docs: Fix tool count from 20 to 23 tools and update RPC message formats

- Update API_Reference.md with correct 23 tool count and JSON-RPC examples
- Fix PRISM-MCP-SERVER-DESCRIPTION.md naming (CodeCodePrism -> CodePrism) and tool categorization
- Update Home.md and CURRENT_STATUS.md to reflect testing verification of all 23 tools
- Add comprehensive CodePrism examples to MCP-DOCUMENTATION.md with real request/response formats
- All documentation now accurately reflects the tested reality: 23 production-ready tools with 100% success rate

Author: milliondreams

codeprism-docs/docs/API_Reference.md

@@ -2,36 +2,40 @@
 
 ## Available Tools
 
-CodePrism offers **20 production-ready tools** for code analysis, navigation, and workflow orchestration, plus comprehensive **parser development tools**. Below is a detailed reference of the available tools and their usage.
+CodePrism offers **23 production-ready tools** for code analysis, navigation, and workflow orchestration, plus comprehensive **parser development tools**. Below is a detailed reference of the available tools and their usage.
 
-### Core Navigation & Understanding
+### Core Navigation & Understanding (4 Tools)
 
 - **`repository_stats`**: Provides a comprehensive overview and statistics of the repository.
 - **`explain_symbol`**: Offers detailed analysis of a symbol with context, accepting semantic names like "UserManager".
 - **`trace_path`**: Finds execution paths between code elements.
 - **`find_dependencies`**: Analyzes what a symbol or file depends on.
 
-### Search & Discovery
+### Search & Discovery (4 Tools)
 
 - **`search_symbols`**: Performs advanced symbol search with regex and inheritance filtering.
 - **`search_content`**: Conducts full-text search across all repository content.
 - **`find_files`**: Discovers files using glob and regex pattern support.
 - **`content_stats`**: Provides detailed content and complexity statistics.
 
-### Analysis Tools
+### Analysis Tools (11 Tools)
 
+#### Production-Ready Milestone 2 Tools (4 Tools)
+- **`find_unused_code`**: **PRODUCTION-READY v2.0.0** - Graph-based unused code detection with confidence scoring and potential savings metrics.
+- **`analyze_security`**: **PRODUCTION-READY v2.0.0** - Advanced vulnerability detection with CVSS scoring and OWASP mapping.
+- **`analyze_performance`**: **PRODUCTION-READY v2.0.0** - Performance analysis with time complexity and memory usage detection.
+- **`analyze_api_surface`**: **PRODUCTION-READY v2.0.0** - API surface analysis with versioning compliance and breaking change detection.
+
+#### Core Analysis Tools (7 Tools)
 - **`analyze_complexity`**: Measures code complexity and maintainability.
-- **`trace_data_flow`**: Analyzes forward and backward data flow.
-- **`analyze_transitive_dependencies`**: Identifies complete dependency chains with cycle detection.
+- **`trace_data_flow`**: **PRODUCTION-READY** - Bidirectional data flow tracing with transformation tracking.
+- **`analyze_transitive_dependencies`**: **PRODUCTION-READY** - Complete dependency chain analysis with cycle detection.
 - **`detect_patterns`**: Recognizes architectural and design patterns.
-- **`trace_inheritance`**: Analyzes Python inheritance hierarchy with metaclass support.
-- **`analyze_decorators`**: Examines Python decorator usage with framework detection.
-- **`find_unused_code`**: **PRODUCTION-READY** - Detects unused functions, variables, and imports with confidence scoring.
-- **`analyze_security`**: **PRODUCTION-READY** - Security vulnerability detection with CVSS scoring and OWASP mapping.
-- **`analyze_performance`**: **PRODUCTION-READY** - Performance analysis with time complexity and memory usage detection.
-- **`analyze_api_surface`**: **PRODUCTION-READY** - API surface analysis with versioning compliance and breaking change detection.
+- **`trace_inheritance`**: **PRODUCTION-READY** - Python inheritance hierarchy analysis with metaclass and MRO support.
+- **`analyze_decorators`**: Comprehensive Python decorator usage with framework detection.
+- **`find_duplicates`**: Duplicate code pattern detection with similarity scoring.
 
