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# Directory Structure

```
├── .actrc
├── .gitattributes
├── .github
│   └── workflows
│       ├── ci.yml
│       ├── mcp-compliance.yml
│       └── pr-validation.yml
├── .gitignore
├── agent.md
├── assets
│   └── logo.png
├── CLAUDE.md
├── config
│   └── framework-state.json
├── docs
│   ├── architecture.md
│   ├── chain-modification-examples.md
│   ├── contributing.md
│   ├── enhanced-gate-system.md
│   ├── execution-architecture-guide.md
│   ├── installation-guide.md
│   ├── mcp-tool-usage-guide.md
│   ├── mcp-tools-reference.md
│   ├── prompt-format-guide.md
│   ├── prompt-management.md
│   ├── prompt-vs-template-guide.md
│   ├── README.md
│   ├── template-development-guide.md
│   ├── TODO.md
│   ├── troubleshooting.md
│   └── version-history.md
├── LICENSE
├── local-test.sh
├── plans
│   ├── nunjucks-dynamic-chain-orchestration.md
│   ├── outputschema-realtime-progress-and-validation.md
│   ├── parallel-conditional-execution-analysis.md
│   ├── sqlite-storage-migration.md
│   └── symbolic-command-language-implementation.md
├── README.md
├── scripts
│   ├── setup-windows-testing.sh
│   ├── test_server.js
│   ├── test-all-platforms.sh
│   └── windows-tests
│       ├── test-windows-paths.js
│       ├── test-windows-startup.sh
│       └── windows-env.sh
└── server
    ├── config
    │   ├── framework-state.json
    │   └── tool-descriptions.json
    ├── config.json
    ├── jest.config.cjs
    ├── LICENSE
    ├── package-lock.json
    ├── package.json
    ├── prompts
    │   ├── analysis
    │   │   ├── advanced_analysis_engine.md
    │   │   ├── content_analysis.md
    │   │   ├── deep_analysis.md
    │   │   ├── deep_research.md
    │   │   ├── markdown_notebook.md
    │   │   ├── note_integration.md
    │   │   ├── note_refinement.md
    │   │   ├── notes.md
    │   │   ├── progressive_research.md
    │   │   ├── prompts.json
    │   │   ├── query_refinement.md
    │   │   └── review.md
    │   ├── architecture
    │   │   ├── prompts.json
    │   │   └── strategic-system-alignment.md
    │   ├── content_processing
    │   │   ├── format_enhancement.md
    │   │   ├── noteIntegration.md
    │   │   ├── obsidian_metadata_optimizer.md
    │   │   ├── prompts.json
    │   │   ├── vault_related_notes_finder.md
    │   │   └── video_notes_enhanced.md
    │   ├── debugging
    │   │   ├── analyze_logs.md
    │   │   └── prompts.json
    │   ├── development
    │   │   ├── analyze_code_structure.md
    │   │   ├── analyze_file_structure.md
    │   │   ├── code_review_optimization_chain.md
    │   │   ├── component_flow_analysis.md
    │   │   ├── create_modularization_plan.md
    │   │   ├── detect_code_issues.md
    │   │   ├── detect_project_commands.md
    │   │   ├── expert_code_implementation.md
    │   │   ├── generate_comprehensive_claude_md.md
    │   │   ├── prompts.json
    │   │   ├── strategicImplement.md
    │   │   ├── suggest_code_improvements.md
    │   │   └── transform_code_to_modules.md
    │   ├── documentation
    │   │   ├── create_docs_chain.md
    │   │   ├── docs-content-creation.md
    │   │   ├── docs-content-planning.md
    │   │   ├── docs-final-assembly.md
    │   │   ├── docs-project-analysis.md
    │   │   ├── docs-review-refinement.md
    │   │   └── prompts.json
    │   ├── education
    │   │   ├── prompts.json
    │   │   └── vault_integrated_notes.md
    │   ├── general
    │   │   ├── diagnose.md
    │   │   └── prompts.json
    │   ├── promptsConfig.json
    │   └── testing
    │       ├── final_verification_test.md
    │       └── prompts.json
    ├── README.md
    ├── scripts
    │   └── validate-dependencies.js
    ├── src
    │   ├── api
    │   │   └── index.ts
    │   ├── chain-session
    │   │   └── manager.ts
    │   ├── config
    │   │   └── index.ts
    │   ├── Dockerfile
    │   ├── execution
    │   │   ├── context
    │   │   │   ├── context-resolver.ts
    │   │   │   ├── framework-injector.ts
    │   │   │   └── index.ts
    │   │   ├── index.ts
    │   │   ├── parsers
    │   │   │   ├── argument-parser.ts
    │   │   │   ├── index.ts
    │   │   │   └── unified-command-parser.ts
    │   │   └── types.ts
    │   ├── frameworks
    │   │   ├── framework-manager.ts
    │   │   ├── framework-state-manager.ts
    │   │   ├── index.ts
    │   │   ├── integration
    │   │   │   ├── framework-semantic-integration.ts
    │   │   │   └── index.ts
    │   │   ├── methodology
    │   │   │   ├── guides
    │   │   │   │   ├── 5w1h-guide.ts
    │   │   │   │   ├── cageerf-guide.ts
    │   │   │   │   ├── react-guide.ts
    │   │   │   │   └── scamper-guide.ts
    │   │   │   ├── index.ts
    │   │   │   ├── interfaces.ts
    │   │   │   └── registry.ts
    │   │   ├── prompt-guidance
    │   │   │   ├── index.ts
    │   │   │   ├── methodology-tracker.ts
    │   │   │   ├── service.ts
    │   │   │   ├── system-prompt-injector.ts
    │   │   │   └── template-enhancer.ts
    │   │   └── types
    │   │       ├── index.ts
    │   │       ├── integration-types.ts
    │   │       ├── methodology-types.ts
    │   │       └── prompt-guidance-types.ts
    │   ├── gates
    │   │   ├── constants.ts
    │   │   ├── core
    │   │   │   ├── gate-definitions.ts
    │   │   │   ├── gate-loader.ts
    │   │   │   ├── gate-validator.ts
    │   │   │   ├── index.ts
    │   │   │   └── temporary-gate-registry.ts
    │   │   ├── definitions
    │   │   │   ├── code-quality.json
    │   │   │   ├── content-structure.json
    │   │   │   ├── educational-clarity.json
    │   │   │   ├── framework-compliance.json
    │   │   │   ├── research-quality.json
    │   │   │   ├── security-awareness.json
    │   │   │   └── technical-accuracy.json
    │   │   ├── gate-state-manager.ts
    │   │   ├── guidance
    │   │   │   ├── FrameworkGuidanceFilter.ts
    │   │   │   └── GateGuidanceRenderer.ts
    │   │   ├── index.ts
    │   │   ├── intelligence
    │   │   │   ├── GatePerformanceAnalyzer.ts
    │   │   │   └── GateSelectionEngine.ts
    │   │   ├── templates
    │   │   │   ├── code_quality_validation.md
    │   │   │   ├── educational_clarity_validation.md
    │   │   │   ├── framework_compliance_validation.md
    │   │   │   ├── research_self_validation.md
    │   │   │   ├── security_validation.md
    │   │   │   ├── structure_validation.md
    │   │   │   └── technical_accuracy_validation.md
    │   │   └── types.ts
    │   ├── index.ts
    │   ├── logging
    │   │   └── index.ts
    │   ├── mcp-tools
    │   │   ├── config-utils.ts
    │   │   ├── constants.ts
    │   │   ├── index.ts
    │   │   ├── prompt-engine
    │   │   │   ├── core
    │   │   │   │   ├── engine.ts
    │   │   │   │   ├── executor.ts
    │   │   │   │   ├── index.ts
    │   │   │   │   └── types.ts
    │   │   │   ├── index.ts
    │   │   │   ├── processors
    │   │   │   │   ├── response-formatter.ts
    │   │   │   │   └── template-processor.ts
    │   │   │   └── utils
    │   │   │       ├── category-extractor.ts
    │   │   │       ├── classification.ts
    │   │   │       ├── context-builder.ts
    │   │   │       └── validation.ts
    │   │   ├── prompt-manager
    │   │   │   ├── analysis
    │   │   │   │   ├── comparison-engine.ts
    │   │   │   │   ├── gate-analyzer.ts
    │   │   │   │   └── prompt-analyzer.ts
    │   │   │   ├── core
    │   │   │   │   ├── index.ts
    │   │   │   │   ├── manager.ts
    │   │   │   │   └── types.ts
    │   │   │   ├── index.ts
    │   │   │   ├── operations
    │   │   │   │   └── file-operations.ts
    │   │   │   ├── search
    │   │   │   │   ├── filter-parser.ts
    │   │   │   │   └── prompt-matcher.ts
    │   │   │   └── utils
    │   │   │       ├── category-manager.ts
    │   │   │       └── validation.ts
    │   │   ├── shared
    │   │   │   └── structured-response-builder.ts
    │   │   ├── system-control.ts
    │   │   ├── tool-description-manager.ts
    │   │   └── types
    │   │       └── shared-types.ts
    │   ├── metrics
    │   │   ├── analytics-service.ts
    │   │   ├── index.ts
    │   │   └── types.ts
    │   ├── performance
    │   │   ├── index.ts
    │   │   └── monitor.ts
    │   ├── prompts
    │   │   ├── category-manager.ts
    │   │   ├── converter.ts
    │   │   ├── file-observer.ts
    │   │   ├── hot-reload-manager.ts
    │   │   ├── index.ts
    │   │   ├── loader.ts
    │   │   ├── promptUtils.ts
    │   │   ├── registry.ts
    │   │   └── types.ts
    │   ├── runtime
    │   │   ├── application.ts
    │   │   └── startup.ts
    │   ├── semantic
    │   │   ├── configurable-semantic-analyzer.ts
    │   │   └── integrations
    │   │       ├── index.ts
    │   │       └── llm-clients.ts
    │   ├── server
    │   │   ├── index.ts
    │   │   └── transport
    │   │       └── index.ts
    │   ├── smithery.yaml
    │   ├── text-references
    │   │   ├── conversation.ts
    │   │   └── index.ts
    │   ├── types
    │   │   └── index.ts
    │   ├── types.ts
    │   └── utils
    │       ├── chainUtils.ts
    │       ├── errorHandling.ts
    │       ├── global-resource-tracker.ts
    │       ├── index.ts
    │       └── jsonUtils.ts
    ├── tests
    │   ├── ci-startup-validation.js
    │   ├── enhanced-validation
    │   │   ├── contract-validation
    │   │   │   ├── contract-test-suite.js
    │   │   │   ├── interface-contracts.js
    │   │   │   └── interface-contracts.ts
    │   │   ├── environment-validation
    │   │   │   ├── environment-parity-checker.js
    │   │   │   └── environment-test-suite.js
    │   │   ├── lifecycle-validation
    │   │   │   ├── lifecycle-test-suite.js
    │   │   │   └── process-lifecycle-validator.js
    │   │   └── validation-orchestrator.js
    │   ├── helpers
    │   │   └── test-helpers.js
    │   ├── integration
    │   │   ├── mcp-tools.test.ts
    │   │   ├── server-startup.test.ts
    │   │   └── unified-parsing-integration.test.ts
    │   ├── performance
    │   │   ├── parsing-system-benchmark.test.ts
    │   │   └── server-performance.test.ts
    │   ├── scripts
    │   │   ├── consolidated-tools.js
    │   │   ├── establish-performance-baselines.js
    │   │   ├── functional-mcp-validation.js
    │   │   ├── integration-mcp-tools.js
    │   │   ├── integration-routing-system.js
    │   │   ├── integration-server-startup.js
    │   │   ├── integration-unified-parsing.js
    │   │   ├── methodology-guides.js
    │   │   ├── performance-memory.js
    │   │   ├── runtime-integration.js
    │   │   ├── unit-conversation-manager.js
    │   │   ├── unit-semantic-analyzer.js
    │   │   └── unit-unified-parsing.js
    │   ├── setup.ts
    │   ├── test-enhanced-parsing.js
    │   └── unit
    │       ├── conversation-manager.test.ts
    │       ├── semantic-analyzer-three-tier.test.ts
    │       └── unified-parsing-system.test.ts
    ├── tsconfig.json
    └── tsconfig.test.json
```

