Phase 06 Tier 1: Complete Backend Implementation - Recovery Tracking & Swap System

COMPLETED TASKS:
✅ 06-01: Workout Swap System
   - Added swapped_from_id to workout_logs
   - Created workout_swaps table for history
   - POST /api/workouts/:id/swap endpoint
   - GET /api/workouts/available endpoint
   - Reversible swaps with audit trail

✅ 06-02: Muscle Group Recovery Tracking
   - Created muscle_group_recovery table
   - Implemented calculateRecoveryScore() function
   - GET /api/recovery/muscle-groups endpoint
   - GET /api/recovery/most-recovered endpoint
   - Auto-tracking on workout log completion

✅ 06-03: Smart Workout Recommendations
   - GET /api/recommendations/smart-workout endpoint
   - 7-day workout analysis algorithm
   - Recovery-based filtering (>30% threshold)
   - Top 3 recommendations with context
   - Context-aware reasoning messages

DATABASE CHANGES:
- Added 4 new tables: muscle_group_recovery, workout_swaps, custom_workouts, custom_workout_exercises
- Extended workout_logs with: swapped_from_id, source_type, custom_workout_id, custom_workout_exercise_id
- Created 7 new indexes for performance

IMPLEMENTATION:
- Recovery service with 4 core functions
- 2 new route handlers (recovery, smartRecommendations)
- Updated workouts router with swap endpoints
- Integrated recovery tracking into POST /api/logs
- Full error handling and logging

TESTING:
- Test file created: /backend/test/phase-06-tests.js
- Ready for E2E and staging validation

STATUS: Ready for frontend integration and production review
Branch: feature/06-phase-06

.claude/commands/monitoring/README.md

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

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

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

.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__claude-flow__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__claude-flow__agent_list`
+2. Get specific agent metrics: Use tool `mcp__claude-flow__agent_metrics` with parameters `{"agentId": "coder-123"}`
+3. Monitor agent performance: Use tool `mcp__claude-flow__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/

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

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+# real-time-view
+
+Real-time view of swarm activity.
+
+## Usage
+```bash
+npx claude-flow 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 claude-flow monitoring real-time-view
+
+# Filter errors
+npx claude-flow monitoring real-time-view --filter errors
+
+# Highlight pattern
+npx claude-flow monitoring real-time-view --highlight "API"
+```

.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__claude-flow__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__claude-flow__swarm_status`
+2. Monitor in real-time: Use tool `mcp__claude-flow__swarm_monitor` with parameters `{"interval": 1000}`
+3. Get agent metrics: Use tool `mcp__claude-flow__agent_metrics` with parameters `{"agentId": "agent-123"}`
+4. Health check: Use tool `mcp__claude-flow__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/

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

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