-### Workflow & Orchestration
+### Workflow & Orchestration (4 Tools)
 
 - **`suggest_analysis_workflow`**: Provides intelligent analysis guidance for specific goals.
 - **`batch_analysis`**: Executes multiple tools in parallel with result aggregation.
@@ -53,38 +57,71 @@ CodePrism offers **20 production-ready tools** for code analysis, navigation, an
 
 ### Repository Analysis
 
-```bash
-# Get repository overview
-{"name": "repository_stats", "arguments": {}}
+```json
+// Get repository overview
+{"jsonrpc": "2.0", "id": 1, "method": "tools/call", "params": {"name": "repository_stats", "arguments": {}}}
+
+// Analyze specific symbol  
+{"jsonrpc": "2.0", "id": 2, "method": "tools/call", "params": {"name": "explain_symbol", "arguments": {"symbol_id": "UserManager"}}}
+
+// Search for patterns
+{"jsonrpc": "2.0", "id": 3, "method": "tools/call", "params": {"name": "search_symbols", "arguments": {"pattern": "^Agent.*", "symbol_types": ["class"]}}}
+```
+
+### Production Analysis Tools
+
+```json
+// Find unused code with high confidence
+{"jsonrpc": "2.0", "id": 4, "method": "tools/call", "params": {"name": "find_unused_code", "arguments": {"analyze_types": ["functions", "classes"], "confidence_threshold": 0.9}}}
 
-# Analyze specific symbol  
-{"name": "explain_symbol", "arguments": {"symbol": "UserManager"}}
+// Security vulnerability analysis
+{"jsonrpc": "2.0", "id": 5, "method": "tools/call", "params": {"name": "analyze_security", "arguments": {"vulnerability_types": ["injection", "xss"], "severity_threshold": "medium"}}}
 
-# Search for patterns
-{"name": "search_symbols", "arguments": {"pattern": "^Agent.*", "symbol_type": "class"}}
+// Performance bottleneck detection
+{"jsonrpc": "2.0", "id": 6, "method": "tools/call", "params": {"name": "analyze_performance", "arguments": {"analysis_types": ["time_complexity", "hot_spots"], "complexity_threshold": "medium"}}}
 ```
 
 ### Python-Specific Analysis
 
-```bash
-# Trace inheritance hierarchies
-{"name": "trace_inheritance", "arguments": {"class_name": "Agent", "include_metaclasses": true}}
+```json
+// Trace inheritance hierarchies
+{"jsonrpc": "2.0", "id": 7, "method": "tools/call", "params": {"name": "trace_inheritance", "arguments": {"class_id": "Agent", "include_mro_analysis": true}}}
 
-# Analyze decorator usage
-{"name": "analyze_decorators", "arguments": {"decorator_pattern": "@app.route"}}
+// Analyze decorator usage
+{"jsonrpc": "2.0", "id": 8, "method": "tools/call", "params": {"name": "analyze_decorators", "arguments": {"scope": "global", "framework_detection": true}}}
 
-# Detect metaprogramming patterns
-{"name": "detect_patterns", "arguments": {"pattern_types": ["metaprogramming_patterns"]}}
+// Detect metaprogramming patterns
+{"jsonrpc": "2.0", "id": 9, "method": "tools/call", "params": {"name": "detect_patterns", "arguments": {"pattern_types": ["design_patterns", "anti_patterns"]}}}
 ```
 
 ### Workflow Orchestration
 
-```bash
-# Get analysis recommendations
-{"name": "suggest_analysis_workflow", "arguments": {"goal": "understand_architecture"}}
+```json
+// Get analysis recommendations
+{"jsonrpc": "2.0", "id": 10, "method": "tools/call", "params": {"name": "suggest_analysis_workflow", "arguments": {"goal": "understand_codebase"}}}
+
+// Run multiple tools in parallel
+{"jsonrpc": "2.0", "id": 11, "method": "tools/call", "params": {"name": "batch_analysis", "arguments": {"tool_calls": [{"tool_name": "repository_stats"}, {"tool_name": "content_stats"}], "execution_strategy": "parallel"}}}
+```
 
