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/optimization/README.md

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

.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__claude-flow__task_orchestrate
+Parameters: {"task": "Fix typo in README.md"}
+Result: Automatically uses star topology with single agent
+```
+
+**Complex Task:**
+```
+Tool: mcp__claude-flow__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 claude-flow hook pre-task --optimize-topology"
+}
+```
+
+## Direct Optimization
+```
+Tool: mcp__claude-flow__topology_optimize
+Parameters: {"swarmId": "current"}
+```
+
+## CLI Usage
+```bash
+# Auto-optimize topology via CLI
+npx claude-flow optimize topology
+```

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

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+# cache-manage
+
+Manage operation cache for performance.
+
+## Usage
+```bash
+npx claude-flow 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 claude-flow optimization cache-manage --action view
+
+# Clear cache
+npx claude-flow optimization cache-manage --action clear
+
+# Set limits
+npx claude-flow optimization cache-manage --max-size 100 --ttl 3600
+```

.claude/commands/optimization/parallel-execute.md

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+# parallel-execute
+
+Execute tasks in parallel for maximum efficiency.
+
+## Usage
+```bash
+npx claude-flow optimization parallel-execute [options]
+```
+
+## Options
+- `--tasks <file>` - Task list file
+- `--max-parallel <n>` - Maximum parallel tasks
+- `--strategy <type>` - Execution strategy
+
+## Examples
+```bash
+# Execute task list
+npx claude-flow optimization parallel-execute --tasks tasks.json
+
+# Limit parallelism
+npx claude-flow optimization parallel-execute --tasks tasks.json --max-parallel 5
+
+# Custom strategy
+npx claude-flow optimization parallel-execute --strategy adaptive
+```

.claude/commands/optimization/parallel-execution.md

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+# Parallel Task Execution
+
+## Purpose
+Execute independent subtasks in parallel for maximum efficiency.
+
+## Coordination Strategy
+
+### 1. Task Decomposition
+```
+Tool: mcp__claude-flow__task_orchestrate
+Parameters: {
+  "task": "Build complete REST API with auth, CRUD operations, and tests",
+  "strategy": "parallel",
+  "maxAgents": 8
+}
+```
+
+### 2. Parallel Workflows
+The system automatically:
+- Identifies independent components
+- Assigns specialized agents
+- Executes in parallel where possible
+- Synchronizes at dependency points
+
+### 3. Example Breakdown
+For the REST API task:
+- **Agent 1 (Architect)**: Design API structure
+- **Agent 2-3 (Coders)**: Implement auth & CRUD in parallel
+- **Agent 4 (Tester)**: Write tests as features complete
+- **Agent 5 (Documenter)**: Update docs continuously
+
+## CLI Usage
+```bash
+# Execute parallel tasks via CLI
+npx claude-flow parallel "Build REST API" --max-agents 8
+```
+
+## Performance Gains
+- 🚀 2.8-4.4x faster execution
+- 💪 Optimal CPU utilization
+- 🔄 Automatic load balancing
+- 📈 Linear scalability with agents
+
+## Monitoring
+```
+Tool: mcp__claude-flow__swarm_monitor
+Parameters: {"interval": 1000, "swarmId": "current"}
+```
+
+Watch real-time parallel execution progress!

.claude/commands/optimization/topology-optimize.md

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+# topology-optimize
+
+Optimize swarm topology for current workload.
+
+## Usage
+```bash
+npx claude-flow optimization topology-optimize [options]
+```
+
+## Options
+- `--analyze-first` - Analyze before optimizing
+- `--target <metric>` - Optimization target
+- `--apply` - Apply optimizations
+
+## Examples
+```bash
+# Analyze and suggest
+npx claude-flow optimization topology-optimize --analyze-first
+
+# Optimize for speed
+npx claude-flow optimization topology-optimize --target speed
+
+# Apply changes
+npx claude-flow optimization topology-optimize --target efficiency --apply
+```