Handles MCP tool-related requests (tools/list and tools/call).

Implements the full Ragex MCP tool catalogue (~50 tools across categories):

• Core analysis: analyze_file, analyze_directory, query_graph, list_nodes
• File watching: watch_directory, unwatch_directory, list_watched
• Semantic search: semantic_search, hybrid_search, get_embeddings_stats, metaast_search, cross_language_alternatives, expand_query, find_metaast_pattern
• Graph algorithms: find_paths, find_callers, graph_stats, betweenness_centrality, closeness_centrality, detect_communities, export_graph
• Code editing: edit_file, edit_files, validate_edit, rollback_edit, edit_history, refactor_code, advanced_refactor
• Refactor previews: preview_refactor, refactor_conflicts, undo_refactor, refactor_history, visualize_impact
• Quality & complexity: analyze_quality, quality_report, find_complex_code
• Security: scan_security, security_audit, check_secrets, analyze_security_issues
• Code analysis: find_dead_code, analyze_dead_code_patterns, find_duplicates, find_similar_code, detect_smells, analyze_business_logic
• Dependencies: analyze_dependencies, find_circular_dependencies, coupling_report
• Impact & suggestions: analyze_impact, estimate_refactoring_effort, risk_assessment, suggest_refactorings, explain_suggestion
• Semantic / OpKind: semantic_operations, semantic_analysis
• RAG pipeline: rag_query, rag_explain, rag_suggest (+ _stream variants)
• AI features: validate_with_ai
• AI usage tracking: get_ai_usage, get_ai_cache_stats, clear_ai_cache
• Agent: agent_analyze, agent_chat, agent_session_info, agent_list_sessions, agent_clear_session, read_file