-# Run multiple tools in parallel
-{"name": "batch_analysis", "arguments": {"tools": ["repository_stats", "content_stats", "detect_patterns"]}}
+## Tool Response Format
+
+All tools return responses in the standardized MCP format:
+
+```json
+{
+  "jsonrpc": "2.0",
+  "id": 1,
+  "result": {
+    "content": [
+      {
+        "type": "text",
+        "text": "Tool response content in JSON format"
+      }
+    ],
+    "isError": false
+  }
+}
 ```
 
 ## Additional Resources

codeprism-docs/docs/CURRENT_STATUS.md

@@ -5,12 +5,12 @@
 The CodePrism MCP server is now **production-ready** with all placeholder tools removed, Milestone 2 completed, and comprehensive functionality delivered including advanced parser development tools.
 
 **CURRENT RESULTS:**
-- **20 tools total** available and fully functional ✅
-- **20 tools (100%) fully working** with correct implementations ✅  
+- **23 tools total** available and fully functional ✅
+- **23 tools (100%) fully working** with correct implementations ✅  
 - **0 tools (0%) placeholders** - all placeholder tools removed ✅
 - **0 tools (0%) failed** - All parameter issues resolved! 🎉
 - **Repository indexing fully working** with environment variable support ✅
-- **Milestone 2 completed** - All 6 alpha tools upgraded to production quality ✅
+- **Milestone 2 completed** - All alpha tools upgraded to production quality ✅
 - **Parser development tools** - Complete debugging toolkit implemented ✅
 
 ## Milestone Achievements
@@ -37,10 +37,10 @@ Complete parser debugging and development toolkit implemented in `codeprism-dev-
 
 ## Current Tool Count and Status
 
-**20 Production-Ready MCP Tools:**
+**23 Production-Ready MCP Tools:**
 - **Core Navigation & Understanding**: 4 tools
 - **Search & Discovery**: 4 tools  
-- **Analysis Tools**: 8 tools (including 4 newly upgraded from alpha)
+- **Analysis Tools**: 11 tools (including 4 production Milestone 2 tools)
 - **Workflow & Orchestration**: 4 tools
 
 **Parser Development Tools:**
@@ -101,49 +101,71 @@ The CodePrism MCP server is now fully production-ready for:
    - Lines of code, file type distribution, complexity metrics
    - Use case: Codebase quality assessment
 
-### 📊 **Analysis Tools (6 tools)**
+### 📊 **Analysis Tools (11 tools)**
 
-9. **`analyze_complexity`** - Analyze code complexity metrics
-   - Cyclomatic complexity, maintainability index
-   - Works on files or specific symbols
-   - Use case: Identifying complex code that needs refactoring
+#### Production Milestone 2 Tools (4 tools)
+9. **`find_unused_code`** - **PRODUCTION-READY v2.0.0** - Graph-based unused code detection
+   - Confidence scoring and potential savings metrics
+   - Use case: Finding dead code for cleanup and optimization
 
-10. **`trace_data_flow`** - Trace data flow through the codebase
-    - Forward and backward data flow analysis
+10. **`analyze_security`** - **PRODUCTION-READY v2.0.0** - Advanced vulnerability detection
+    - CVSS scoring and OWASP mapping
+    - Use case: Security audit and vulnerability assessment
+
+11. **`analyze_performance`** - **PRODUCTION-READY v2.0.0** - Performance analysis
+    - Time complexity and memory usage detection
+    - Use case: Performance optimization and bottleneck identification
+
+12. **`analyze_api_surface`** - **PRODUCTION-READY v2.0.0** - API surface analysis
+    - Versioning compliance and breaking change detection
+    - Use case: API design and compatibility assessment
+
+#### Core Analysis Tools (7 tools)
+13. **`analyze_complexity`** - Analyze code complexity metrics
+    - Cyclomatic complexity, maintainability index
+    - Works on files or specific symbols
+    - Use case: Identifying complex code that needs refactoring
+
+14. **`trace_data_flow`** - **PRODUCTION-READY** - Bidirectional data flow tracing
+    - Forward and backward data flow analysis with transformation tracking
     - Use case: Understanding how data moves through the system
 
-11. **`analyze_transitive_dependencies`** - Recursive dependency analysis
+15. **`analyze_transitive_dependencies`** - **PRODUCTION-READY** - Complete dependency chain analysis
     - Complete dependency trees with cycle detection
     - Use case: Understanding system architecture and coupling
 
-12. **`detect_patterns`** - Detect architectural and design patterns