# Files

--------------------------------------------------------------------------------
/server/prompts/debugging/analyze_logs.md:
--------------------------------------------------------------------------------

```markdown
# Advanced Log Analysis & Debugging

## Description
Comprehensive log analysis template incorporating advanced debugging strategies used by senior developers and SREs for systematic root cause analysis

## System Message
You are a SENIOR DIAGNOSTIC AGENT with expertise in advanced log analysis and production system debugging. Your mission is to methodically analyze logs using professional debugging strategies to identify root causes and provide comprehensive actionable insights.

You have access to all necessary tools for thorough investigation: codebase search, file reading, web research, and MCP tools. Use them systematically to build evidence-based conclusions.

## User Message Template
## Advanced Log Analysis Request

**Logs to Analyze:**
```
{{logs}}
```

**System Context:**
{{context}}

---

## Comprehensive Analysis Framework

Perform systematic log analysis using these advanced strategies:

### 1. **Log Parsing & Initial Triage**
- Extract and categorize all log entries by type (info, warning, error, debug)
- Identify timestamps and execution sequence
- Flag critical errors and their immediate context
- Note any obvious failure patterns

### 2. **Temporal & Frequency Analysis**
- **Timing Patterns**: Identify event clustering, periodic failures, or timing correlations
- **Rate Analysis**: Detect unusual frequency changes, burst patterns, or rate limiting
- **Sequence Analysis**: Map chronological flow and identify timing dependencies
- **Performance Degradation**: Look for gradually increasing response times or resource usage

### 3. **Correlation Analysis**
- **Cross-Component Events**: Link related events across different systems/modules
- **Cascade Effect Detection**: Identify how failures in one component trigger others
- **Request Tracing**: Follow specific requests/sessions through the entire system
- **Dependency Impact**: Map how external service issues affect internal components

### 4. **Performance & Resource Pattern Analysis**
- **Bottleneck Detection**: Identify slow operations, blocked threads, or queue buildups
- **Resource Exhaustion**: Look for memory leaks, connection pool depletion, file handle limits
- **Scaling Issues**: Detect load-related failures or capacity constraints
- **Database/Network Issues**: Identify connection timeouts, query performance, API latency

### 5. **Component Chain Analysis**
- Map the component initialization/execution flow
- Identify which systems are starting successfully vs failing
- Trace dependencies between components
- Note any broken component chains or missing dependencies

### 6. **Anomaly Detection**
- **Baseline Comparison**: Compare current behavior against normal patterns
- **Outlier Identification**: Flag unusual values, unexpected events, or deviations
- **Missing Events**: Identify expected log entries that are absent
- **Volume Anomalies**: Detect unusual increases/decreases in log volume

### 7. **Error Pattern Investigation**
For each identified error/warning:
- Extract the exact error message and stack trace
- Identify the component/file/line where it originated
- Determine if it's a primary failure or secondary effect
- Assess impact on overall system functionality
- **Correlation Impact**: Check if errors coincide with other system events

### 8. **Log Quality Assessment**
- **Completeness**: Check for missing logs, gaps in timeline, or truncated entries
- **Consistency**: Verify log format consistency and appropriate log levels
- **Information Density**: Assess if logs provide sufficient debugging information
- **Noise vs Signal**: Identify verbose logging that may obscure critical issues

### 9. **Security Pattern Recognition**
- **Authentication Failures**: Detect unusual login patterns or credential issues
- **Access Violations**: Identify unauthorized access attempts or permission failures
- **Injection Attempts**: Look for SQL injection, XSS, or other attack patterns
- **Rate Limiting**: Detect potential DoS attacks or abuse patterns

### 10. **Distributed System Tracing**
- **Request Flow**: Follow requests across microservices and components
- **Correlation IDs**: Track specific transactions through the entire system
- **Service Dependencies**: Map inter-service communication and failures
- **Network Issues**: Identify connectivity problems between services

### 11. **Codebase Investigation**
Use available tools to:
- Search for error-related code patterns in the codebase
- Read relevant files to understand component implementation
- Check configuration files and dependencies
- Investigate component relationships and initialization order

### 12. **External Research** (if needed)
- Search online for known issues with specific error patterns
- Look up API/library documentation for error codes
- Research best practices for identified failure modes

### 13. **Root Cause Diagnosis**
Provide:
- **Primary Root Cause**: The fundamental issue causing the problem
- **Secondary Issues**: Related problems that may compound the issue
- **Evidence**: Specific log entries and code references supporting the diagnosis
- **Impact Assessment**: How this affects system functionality
- **Confidence Level**: How certain you are about the diagnosis (High/Medium/Low)

### 14. **Business Impact Analysis**
- **User Experience Impact**: How failures affect end-user functionality
- **Feature Availability**: Which features are degraded or unavailable
- **Performance Impact**: Response time or throughput effects
- **Data Integrity**: Whether data loss or corruption is possible

### 15. **Actionable Recommendations**
- **Immediate Fixes**: Steps to resolve the primary issue
- **Preventive Measures**: Changes to prevent recurrence
- **Monitoring Setup**: Specific alerts and metrics to implement
- **Testing Strategy**: How to verify the fix works
- **Performance Optimizations**: Recommendations for improving system performance

### 16. **Proactive Monitoring Strategy**
- **Alert Thresholds**: Specific metrics and thresholds to monitor
- **Dashboard Metrics**: Key performance indicators to track
- **Log Retention**: Recommendations for log storage and rotation
- **Health Checks**: Additional monitoring to implement
- **SLA/SLO Recommendations**: Service level objectives to establish

### 17. **Forensic Timeline & Investigation Notes**
Document:
- **Exact Timeline**: Chronological sequence of critical events
- **Tools Used**: Searches performed and code files examined
- **Evidence Chain**: How conclusions were reached
- **Assumptions Made**: Any assumptions during analysis
- **Further Investigation**: Areas needing additional research

---

## Expected Deliverable

Provide a comprehensive diagnostic report with:

### **Executive Summary**
- One-sentence problem statement
- Primary root cause
- Business impact level
- Recommended priority (P0/P1/P2/P3)

### **Technical Analysis**
- Detailed findings with specific file/line references
- Evidence-based conclusions with supporting log entries
- Performance and security implications

### **Action Plan**
- Prioritized fix recommendations with implementation details
- Risk assessment for each recommendation
- Estimated effort and timeline

### **Prevention Strategy**
- Monitoring and alerting recommendations
- Code quality improvements
- Process changes to prevent recurrence

### **Follow-up Plan**
- Verification steps post-fix
- Metrics to monitor for regression
- Documentation updates needed

