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>

setup/utils/environment.py

@@ -466,4 +466,48 @@ def create_env_file(api_keys: Dict[str, str], env_file_path: Optional[Path] = No
     except Exception as e:
         logger.error(f"Failed to create .env file: {e}")
         display_warning(f"Could not create .env file: {e}")
-        return False
+        return False
+
+
+def check_research_prerequisites() -> tuple[bool, list[str]]:
+    """
+    Check if deep research prerequisites are met
+    
+    Returns:
+        Tuple of (success: bool, warnings: List[str])
+    """
+    warnings = []
+    logger = get_logger()
+    
+    # Check Tavily API key
+    if not os.environ.get("TAVILY_API_KEY"):
+        warnings.append(
+            "TAVILY_API_KEY not set - Deep research web search will not work\n"
+            "Get your key from: https://app.tavily.com"
+        )
+        logger.warning("TAVILY_API_KEY not found in environment")
+    else:
+        logger.info("Found TAVILY_API_KEY in environment")
+    
+    # Check Node.js for MCP
+    import shutil
+    if not shutil.which("node"):
+        warnings.append(
+            "Node.js not found - Required for Tavily MCP\n"
+            "Install from: https://nodejs.org"
+        )
+        logger.warning("Node.js not found - required for Tavily MCP")
+    else:
+        logger.info("Node.js found")
+    
+    # Check npm
+    if not shutil.which("npm"):
+        warnings.append(
+            "npm not found - Required for MCP server installation\n"
+            "Usually installed with Node.js"
+        )
+        logger.warning("npm not found - required for MCP installation")
+    else:
+        logger.info("npm found")
+    
+    return len(warnings) == 0, warnings