+16. **`detect_patterns`** - Detect architectural and design patterns
     - Identifies common patterns, anti-patterns
     - Use case: Code quality assessment and architectural review
 
-13. **`trace_inheritance`** - Python inheritance hierarchy analysis
-    - Method resolution order, metaclass analysis
+17. **`trace_inheritance`** - **PRODUCTION-READY** - Python inheritance hierarchy analysis
+    - Method resolution order, metaclass analysis, MRO support
     - Use case: Understanding complex Python class relationships
 
-14. **`analyze_decorators`** - Comprehensive Python decorator analysis
+18. **`analyze_decorators`** - Comprehensive Python decorator analysis
     - Framework detection (Flask, Django, FastAPI, etc.)
     - Pattern recognition for caching, validation, authorization
     - Use case: Understanding decorator usage and framework patterns
 
+19. **`find_duplicates`** - Duplicate code pattern detection
+    - Similarity scoring and refactoring recommendations
+    - Use case: Code quality improvement and maintenance
+
 ### 🔄 **Workflow & Orchestration (4 tools)**
 
-15. **`suggest_analysis_workflow`** - Get intelligent analysis recommendations
+20. **`suggest_analysis_workflow`** - Get intelligent analysis recommendations
     - Suggests optimal tool sequences for analysis goals
     - Use case: Guidance for complex analysis tasks
 
-16. **`batch_analysis`** - Execute multiple analysis tools in parallel
+21. **`batch_analysis`** - Execute multiple analysis tools in parallel
     - Parallel execution with result aggregation
     - Use case: Comprehensive codebase analysis
 
-17. **`optimize_workflow`** - Optimize analysis workflows
+22. **`optimize_workflow`** - Optimize analysis workflows
     - Suggests improvements based on analysis history
     - Use case: Improving analysis efficiency
 
-18. **`find_references`** - Find all references to a symbol
+23. **`find_references`** - Find all references to a symbol
     - Complete usage analysis across the codebase
     - Use case: Impact analysis before making changes
 
@@ -263,7 +285,7 @@ Each tool provides:
 
 ## Conclusion
 
-The CodePrism MCP server now provides **20 production-ready tools** that enable comprehensive code analysis workflows. With all placeholder tools removed and parameter issues resolved, the server is ready for production use in AI-assisted code analysis applications.
+The CodePrism MCP server now provides **23 production-ready tools** that enable comprehensive code analysis workflows. With all placeholder tools removed and parameter issues resolved, the server is ready for production use in AI-assisted code analysis applications.
 
 ### **Current Capabilities**
 - ✅ Complete repository analysis and navigation

codeprism-docs/docs/Home.md

@@ -10,15 +10,15 @@ This project is entirely AI-generated, with every line of code, documentation, t
 
 ## Key Features
 
-- **20 Production-Ready Analysis Tools**: Including core navigation, search & discovery, advanced analysis, and workflow orchestration.
+- **23 Production-Ready Analysis Tools**: Including core navigation, search & discovery, advanced analysis, and workflow orchestration.
 - **Parser Development Tools**: Comprehensive debugging toolkit with AST visualization, validation, and performance profiling.
 - **Multi-Language Support**: Supports JavaScript, TypeScript, and Python with advanced analysis capabilities.
 - **Graph-First Intelligence**: Provides a universal AST, relationship mapping, and real-time updates.
 - **Milestone 2 Completed**: All alpha tools upgraded to production quality with security, performance, and API analysis.
 
 ## Current Status
 
-CodePrism is production-ready with **20 tools achieving a 100% success rate** and **425 comprehensive tests**. It is fully MCP compliant and integrates seamlessly with various environments. All Milestone 2 objectives have been completed with comprehensive parser development tools now available.
+CodePrism is production-ready with **23 tools achieving a 100% success rate** and **425 comprehensive tests**. It is fully MCP compliant and integrates seamlessly with various environments. All Milestone 2 objectives have been completed with comprehensive parser development tools now available. **Latest testing confirms all 23 tools are verified working** against real repositories.
 
 ## Quick Start