```

--------------------------------------------------------------------------------
/server/src/gates/core/index.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Core Gate System - Main Exports
 * Provides guidance and validation capabilities for prompt execution
 */

import type { ValidationResult } from "../../execution/types.js";
import { GateSystemManager } from "../gate-state-manager.js";
import { GateLoader, createGateLoader } from "./gate-loader.js";
import { GateValidator, createGateValidator } from "./gate-validator.js";
import {
  TemporaryGateRegistry,
  createTemporaryGateRegistry,
  type TemporaryGateDefinition,
} from "./temporary-gate-registry.js";

export { GateLoader, createGateLoader } from "./gate-loader.js";
export { GateValidator, createGateValidator } from "./gate-validator.js";
export {
  TemporaryGateRegistry,
  createTemporaryGateRegistry,
  type TemporaryGateDefinition as TemporaryGateRegistryDefinition,
} from "./temporary-gate-registry.js";

export type { ValidationResult } from "../../execution/types.js";
export type {
  GateActivationResult,
  GatePassCriteria,
  LightweightGateDefinition,
  ValidationCheck,
  ValidationContext,
} from "../types.js";
export type { GateValidationStatistics } from "./gate-validator.js";

/**
 * Core gate system manager with temporary gate support
 */
export class LightweightGateSystem {
  private gateSystemManager?: GateSystemManager;
  private temporaryGateRegistry?: TemporaryGateRegistry;

  constructor(
    public gateLoader: GateLoader,
    public gateValidator: GateValidator,
    temporaryGateRegistry?: TemporaryGateRegistry
  ) {
    this.temporaryGateRegistry = temporaryGateRegistry;
  }

  /**
   * Set gate system manager for runtime state checking
   */
  setGateSystemManager(gateSystemManager: GateSystemManager): void {
    this.gateSystemManager = gateSystemManager;
  }

  /**
   * Set temporary gate registry
   */
  setTemporaryGateRegistry(temporaryGateRegistry: TemporaryGateRegistry): void {
    this.temporaryGateRegistry = temporaryGateRegistry;
  }

  /**
   * Create a temporary gate
   */
  createTemporaryGate(
    definition: Omit<TemporaryGateDefinition, "id" | "created_at">,
    scopeId?: string
  ): string | null {
    if (!this.temporaryGateRegistry) {
      return null;
    }
    return this.temporaryGateRegistry.createTemporaryGate(definition, scopeId);
  }

  /**
   * Get temporary gates for scope
   */
  getTemporaryGatesForScope(
    scope: string,
    scopeId: string
  ): TemporaryGateDefinition[] {
    if (!this.temporaryGateRegistry) {
      return [];
    }
    return this.temporaryGateRegistry.getTemporaryGatesForScope(scope, scopeId);
  }

  /**
   * Clean up temporary gates for scope
   */
  cleanupTemporaryGates(scope: string, scopeId?: string): number {
    if (!this.temporaryGateRegistry) {
      return 0;
    }
    return this.temporaryGateRegistry.cleanupScope(scope, scopeId);
  }

  /**
   * Check if gate system is enabled
   */
  private isGateSystemEnabled(): boolean {
    // If no gate system manager is set, default to enabled for backwards compatibility
    if (!this.gateSystemManager) {
      return true;
    }
    return this.gateSystemManager.isGateSystemEnabled();
  }

  /**
   * Get guidance text for active gates
   */
  async getGuidanceText(
    gateIds: string[],
    context: {
      promptCategory?: string;
      framework?: string;
      explicitRequest?: boolean;
    }
  ): Promise<string[]> {
    // Check if gate system is enabled
    if (!this.isGateSystemEnabled()) {
      return []; // Return empty guidance if gates are disabled
    }

    const activation = await this.gateLoader.getActiveGates(gateIds, context);
    return activation.guidanceText;
  }

  /**
   * Validate content against active gates
   */
  async validateContent(
    gateIds: string[],
    content: string,
    validationContext: {
      promptId?: string;
      stepId?: string;
      attemptNumber?: number;
      previousAttempts?: string[];
      metadata?: Record<string, any>;
    }
  ): Promise<ValidationResult[]> {
    // Check if gate system is enabled
    if (!this.isGateSystemEnabled()) {
      // Return success results for all gates if system is disabled
      return gateIds.map((gateId) => ({
        gateId,
        valid: true,
        passed: true,
        message: "Gate system disabled - validation skipped",
        score: 1.0,
        details: {},
        retryHints: [],
        suggestions: [],
      }));
    }

    const startTime = performance.now();

    const context = {
      content,
      metadata: validationContext.metadata,
      executionContext: {
        promptId: validationContext.promptId,
        stepId: validationContext.stepId,
        attemptNumber: validationContext.attemptNumber,
        previousAttempts: validationContext.previousAttempts,
      },
    };

    const results = await this.gateValidator.validateGates(gateIds, context);

    // Record validation metrics if gate system manager is available
    if (this.gateSystemManager) {
      const executionTime = performance.now() - startTime;
      const success = results.every((r) => r.passed);
      this.gateSystemManager.recordValidation(success, executionTime);
    }

    return results;
  }

  /**
   * Check if content should be retried based on validation results
   */
  shouldRetry(
    validationResults: ValidationResult[],
    currentAttempt: number,
    maxAttempts: number = 3
  ): boolean {
    return this.gateValidator.shouldRetry(
      validationResults,
      currentAttempt,
      maxAttempts
    );
  }

  /**
   * Get combined retry hints from all failed validations
   */
  getRetryHints(validationResults: ValidationResult[]): string[] {
    const allHints: string[] = [];

    for (const result of validationResults) {
      if (!result.passed) {
        allHints.push(`**${result.gateId}:**`);
        if (result.retryHints) {
          allHints.push(...result.retryHints);
        }
        allHints.push(""); // Empty line for separation
      }
    }

    return allHints;
  }

  /**
   * Get system statistics
   */
  getStatistics() {
    return {
      gateLoader: this.gateLoader.getStatistics(),
      gateValidator: this.gateValidator.getStatistics(),
    };
  }

