/start.md

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+# 🔍 Verification Commands
+
+Truth verification system for ensuring code quality and correctness with a 0.95 accuracy threshold.
+
+## Overview
+
+The verification system provides real-time truth checking and validation for all agent tasks, ensuring high-quality outputs and automatic rollback on failures.
+
+## Subcommands
+
+### `verify check`
+Run verification checks on current code or agent outputs.
+
+```bash
+claude-flow verify check --file src/app.js
+claude-flow verify check --task "task-123"
+claude-flow verify check --threshold 0.98
+```
+
+### `verify rollback`
+Automatically rollback changes that fail verification.
+
+```bash
+claude-flow verify rollback --to-commit abc123
+claude-flow verify rollback --last-good
+claude-flow verify rollback --interactive
+```
+
+### `verify report`
+Generate verification reports and metrics.
+
+```bash
+claude-flow verify report --format json
+claude-flow verify report --export metrics.html
+claude-flow verify report --period 7d
+```
+
+### `verify dashboard`
+Launch interactive verification dashboard.
+
+```bash
+claude-flow verify dashboard
+claude-flow verify dashboard --port 3000
+claude-flow verify dashboard --export
+```
+
+## Configuration
+
+Default threshold: **0.95** (95% accuracy required)
+
+Configure in `.claude-flow/config.json`:
+```json
+{
+  "verification": {
+    "threshold": 0.95,
+    "autoRollback": true,
+    "gitIntegration": true,
+    "hooks": {
+      "preCommit": true,
+      "preTask": true,
+      "postEdit": true
+    }
+  }
+}
+```
+
+## Integration
+
+### With Swarm Commands
+```bash
+claude-flow swarm --verify --threshold 0.98
+claude-flow hive-mind --verify
+```
+
+### With Training Pipeline
+```bash
+claude-flow train --verify --rollback-on-fail
+```
+
+### With Pair Programming
+```bash
+claude-flow pair --verify --real-time
+```
+
+## Metrics
+
+- **Truth Score**: 0.0 to 1.0 (higher is better)
+- **Confidence Level**: Statistical confidence in verification
+- **Rollback Rate**: Percentage of changes rolled back
+- **Quality Improvement**: Trend over time
+
+## Examples
+
+### Basic Verification
+```bash
+# Verify current directory
+claude-flow verify check
+
+# Verify with custom threshold
+claude-flow verify check --threshold 0.99
+
+# Verify and auto-fix
+claude-flow verify check --auto-fix
+```
+
+### Advanced Workflows
+```bash
+# Continuous verification during development
+claude-flow verify watch --directory src/
+
+# Batch verification
+claude-flow verify batch --files "*.js" --parallel
+
+# Integration testing
+claude-flow verify integration --test-suite full
+```
+
+## Performance
+
+- Verification latency: <100ms for most checks
+- Rollback time: <1s for git-based rollback
+- Dashboard refresh: Real-time via WebSocket
+
+## Related Commands
+
+- `truth` - View truth scores and metrics
+- `pair` - Collaborative development with verification
+- `train` - Training with verification feedback

package/.claude/commands/workflows/README.md

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+# Workflows Commands
+
+Commands for workflows operations in Claude Flow.
+
+## Available Commands
+
+- [workflow-create](./workflow-create.md)
+- [workflow-execute](./workflow-execute.md)
+- [workflow-export](./workflow-export.md)

package/.claude/commands/workflows/development.md

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+# Development Workflow Coordination
+
+## Purpose
+Structure Claude Code's approach to complex development tasks for maximum efficiency.
+
+## Step-by-Step Coordination
+
+### 1. Initialize Development Framework
+```
+Tool: mcp__claude-flow__swarm_init
+Parameters: {"topology": "hierarchical", "maxAgents": 8, "strategy": "specialized"}
+```
+Creates hierarchical structure for organized, top-down development.
+
+### 2. Define Development Perspectives
+```
+Tool: mcp__claude-flow__agent_spawn
+Parameters: {
+  "type": "architect",
+  "name": "System Design",
+  "capabilities": ["api-design", "database-schema"]
+}
+```
+```
+Tool: mcp__claude-flow__agent_spawn
+Parameters: {
+  "type": "coder",
+  "name": "Implementation Focus",
+  "capabilities": ["nodejs", "typescript", "express"]
+}
+```
+```
+Tool: mcp__claude-flow__agent_spawn
+Parameters: {
+  "type": "tester",
+  "name": "Quality Assurance",
+  "capabilities": ["unit-testing", "integration-testing"]
+}
+```
+Sets up architectural and implementation thinking patterns.
+
+### 3. Coordinate Implementation
+```
+Tool: mcp__claude-flow__task_orchestrate
+Parameters: {
+  "task": "Build REST API with authentication",
+  "strategy": "parallel",
+  "priority": "high",
+  "dependencies": ["database setup", "auth system"]
+}
+```
+
+### 4. Monitor Progress
+```
+Tool: mcp__claude-flow__task_status
+Parameters: {"taskId": "api-build-task-123"}
+```
+
+## What Claude Code Actually Does
+1. Uses **Write** tool to create new files
+2. Uses **Edit/MultiEdit** tools for code modifications
+3. Uses **Bash** tool for testing and building
+4. Uses **TodoWrite** tool for task tracking
+5. Follows coordination patterns for systematic implementation
+
+Remember: All code is written by Claude Code using its native tools!
+
+## CLI Usage
+```bash
+# Start development workflow via CLI
+npx claude-flow workflow dev "REST API with auth"
+
+# Create custom workflow
+npx claude-flow workflow create --name "api-dev" --steps "design,implement,test,deploy"
+
+# Execute saved workflow
+npx claude-flow workflow execute api-dev
+```