feat: Add Deep Research System v4.2.0 (#380)

feat: Add Deep Research System v4.2.0 - Autonomous web research capabilities

## Overview
Comprehensive implementation of Deep Research framework aligned with DR Agent architecture, enabling autonomous, adaptive, and intelligent web research capabilities.

## Key Features

### 🔬 Deep Research Agent
- 15th specialized agent for comprehensive research orchestration
- Adaptive planning strategies: Planning-Only, Intent-Planning, Unified Intent-Planning
- Multi-hop reasoning with genealogy tracking (up to 5 hops)
- Self-reflective mechanisms with confidence scoring (0.0-1.0)
- Case-based learning for cross-session intelligence

### 🎯 New /sc:research Command
- Intelligent web research with depth control (quick/standard/deep/exhaustive)
- Parallel-first execution for optimal performance
- Domain filtering and time-based search options
- Automatic report generation in claudedocs/

### 🔍 Tavily MCP Integration
- 7th MCP server for real-time web search
- News search with time filtering
- Content extraction from search results
- Multi-round searching with iterative refinement
- Free tier available with optional API key

### 🎨 MODE_DeepResearch
- 7th behavioral mode for systematic investigation
- 6-phase workflow: Understand → Plan → TodoWrite → Execute → Track → Validate
- Evidence-based reasoning with citation management
- Parallel operation defaults for efficiency

## Technical Changes

### Framework Updates
- Updated agent count: 14 → 15 agents
- Updated mode count: 6 → 7 modes
- Updated MCP server count: 6 → 7 servers
- Updated command count: 24 → 25 commands

### Configuration
- Added RESEARCH_CONFIG.md for research settings
- Added deep_research_workflows.md with examples
- Standardized file naming conventions (UPPERCASE for Core)
- Removed multi-source investigation features for simplification

### Integration Points
- Enhanced MCP component with remote server support
- Added check_research_prerequisites() in environment.py
- Created verify_research_integration.sh script
- Updated all documentation guides

## Requirements
- TAVILY_API_KEY environment variable (free tier available)
- Node.js and npm for Tavily MCP execution

## Documentation
- Complete user guide integration
- Workflow examples and best practices
- API configuration instructions
- Depth level explanations

🤖 Generated with Claude Code

Co-authored-by: moshe_anconina <moshe_a@ituran.com>
Co-authored-by: Claude <noreply@anthropic.com>

Docs/User-Guide/commands.md

@@ -1,6 +1,6 @@
 # SuperClaude Commands Guide
 
-SuperClaude provides 24 commands for Claude Code: `/sc:*` commands for workflows and `@agent-*` for specialists.
+SuperClaude provides 25 commands for Claude Code: `/sc:*` commands for workflows and `@agent-*` for specialists.
 
 ## Command Types
 
@@ -106,7 +106,7 @@ python3 -m SuperClaude install --list-components | grep mcp
 
 - [Essential Commands](#essential-commands) - Start here (8 core commands)
 - [Common Workflows](#common-workflows) - Command combinations that work
-- [Full Command Reference](#full-command-reference) - All 23 commands organized by category
+- [Full Command Reference](#full-command-reference) - All 25 commands organized by category
 - [Troubleshooting](#troubleshooting) - Common issues and solutions
 - [Command Index](#command-index) - Find commands by category
 
@@ -133,6 +133,24 @@ python3 -m SuperClaude install --list-components | grep mcp
 - Discovering available commands: `/sc:help`
 - Getting a quick reminder of command names: `/sc:help`
 
+### `/sc:research` - Deep Research Command
+**Purpose**: Comprehensive web research with adaptive planning and intelligent search  
+**Syntax**: `/sc:research "[query]"` `[--depth quick|standard|deep|exhaustive] [--strategy planning|intent|unified]`
+
+**Use Cases**:
+- Technical research: `/sc:research "latest React 19 features" --depth deep`
+- Market analysis: `/sc:research "AI coding assistant landscape 2024" --strategy unified`
+- Academic investigation: `/sc:research "quantum computing breakthroughs" --depth exhaustive`
+- Current events: `/sc:research "latest AI developments 2024"`
+
+**Key Capabilities**:
+- **6-Phase Workflow**: Understand → Plan → TodoWrite → Execute → Track → Validate
+- **Adaptive Depth**: Quick (basic search), Standard (extended), Deep (comprehensive), Exhaustive (maximum depth)
+- **Planning Strategies**: Planning (direct), Intent (clarify first), Unified (collaborative)
+- **Parallel Execution**: Default parallel searches and extractions
+- **Evidence Management**: Clear citations with relevance scoring
+- **Output Standards**: Reports saved to `claudedocs/research_[topic]_[timestamp].md`
+
 ### `/sc:implement` - Feature Development  
 **Purpose**: Full-stack feature implementation with intelligent specialist routing  
 **Syntax**: `/sc:implement "feature description"` `[--type frontend|backend|fullstack] [--focus security|performance]`  
@@ -277,6 +295,7 @@ python3 -m SuperClaude install --list-components | grep mcp
 | Command | Purpose | Best For |
 |---------|---------|----------|
 | **analyze** | Code assessment | Quality audits, security reviews |
+| **research** | Web research with intelligent search | Technical research, current events, market analysis |
 | **business-panel** | Strategic analysis | Business decisions, competitive assessment |
 | **spec-panel** | Specification review | Requirements validation, architecture analysis |
 | **troubleshoot** | Problem diagnosis | Bug investigation, performance issues |