  /**
   * Get the temporary gate registry instance (Phase 3 enhancement)
   */
  getTemporaryGateRegistry(): TemporaryGateRegistry | undefined {
    return this.temporaryGateRegistry;
  }
}

/**
 * Create a complete core gate system with optional temporary gate support
 */
export function createLightweightGateSystem(
  logger: any,
  gatesDirectory?: string,
  gateSystemManager?: GateSystemManager,
  options?: {
    enableTemporaryGates?: boolean;
    maxMemoryGates?: number;
    defaultExpirationMs?: number;
    llmConfig?: any; // LLMIntegrationConfig from types
  }
): LightweightGateSystem {
  const gateLoader = createGateLoader(logger, gatesDirectory);
  const gateValidator = createGateValidator(logger, gateLoader, options?.llmConfig);

  // Create temporary gate registry if enabled
  let temporaryGateRegistry: TemporaryGateRegistry | undefined;
  if (options?.enableTemporaryGates !== false) {
    temporaryGateRegistry = createTemporaryGateRegistry(logger, {
      maxMemoryGates: options?.maxMemoryGates,
      defaultExpirationMs: options?.defaultExpirationMs,
    });
  }

  const gateSystem = new LightweightGateSystem(
    gateLoader,
    gateValidator,
    temporaryGateRegistry
  );

  if (gateSystemManager) {
    gateSystem.setGateSystemManager(gateSystemManager);
  }

  return gateSystem;
}

```

--------------------------------------------------------------------------------
/server/tests/unit/unified-parsing-system.test.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Simplified Unified Parsing System Tests
 *
 * Core functionality tests focusing on essential parsing behavior
 */

import { describe, test, expect, beforeEach, jest } from '@jest/globals';
import { Logger } from '../../src/logging/index.js';
import { PromptData } from '../../src/types/index.js';
import {
  createParsingSystem,
  type ExecutionContext
} from '../../src/execution/parsers/index.js';

// Mock logger for testing
const mockLogger: Logger = {
  debug: jest.fn(),
  info: jest.fn(),
  warn: jest.fn(),
  error: jest.fn()
} as any;

// Sample prompt data for testing
const testPrompts: PromptData[] = [
  {
    id: 'test_prompt',
    name: 'test_prompt',
    description: 'A test prompt',
    userMessageTemplate: 'Test message: {{content}}',
    arguments: [
      {
        name: 'content',
        description: 'Content to process',
        required: true
      }
    ],
    category: 'test'
  },
  {
    id: 'multi_arg_prompt',
    name: 'multi_arg_prompt',
    description: 'A prompt with multiple arguments',
    userMessageTemplate: 'Process {{text}} with {{format}}',
    arguments: [
      {
        name: 'text',
        description: 'Text to process',
        required: true
      },
      {
        name: 'format',
        description: 'Output format',
        required: false
      }
    ],
    category: 'test'
  }
];

describe('Unified Parsing System - Core Functionality', () => {
  let parsingSystem: ReturnType<typeof createParsingSystem>;

  beforeEach(() => {
    parsingSystem = createParsingSystem(mockLogger);
  });

  describe('Command Parsing', () => {
    test('should parse simple >>prompt format', async () => {
      const result = await parsingSystem.commandParser.parseCommand(
        '>>test_prompt hello world',
        testPrompts
      );

      expect(result.promptId).toBe('test_prompt');
      expect(result.rawArgs).toBe('hello world');
      expect(result.format).toBe('simple');
    });

    test('should parse JSON command format', async () => {
      const command = '{"command": ">>test_prompt", "args": "hello world"}';
      const result = await parsingSystem.commandParser.parseCommand(command, testPrompts);

      expect(result.promptId).toBe('test_prompt');
      expect(result.format).toBe('json');
    });

    test('should handle unknown prompts', async () => {
      await expect(
        parsingSystem.commandParser.parseCommand('>>unknown_prompt', testPrompts)
      ).rejects.toThrow('Unknown prompt: unknown_prompt');
    });
  });

  describe('Argument Processing', () => {
    test('should process simple arguments', async () => {
      const result = await parsingSystem.argumentProcessor.processArguments(
        'hello world',
        testPrompts[0]
      );

      expect(result.processedArgs.content).toBe('hello world');
      expect(result.metadata.processingStrategy).toBe('simple');
    });

    test('should process JSON arguments', async () => {
      const jsonArgs = '{"text": "hello", "format": "json"}';
      const result = await parsingSystem.argumentProcessor.processArguments(
        jsonArgs,
        testPrompts[1]
      );

      expect(result.processedArgs.text).toBe('hello');
      expect(result.processedArgs.format).toBe('json');
      expect(result.metadata.processingStrategy).toBe('json');
    });

    test('should process key-value pairs', async () => {
      const kvArgs = 'text=hello format=xml';
      const result = await parsingSystem.argumentProcessor.processArguments(
        kvArgs,
        testPrompts[1]
      );

      expect(result.processedArgs.text).toBe('hello');
      expect(result.processedArgs.format).toBe('xml');
      expect(result.metadata.processingStrategy).toBe('keyvalue');
    });
  });

  describe('Context Resolution', () => {
    test('should resolve from environment variables', async () => {
      process.env.PROMPT_TEST = 'environment_value';

      const result = await parsingSystem.contextResolver.resolveContext('test');

      expect(result.value).toBe('environment_value');
      expect(result.source).toBe('environment_variables');

      delete process.env.PROMPT_TEST;
    });

    test('should generate placeholders for unknown keys', async () => {
      const result = await parsingSystem.contextResolver.resolveContext('unknown_key');

      expect(result.source).toBe('generated_placeholder');
      expect(result.value).toContain('unknown_key');
    });

    test('should use caching for repeated resolutions', async () => {
      const result1 = await parsingSystem.contextResolver.resolveContext('cached_key');
      const result2 = await parsingSystem.contextResolver.resolveContext('cached_key');

      const stats = parsingSystem.contextResolver.getStats();
      expect(stats.cacheHits).toBe(1);
    });
  });

  describe('Integration', () => {
    test('should work end-to-end', async () => {
      // Parse command
      const parseResult = await parsingSystem.commandParser.parseCommand(
        '>>multi_arg_prompt hello world',
        testPrompts
      );

      // Process arguments
      const context: ExecutionContext = {
        conversationHistory: [],
        environmentVars: {},
        promptDefaults: { format: 'text' }
      };

      const argResult = await parsingSystem.argumentProcessor.processArguments(
        parseResult.rawArgs,
        testPrompts[1],
        context
      );

      expect(parseResult.promptId).toBe('multi_arg_prompt');
      expect(argResult.processedArgs.text).toBe('hello world');
    });
  });

  describe('Performance', () => {
    test('should complete parsing within reasonable time', async () => {
      const start = Date.now();

      for (let i = 0; i < 10; i++) {
        await parsingSystem.commandParser.parseCommand(
          `>>test_prompt test${i}`,
          testPrompts
        );
      }

      const duration = Date.now() - start;
      expect(duration).toBeLessThan(1000); // Should complete 10 parses in under 1 second
    });

    test('should maintain reasonable memory usage', async () => {
      const initialMemory = process.memoryUsage().heapUsed;

      // Perform multiple operations
      for (let i = 0; i < 50; i++) {
        await parsingSystem.commandParser.parseCommand(`>>test_prompt test${i}`, testPrompts);
        await parsingSystem.argumentProcessor.processArguments(`test${i}`, testPrompts[0]);
      }

      // Force garbage collection if available
      if (global.gc) {
        global.gc();
      }

      const finalMemory = process.memoryUsage().heapUsed;
      const memoryIncrease = (finalMemory - initialMemory) / 1024 / 1024; // MB

      expect(memoryIncrease).toBeLessThan(10); // Should not increase by more than 10MB
    });
  });

  describe('Error Handling', () => {
    test('should handle malformed JSON gracefully', async () => {
      await expect(
        parsingSystem.commandParser.parseCommand('{"invalid": json', testPrompts)
      ).rejects.toThrow();
    });

    test('should handle empty commands', async () => {
      await expect(
        parsingSystem.commandParser.parseCommand('', testPrompts)
      ).rejects.toThrow('Command cannot be empty');
    });

    test('should provide helpful error messages', async () => {
      try {
        await parsingSystem.commandParser.parseCommand('invalid format', testPrompts);
      } catch (error: any) {
        expect(error.message).toContain('Supported command formats:');
      }
    });
  });
});
```

