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/modes.md

@@ -9,6 +9,7 @@ Test modes by using `/sc:` commands - they activate automatically based on task
 |------|---------|---------------|---------------|---------------|
 | **🧠 Brainstorming** | Interactive discovery | "brainstorm", "maybe", vague requests | Socratic questions, requirement elicitation | New project planning, unclear requirements |
 | **🔍 Introspection** | Meta-cognitive analysis | Error recovery, "analyze reasoning" | Transparent thinking markers (🤔, 🎯, 💡) | Debugging, learning, optimization |
+| **🔬 Deep Research** | Systematic investigation mindset | `/sc:research`, investigation keywords | 6-phase workflow, evidence-based reasoning | Technical research, current events, market analysis |
 | **📋 Task Management** | Complex coordination | >3 steps, >2 directories | Phase breakdown, memory persistence | Multi-step operations, project management |
 | **🎯 Orchestration** | Intelligent tool selection | Multi-tool ops, high resource usage | Optimal tool routing, parallel execution | Complex analysis, performance optimization |
 | **⚡ Token Efficiency** | Compressed communication | High context usage, `--uc` flag | Symbol systems, estimated 30-50% token reduction | Resource constraints, large operations |
@@ -120,6 +121,60 @@ Introspective Approach:
 
 ---
 
+### 🔬 Deep Research Mode - Systematic Investigation Mindset
+
+**Purpose**: Research mindset for systematic investigation and evidence-based reasoning.
+
+**Auto-Activation Triggers:**
+- `/sc:research` command invocation
+- Research-related keywords: investigate, explore, discover, analyze
+- Questions requiring current information beyond knowledge cutoff
+- Complex research requirements
+- Manual flag: `--research`
+
+**Behavioral Modifications:**
+- **Thinking Style**: Systematic over casual, evidence over assumption, progressive depth exploration
+- **Communication**: Lead with confidence levels, provide inline citations, acknowledge uncertainties
+- **Priority Shifts**: Completeness over speed, accuracy over speculation, verification over assumption
+- **Process Adaptations**: Always create investigation plans, default to parallel operations, maintain evidence chains
+
+**6-Phase Research Workflow:**
+- 📋 **Understand** (5-10%): Assess query complexity and requirements
+- 📝 **Plan** (10-15%): Select strategy (planning/intent/unified) and identify parallelization
+- ✅ **TodoWrite** (5%): Create adaptive task hierarchy (3-15 tasks based on complexity)
+- 🔄 **Execute** (50-60%): Parallel-first searches and smart extraction routing
+- 📊 **Track** (Continuous): Monitor progress and update confidence scores
+- ✓ **Validate** (10-15%): Verify evidence chains and ensure completeness
+
+**Example Experience:**
+```
+Standard Mode: "Here are some search results about quantum computing..."
+Deep Research Mode: 
+"📊 Research Plan: Quantum computing breakthroughs
+ ✓ TodoWrite: Created 8 research tasks
+ 🔄 Executing parallel searches across domains
+ 📈 Confidence: 0.82 across 15 verified sources
+ 📝 Report saved: claudedocs/research_quantum_[timestamp].md"
+```
+
+#### Quality Standards
+- [ ] Minimum 2 sources per claim with inline citations
+- [ ] Confidence scoring (0.0-1.0) for all findings
+- [ ] Parallel execution by default for independent operations
+- [ ] Reports saved to claudedocs/ with proper structure
+- [ ] Clear methodology and evidence presentation
+
+**Verify:** `/sc:research "test topic"` should create TodoWrite and execute systematically  
+**Test:** All research should include confidence scores and citations  
+**Check:** Reports should be saved to claudedocs/ automatically
+
+**Works Best With:**
+- **→ Task Management**: Research planning with TodoWrite integration
+- **→ Orchestration**: Parallel Tavily/Playwright coordination
+- **Manual Override**: Use `--depth` and `--strategy` for fine control
+
+---
+
 ### 📋 Task Management Mode - Complex Coordination
 
 **Purpose**: Hierarchical task organization with session persistence for multi-step operations.