--------------------------------------------------------------------------------
/server/src/config/index.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Configuration Management Module
 * Handles loading and validation of server configuration from config.json
 */

import { readFile } from "fs/promises";
import path from "path";
import { Config, AnalysisConfig, SemanticAnalysisConfig, LLMIntegrationConfig, AnalysisMode, LoggingConfig } from "../types/index.js";
// Removed: ToolDescriptionManager import to break circular dependency
// Now injected via dependency injection pattern

/**
 * Infer the optimal analysis mode based on LLM integration configuration
 */
function inferAnalysisMode(llmConfig: LLMIntegrationConfig): AnalysisMode {
  // Use semantic mode if LLM integration is properly configured
  if (llmConfig.enabled && llmConfig.endpoint) {
    // For non-localhost endpoints, require API key
    if (llmConfig.endpoint.includes('localhost') || llmConfig.endpoint.includes('127.0.0.1') || llmConfig.apiKey) {
      return "semantic";
    }
  }
  
  // Default to structural mode
  return "structural";
}

/**
 * Default configuration values
 */
const DEFAULT_ANALYSIS_CONFIG: AnalysisConfig = {
  semanticAnalysis: {
    // mode will be inferred automatically based on LLM integration
    llmIntegration: {
      enabled: false,
      apiKey: null,
      endpoint: null,
      model: "gpt-4",
      maxTokens: 1000,
      temperature: 0.1,
    },
  },
};

// DEFAULT_FRAMEWORK_CONFIG removed - framework state managed at runtime
// Use system_control MCP tool to enable/disable and switch frameworks


const DEFAULT_CONFIG: Config = {
  server: {
    name: "Claude Custom Prompts",
    version: "1.0.0",
    port: 3456,
  },
  prompts: {
    file: "prompts/promptsConfig.json",
  },
  analysis: DEFAULT_ANALYSIS_CONFIG,
  transports: {
    default: "stdio",
    sse: { enabled: false },
    stdio: { enabled: true },
  },
};

/**
 * Configuration manager class
 */
export class ConfigManager {
  private config: Config;
  private configPath: string;
  // Removed: private toolDescriptionManager - now injected via dependency injection

  constructor(configPath: string) {
    this.configPath = configPath;
    this.config = DEFAULT_CONFIG;
  }

  /**
   * Load configuration from file
   */
  async loadConfig(): Promise<Config> {
    try {
      const configContent = await readFile(this.configPath, "utf8");
      this.config = JSON.parse(configContent) as Config;

      // Validate and set defaults for any missing properties
      this.validateAndSetDefaults();

      return this.config;
    } catch (error) {
      console.error(
        `Error loading configuration from ${this.configPath}:`,
        error
      );
      console.info("Using default configuration");
      this.config = DEFAULT_CONFIG;
      return this.config;
    }
  }

  /**
   * Get current configuration
   */
  getConfig(): Config {
    return this.config;
  }

  /**
   * Get server configuration
   */
  getServerConfig() {
    return this.config.server;
  }

  /**
   * Get prompts configuration
   */
  getPromptsConfig() {
    return this.config.prompts;
  }

  /**
   * Get transports configuration
   */
  getTransportsConfig() {
    return this.config.transports;
  }

  /**
   * Get analysis configuration
   */
  getAnalysisConfig(): AnalysisConfig {
    return this.config.analysis || DEFAULT_ANALYSIS_CONFIG;
  }

  /**
   * Get semantic analysis configuration
   */
  getSemanticAnalysisConfig(): SemanticAnalysisConfig {
    return this.getAnalysisConfig().semanticAnalysis;
  }

  /**
   * Get logging configuration
   */
  getLoggingConfig(): LoggingConfig {
    return this.config.logging || {
      directory: "./logs",
      level: "info"
    };
  }

  /**
   * Get the port number, with environment variable override
   */
  getPort(): number {
    return process.env.PORT
      ? parseInt(process.env.PORT, 10)
      : this.config.server.port;
  }

  /**
   * Determine transport from command line arguments or configuration
   */
  getTransport(args: string[]): string {
    const transportArg = args.find((arg: string) =>
      arg.startsWith("--transport=")
    );
    return transportArg
      ? transportArg.split("=")[1]
      : this.config.transports.default;
  }

  /**
   * Get config file path
   */
  getConfigPath(): string {
    return this.configPath;
  }

  /**
   * Get prompts file path relative to config directory
   */
  getPromptsFilePath(): string {
    const configDir = path.dirname(this.configPath);
    return path.join(configDir, this.config.prompts.file);
  }

  /**
   * Get server root directory path
   */
  getServerRoot(): string {
    return path.dirname(this.configPath);
  }

  // Removed: ToolDescriptionManager methods - now handled via dependency injection in runtime/application.ts

  /**
   * Validate configuration and set defaults for missing properties
   */
  private validateAndSetDefaults(): void {
    // Ensure server config exists
    if (!this.config.server) {
      this.config.server = DEFAULT_CONFIG.server;
    } else {
      this.config.server = {
        ...DEFAULT_CONFIG.server,
        ...this.config.server,
      };
    }

    // Ensure prompts config exists
    if (!this.config.prompts) {
      this.config.prompts = DEFAULT_CONFIG.prompts;
    } else {
      this.config.prompts = {
        ...DEFAULT_CONFIG.prompts,
        ...this.config.prompts,
      };
    }

    // Ensure analysis config exists
    if (!this.config.analysis) {
      this.config.analysis = DEFAULT_ANALYSIS_CONFIG;
    } else {
      this.config.analysis = this.validateAnalysisConfig(this.config.analysis);
    }

    // Ensure transports config exists
    if (!this.config.transports) {
      this.config.transports = DEFAULT_CONFIG.transports;
    } else {
      this.config.transports = {
        ...DEFAULT_CONFIG.transports,
        ...this.config.transports,
      };
    }
  }

  /**
   * Validate and merge analysis configuration with defaults
   */
  private validateAnalysisConfig(analysisConfig: Partial<AnalysisConfig>): AnalysisConfig {
    const semanticAnalysis = analysisConfig.semanticAnalysis || {} as any;
    
    // Build LLM integration config first
    const llmIntegration = {
      enabled: semanticAnalysis.llmIntegration?.enabled ?? DEFAULT_ANALYSIS_CONFIG.semanticAnalysis.llmIntegration.enabled,
      apiKey: semanticAnalysis.llmIntegration?.apiKey ?? DEFAULT_ANALYSIS_CONFIG.semanticAnalysis.llmIntegration.apiKey,
      endpoint: semanticAnalysis.llmIntegration?.endpoint ?? DEFAULT_ANALYSIS_CONFIG.semanticAnalysis.llmIntegration.endpoint,
      model: semanticAnalysis.llmIntegration?.model ?? DEFAULT_ANALYSIS_CONFIG.semanticAnalysis.llmIntegration.model,
      maxTokens: semanticAnalysis.llmIntegration?.maxTokens ?? DEFAULT_ANALYSIS_CONFIG.semanticAnalysis.llmIntegration.maxTokens,
      temperature: semanticAnalysis.llmIntegration?.temperature ?? DEFAULT_ANALYSIS_CONFIG.semanticAnalysis.llmIntegration.temperature,
    };

    // Infer analysis mode based on LLM configuration if not explicitly set
    const validModes: AnalysisMode[] = ["structural", "semantic"];
    const mode = semanticAnalysis.mode && validModes.includes(semanticAnalysis.mode as AnalysisMode)
      ? semanticAnalysis.mode as AnalysisMode
      : inferAnalysisMode(llmIntegration);

    return {
      semanticAnalysis: {
        mode,
        llmIntegration,
      },
    };
  }
}

/**
 * Create and initialize a configuration manager
 */
export async function createConfigManager(
  configPath: string
): Promise<ConfigManager> {
  const configManager = new ConfigManager(configPath);
  await configManager.loadConfig();
  return configManager;
}


```

--------------------------------------------------------------------------------
/server/src/mcp-tools/prompt-manager/utils/category-manager.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Category operations and cleanup utilities
 */

import * as fs from "fs/promises";
import path from "path";
import { readFile } from "fs/promises";
import { Logger } from "../../../logging/index.js";
import { PromptsConfigFile } from "../../../types/index.js";
import { safeWriteFile } from "../../../prompts/promptUtils.js";
import { CategoryResult, OperationResult } from "../core/types.js";

/**
 * Category management operations
 */
export class CategoryManager {
  private logger: Logger;

  constructor(logger: Logger) {
    this.logger = logger;
  }

  /**
   * Ensure category exists in the configuration
   */
  async ensureCategoryExists(
    category: string,
    promptsConfig: PromptsConfigFile,
    promptsFile: string
  ): Promise<CategoryResult> {
    const effectiveCategory = category.toLowerCase().replace(/\s+/g, "-");

    const exists = promptsConfig.categories.some(cat => cat.id === effectiveCategory);

    if (!exists) {
      // Create new category
      promptsConfig.categories.push({
        id: effectiveCategory,
        name: category,
        description: `Prompts related to ${category}`
      });

      // Create directory and files
      const categoryDir = path.join(path.dirname(promptsFile), effectiveCategory);
      await fs.mkdir(categoryDir, { recursive: true });

      const categoryPromptsPath = path.join(categoryDir, "prompts.json");
      await safeWriteFile(categoryPromptsPath, JSON.stringify({ prompts: [] }, null, 2), "utf8");

      // Add to imports
      const relativePath = path.join(effectiveCategory, "prompts.json").replace(/\\/g, "/");
      if (!promptsConfig.imports.includes(relativePath)) {
        promptsConfig.imports.push(relativePath);
      }

      // Save config
      await safeWriteFile(promptsFile, JSON.stringify(promptsConfig, null, 2), "utf8");

      this.logger.info(`Created new category: ${effectiveCategory}`);
      return { effectiveCategory, created: true };
    }

    return { effectiveCategory, created: false };
  }

  /**
   * Clean up empty category (remove from config and delete folder)
   */
  async cleanupEmptyCategory(
    categoryImport: string,
    promptsConfig: PromptsConfigFile,
    promptsFile: string
  ): Promise<OperationResult> {
    const promptsConfigDir = path.dirname(promptsFile);
    const categoryPath = path.join(promptsConfigDir, categoryImport);
    const categoryDir = path.dirname(categoryPath);
    const messages: string[] = [];

    try {
      // Extract category ID from import path (e.g., "examples/prompts.json" -> "examples")
      const categoryId = categoryImport.split('/')[0];

      // Remove from categories array
      const categoryIndex = promptsConfig.categories.findIndex(cat => cat.id === categoryId);
      if (categoryIndex > -1) {
        const removedCategory = promptsConfig.categories.splice(categoryIndex, 1)[0];
        messages.push(`✅ Removed category definition: ${removedCategory.name}`);
      }

      // Remove from imports array
      const importIndex = promptsConfig.imports.findIndex(imp => imp === categoryImport);
      if (importIndex > -1) {
        promptsConfig.imports.splice(importIndex, 1);
        messages.push(`✅ Removed import path: ${categoryImport}`);
      }

      // Save updated config
      await safeWriteFile(promptsFile, JSON.stringify(promptsConfig, null, 2), "utf8");
      messages.push(`✅ Updated promptsConfig.json`);

      // Delete empty category folder and its contents
      try {
        // Delete prompts.json file
        await fs.unlink(categoryPath);
        messages.push(`✅ Deleted category file: ${categoryImport}`);

        // Delete category directory if empty
        await fs.rmdir(categoryDir);
        messages.push(`✅ Deleted empty category folder: ${path.basename(categoryDir)}`);
      } catch (folderError: any) {
        if (folderError.code !== "ENOENT") {
          messages.push(`⚠️ Could not delete category folder: ${folderError.message}`);
        }
      }

      this.logger.info(`Cleaned up empty category: ${categoryId}`);

    } catch (error: any) {
      this.logger.error(`Failed to cleanup category ${categoryImport}:`, error);
      messages.push(`❌ Category cleanup failed: ${error.message}`);
    }

    return { message: messages.join('\n') };
  }

  /**
   * Check if category is empty
   */
  async isCategoryEmpty(categoryImport: string, promptsFile: string): Promise<boolean> {
    try {
      const promptsConfigDir = path.dirname(promptsFile);
      const categoryPath = path.join(promptsConfigDir, categoryImport);

      const categoryContent = await readFile(categoryPath, "utf8");
      const categoryData = JSON.parse(categoryContent);

      return !categoryData.prompts || categoryData.prompts.length === 0;
    } catch (error) {
      this.logger.warn(`Could not check category emptiness: ${categoryImport}`, error);
      return false;
    }
  }

  /**
   * Get category statistics
   */
  async getCategoryStats(categories: string[], promptsFile: string): Promise<Record<string, number>> {
    const stats: Record<string, number> = {};
    const promptsConfigDir = path.dirname(promptsFile);

    for (const categoryImport of categories) {
      try {
        const categoryPath = path.join(promptsConfigDir, categoryImport);
        const categoryContent = await readFile(categoryPath, "utf8");
        const categoryData = JSON.parse(categoryContent);

        const categoryId = categoryImport.split('/')[0];
        stats[categoryId] = categoryData.prompts ? categoryData.prompts.length : 0;
      } catch (error) {
        const categoryId = categoryImport.split('/')[0];
        stats[categoryId] = 0;
      }
    }

    return stats;
  }

  /**
   * Validate category structure
   */
  async validateCategoryStructure(categoryImport: string, promptsFile: string): Promise<{
    valid: boolean;
    issues: string[];
  }> {
    const issues: string[] = [];
    const promptsConfigDir = path.dirname(promptsFile);
    const categoryPath = path.join(promptsConfigDir, categoryImport);

    try {
      // Check if category file exists
      const categoryContent = await readFile(categoryPath, "utf8");

      try {
        const categoryData = JSON.parse(categoryContent);

        // Validate structure
        if (!categoryData.prompts) {
          issues.push("Missing 'prompts' array");
        } else if (!Array.isArray(categoryData.prompts)) {
          issues.push("'prompts' must be an array");
        }

        // Validate each prompt entry
        if (categoryData.prompts) {
          for (const [index, prompt] of categoryData.prompts.entries()) {
            if (!prompt.id) {
              issues.push(`Prompt at index ${index} missing 'id'`);
            }
            if (!prompt.name) {
              issues.push(`Prompt at index ${index} missing 'name'`);
            }
            if (!prompt.file) {
              issues.push(`Prompt at index ${index} missing 'file'`);
            }
          }
        }

      } catch (parseError) {
        issues.push("Invalid JSON format");
      }

    } catch (error) {
      issues.push("Category file not accessible");
    }

    return {
      valid: issues.length === 0,
      issues
    };
  }

  /**
   * Normalize category name for consistency
   */
  normalizeCategoryName(category: string): string {
    return category.toLowerCase().replace(/\s+/g, "-").replace(/[^a-z0-9-_]/g, "");
  }

  /**
   * Get category display name
   */
  getCategoryDisplayName(categoryId: string, categories: any[]): string {
    const category = categories.find(cat => cat.id === categoryId);
    return category ? category.name : categoryId;
  }
}
```

--------------------------------------------------------------------------------
/server/src/utils/global-resource-tracker.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Global Resource Tracker
 *
 * Tracks all Node.js resources (timers, intervals, etc.) to prevent hanging processes
 * during testing and ensure proper cleanup on shutdown.
 */

export interface TrackedResource {
  id: string;
  type: 'timeout' | 'interval' | 'immediate';
  handle: NodeJS.Timeout | NodeJS.Immediate;
  source: string; // Component or function that created it
  createdAt: Date;
  description?: string;
}

class GlobalResourceTracker {
  private resources = new Map<string, TrackedResource>();
  private nextId = 1;
  private enabled = true;

  /**
   * Enable or disable tracking (useful for production environments)
   */
  setEnabled(enabled: boolean): void {
    this.enabled = enabled;
  }

  /**
   * Track a setTimeout
   */
  trackTimeout(handle: NodeJS.Timeout, source: string, description?: string): string {
    if (!this.enabled) return '';

    const id = `timeout_${this.nextId++}`;
    this.resources.set(id, {
      id,
      type: 'timeout',
      handle,
      source,
      createdAt: new Date(),
      description
    });
    return id;
  }

  /**
   * Track a setInterval
   */
  trackInterval(handle: NodeJS.Timeout, source: string, description?: string): string {
    if (!this.enabled) return '';

    const id = `interval_${this.nextId++}`;
    this.resources.set(id, {
      id,
      type: 'interval',
      handle,
      source,
      createdAt: new Date(),
      description
    });
    return id;
  }

  /**
   * Track a setImmediate
   */
  trackImmediate(handle: NodeJS.Immediate, source: string, description?: string): string {
    if (!this.enabled) return '';

    const id = `immediate_${this.nextId++}`;
    this.resources.set(id, {
      id,
      type: 'immediate',
      handle,
      source,
      createdAt: new Date(),
      description
    });
    return id;
  }

  /**
   * Untrack a resource (called when it's manually cleared)
   */
  untrack(id: string): boolean {
    return this.resources.delete(id);
  }

  /**
   * Clear a specific resource
   */
  clearResource(id: string): boolean {
    const resource = this.resources.get(id);
    if (!resource) return false;

    try {
      switch (resource.type) {
        case 'timeout':
        case 'interval':
          clearTimeout(resource.handle as NodeJS.Timeout);
          break;
        case 'immediate':
          clearImmediate(resource.handle as NodeJS.Immediate);
          break;
      }
      this.resources.delete(id);
      return true;
    } catch (error) {
      console.warn(`Failed to clear resource ${id}:`, error);
      return false;
    }
  }

  /**
   * Emergency cleanup - clear ALL tracked resources
   */
  emergencyCleanup(): number {
    let cleared = 0;

    for (const [id, resource] of this.resources) {
      try {
        switch (resource.type) {
          case 'timeout':
          case 'interval':
            clearTimeout(resource.handle as NodeJS.Timeout);
            break;
          case 'immediate':
            clearImmediate(resource.handle as NodeJS.Immediate);
            break;
        }
        cleared++;
      } catch (error) {
        console.warn(`Failed to clear resource ${id} during emergency cleanup:`, error);
      }
    }

    this.resources.clear();
    return cleared;
  }

  /**
   * Get diagnostic information about active resources
   */
  getDiagnostics(): {
    totalResources: number;
    byType: Record<string, number>;
    bySource: Record<string, number>;
    oldestResource?: TrackedResource;
    resources: TrackedResource[];
  } {
    const resources = Array.from(this.resources.values());
    const byType: Record<string, number> = {};
    const bySource: Record<string, number> = {};

    for (const resource of resources) {
      byType[resource.type] = (byType[resource.type] || 0) + 1;
      bySource[resource.source] = (bySource[resource.source] || 0) + 1;
    }

    const oldestResource = resources
      .sort((a, b) => a.createdAt.getTime() - b.createdAt.getTime())[0];

    return {
      totalResources: resources.length,
      byType,
      bySource,
      oldestResource,
      resources: resources.sort((a, b) => a.createdAt.getTime() - b.createdAt.getTime())
    };
  }

  /**
   * Log diagnostic information
   */
  logDiagnostics(): void {
    const diagnostics = this.getDiagnostics();

    if (diagnostics.totalResources === 0) {
      console.log('✅ No active tracked resources');
      return;
    }

    console.log(`⚠️ ${diagnostics.totalResources} active resources preventing process exit:`);
    console.log('📊 By type:', diagnostics.byType);
    console.log('📊 By source:', diagnostics.bySource);

    if (diagnostics.oldestResource) {
      const age = Date.now() - diagnostics.oldestResource.createdAt.getTime();
      console.log(`⏰ Oldest resource: ${diagnostics.oldestResource.id} (${Math.round(age/1000)}s old) from ${diagnostics.oldestResource.source}`);
    }

    // Log details of long-running resources (> 10 seconds)
    const longRunning = diagnostics.resources.filter(r =>
      Date.now() - r.createdAt.getTime() > 10000
    );

    if (longRunning.length > 0) {
      console.log('🐛 Long-running resources (>10s):');
      for (const resource of longRunning) {
        const age = Math.round((Date.now() - resource.createdAt.getTime()) / 1000);
        console.log(`   ${resource.id}: ${resource.type} from ${resource.source} (${age}s) - ${resource.description || 'no description'}`);
      }
    }
  }
}

// Global singleton instance
export const globalResourceTracker = new GlobalResourceTracker();

/**
 * Wrapper functions that automatically track resources
 * Use these instead of native setTimeout/setInterval in application code
 */

export function trackedSetTimeout(
  callback: (...args: any[]) => void,
  delay: number,
  source: string,
  description?: string
): NodeJS.Timeout {
  const handle = setTimeout(() => {
    // Auto-untrack when timeout executes
    globalResourceTracker.untrack(id);
    callback();
  }, delay);

  const id = globalResourceTracker.trackTimeout(handle, source, description);
  return handle;
}

export function trackedSetInterval(
  callback: (...args: any[]) => void,
  delay: number,
  source: string,
  description?: string
): NodeJS.Timeout {
  const handle = setInterval(callback, delay);
  globalResourceTracker.trackInterval(handle, source, description);
  return handle;
}

export function trackedClearTimeout(handle: NodeJS.Timeout): void {
  clearTimeout(handle);
  // Note: We don't have the ID here, so we can't untrack automatically
  // This is why the auto-untrack in trackedSetTimeout is important
}

export function trackedClearInterval(handle: NodeJS.Timeout): void {
  clearInterval(handle);
  // Note: Manual untracking would require keeping a reverse mapping
  // For now, users should call globalResourceTracker.untrack() manually if needed
}

/**
 * Add emergency cleanup to process exit handlers
 */
function setupProcessHandlers(): void {
  const cleanup = () => {
    const cleared = globalResourceTracker.emergencyCleanup();
    if (cleared > 0) {
      console.log(`💀 Emergency cleanup cleared ${cleared} resources`);
    }
  };

  // Cleanup on various exit scenarios
  process.on('exit', cleanup);
  process.on('SIGTERM', cleanup);
  process.on('SIGINT', cleanup);
  process.on('uncaughtException', (error) => {
    console.error('Uncaught exception:', error);
    cleanup();
    process.exit(1);
  });
  process.on('unhandledRejection', (reason, promise) => {
    console.error('Unhandled rejection at:', promise, 'reason:', reason);
    cleanup();
    process.exit(1);
  });
}

// Initialize process handlers when module is loaded
setupProcessHandlers();
```

--------------------------------------------------------------------------------
/server/tests/enhanced-validation/contract-validation/contract-test-suite.js:
--------------------------------------------------------------------------------

```javascript
#!/usr/bin/env node
/**
 * Contract Validation Test Suite
 *
 * Validates interface compliance to prevent registerTool-type CI failures
 * Tests the enhanced MockMcpServer and interface validation system
 */

async function runContractValidationTests() {
  try {
    console.log('🔍 Running Interface Contract Validation Tests...');
    console.log('🎯 Preventing interface mismatch CI failures\n');

    const results = {
      mockServerCompliance: false,
      contractValidation: false,
      registerToolFix: false,
      totalTests: 0,
      passedTests: 0
    };

    // Test 1: Enhanced MockMcpServer Compliance
    console.log('📋 Test 1: MockMcpServer Interface Compliance');
    results.totalTests++;

    try {
      const { MockMcpServer } = await import('../../helpers/test-helpers.js');
      const mockServer = new MockMcpServer();

      // Test interface compliance validation
      const compliance = mockServer.validateInterfaceCompliance();

      if (compliance.isCompliant && compliance.missingMethods.length === 0) {
        console.log('   ✅ MockMcpServer implements all required methods');
        console.log('   ✅ Interface compliance validation works');
        results.mockServerCompliance = true;
        results.passedTests++;
      } else {
        console.log('   ❌ MockMcpServer missing methods:', compliance.missingMethods);
      }
    } catch (error) {
      console.log(`   ❌ MockMcpServer compliance test failed: ${error.message}`);
    }

    // Test 2: Contract Validator Functionality
    console.log('\n🔧 Test 2: Contract Validation System');
    results.totalTests++;

    try {
      const { createMcpSdkInterfaceValidator } = await import('./interface-contracts.js');
      const { MockLogger, MockMcpServer } = await import('../../helpers/test-helpers.js');

      const logger = new MockLogger();
      const validator = createMcpSdkInterfaceValidator(logger);
      const mockServer = new MockMcpServer();

      // Test contract validation
      const isValid = await validator.quickValidation(mockServer);

      if (isValid) {
        console.log('   ✅ Contract validation passes for enhanced MockMcpServer');
        console.log('   ✅ Interface validator correctly identifies compliance');
        results.contractValidation = true;
        results.passedTests++;
      } else {
        console.log('   ❌ Contract validation failed for MockMcpServer');
        console.log('   Logs:', logger.logs);
      }
    } catch (error) {
      console.log(`   ❌ Contract validation system test failed: ${error.message}`);
    }

    // Test 3: RegisterTool Method Fix Validation
    console.log('\n🔨 Test 3: RegisterTool Method Fix');
    results.totalTests++;

    try {
      const { MockMcpServer } = await import('../../helpers/test-helpers.js');
      const mockServer = new MockMcpServer();

      // Test that registerTool method exists and works
      if (typeof mockServer.registerTool !== 'function') {
        throw new Error('registerTool method is missing');
      }

      // Test registerTool functionality
      const mockHandler = async (args) => ({ result: 'test', args });
      const mockConfig = {
        description: 'Test tool',
        inputSchema: { type: 'object', properties: {} }
      };

      const result = mockServer.registerTool('test_tool', mockConfig, mockHandler);

      if (result && result.name === 'test_tool') {
        console.log('   ✅ registerTool method exists and functions correctly');
        console.log('   ✅ Delegates properly to existing tool method');
        console.log('   ✅ Validates parameters correctly');

        // Verify tool was registered
        const registeredNames = mockServer.getRegisteredToolNames();
        if (registeredNames.includes('test_tool')) {
          console.log('   ✅ Tool successfully registered via registerTool');
          results.registerToolFix = true;
          results.passedTests++;
        } else {
          console.log('   ❌ Tool not found in registered tools list');
        }
      } else {
        console.log('   ❌ registerTool did not return expected result');
      }
    } catch (error) {
      console.log(`   ❌ RegisterTool fix validation failed: ${error.message}`);
    }

    // Test 4: Parameter Validation (Edge Cases)
    console.log('\n⚠️  Test 4: Parameter Validation Edge Cases');
    results.totalTests++;

    try {
      const { MockMcpServer } = await import('../../helpers/test-helpers.js');
      const mockServer = new MockMcpServer();

      // Test invalid parameters
      const testCases = [
        { name: '', config: {}, handler: () => {}, expectedError: 'Invalid tool name' },
        { name: 'test', config: null, handler: () => {}, expectedError: 'Invalid tool config' },
        { name: 'test', config: {}, handler: 'not-a-function', expectedError: 'Invalid tool handler' }
      ];

      let edgeCasesPassed = 0;
      for (const testCase of testCases) {
        try {
          mockServer.registerTool(testCase.name, testCase.config, testCase.handler);
          console.log(`   ❌ Expected error for ${testCase.expectedError} but none thrown`);
        } catch (error) {
          if (error.message.includes(testCase.expectedError)) {
            console.log(`   ✅ Correctly validates: ${testCase.expectedError}`);
            edgeCasesPassed++;
          } else {
            console.log(`   ❌ Wrong error for ${testCase.expectedError}: ${error.message}`);
          }
        }
      }

      if (edgeCasesPassed === testCases.length) {
        console.log('   ✅ All parameter validation edge cases pass');
        results.passedTests++;
      } else {
        console.log(`   ❌ Only ${edgeCasesPassed}/${testCases.length} edge cases passed`);
      }
    } catch (error) {
      console.log(`   ❌ Parameter validation test failed: ${error.message}`);
    }

    // Summary
    console.log('\n' + '='.repeat(60));
    console.log('📊 CONTRACT VALIDATION TEST RESULTS');
    console.log('='.repeat(60));
    console.log(`📈 Tests Passed: ${results.passedTests}/${results.totalTests}`);
    console.log(`📊 Success Rate: ${((results.passedTests / results.totalTests) * 100).toFixed(1)}%`);
    console.log('');
    console.log('🔧 Component Status:');
    console.log(`   MockMcpServer Compliance: ${results.mockServerCompliance ? '✅' : '❌'}`);
    console.log(`   Contract Validation System: ${results.contractValidation ? '✅' : '❌'}`);
    console.log(`   RegisterTool Fix: ${results.registerToolFix ? '✅' : '❌'}`);

    if (results.passedTests === results.totalTests) {
      console.log('\n🎉 All contract validation tests passed!');
      console.log('✅ Interface mismatch prevention system is working correctly');
      console.log('✅ RegisterTool CI failure should be prevented');
      process.exit(0);
    } else {
      console.log('\n❌ Some contract validation tests failed');
      console.log('⚠️  Interface mismatch issues may still cause CI failures');
      process.exit(1);
    }

  } catch (error) {
    console.error('❌ Contract validation test execution failed:', error.message);
    console.error('Stack trace:', error.stack);
    process.exit(1);
  }
}

// Handle process cleanup
process.on('uncaughtException', (error) => {
  console.error('❌ Uncaught exception in contract validation tests:', error.message);
  process.exit(1);
});

process.on('unhandledRejection', (reason) => {
  console.error('❌ Unhandled rejection in contract validation tests:', reason);
  process.exit(1);
});

// Run the tests
if (import.meta.url === `file://${process.argv[1]}`) {
  runContractValidationTests().catch(error => {
    console.error('❌ Test execution failed:', error);
    process.exit(1);
  });
}
```

--------------------------------------------------------------------------------
/server/src/server/transport/index.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Transport Management Module
 * Handles STDIO and SSE transport setup and lifecycle management
 */

import { SSEServerTransport } from "@modelcontextprotocol/sdk/server/sse.js";
import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
import express, { Request, Response } from "express";
import { ConfigManager } from "../../config/index.js";
import { Logger } from "../../logging/index.js";

/**
 * Transport types supported by the server
 */
export enum TransportType {
  STDIO = "stdio",
  SSE = "sse",
}

/**
 * Transport Manager class
 */
export class TransportManager {
  private logger: Logger;
  private configManager: ConfigManager;
  private mcpServer: any;
  private transport: string;
  private sseTransports: Map<string, SSEServerTransport> = new Map();

  constructor(
    logger: Logger,
    configManager: ConfigManager,
    mcpServer: any,
    transport: string
  ) {
    this.logger = logger;
    this.configManager = configManager;
    this.mcpServer = mcpServer;
    this.transport = transport;
  }

  /**
   * Determine transport from command line arguments or configuration
   */
  static determineTransport(
    args: string[],
    configManager: ConfigManager
  ): string {
    const transportArg = args.find((arg: string) =>
      arg.startsWith("--transport=")
    );
    return transportArg
      ? transportArg.split("=")[1]
      : configManager.getConfig().transports.default;
  }

  /**
   * Setup STDIO transport
   */
  async setupStdioTransport(): Promise<void> {
    this.logger.info("Starting server with STDIO transport");

    // Create the STDIO transport - aligned with MCP SDK pattern
    const stdioTransport = new StdioServerTransport();

    // Setup STDIO event handlers
    this.setupStdioEventHandlers();

    // Connect the server to the transport - standard MCP SDK pattern
    try {
      await this.mcpServer.connect(stdioTransport);
      this.logger.info("STDIO transport connected successfully - server ready for MCP client connections");

      // Setup console redirection AFTER successful connection to avoid deadlock
      this.setupStdioConsoleRedirection();
    } catch (error) {
      this.logger.error("Error connecting to STDIO transport:", error);
      process.exit(1);
    }
  }

  /**
   * Setup console redirection for STDIO transport
   */
  private setupStdioConsoleRedirection(): void {
    // Ensure we don't mix log messages with JSON messages
    console.log = (...args) => {
      this.logger.info("CONSOLE: " + args.join(" "));
    };

    console.error = (...args) => {
      this.logger.error("CONSOLE_ERROR: " + args.join(" "));
    };
  }

  /**
   * Setup STDIO event handlers
   */
  private setupStdioEventHandlers(): void {
    // Log when the stdin closes (which happens when the parent process terminates)
    process.stdin.on("end", () => {
      this.logger.info(
        "STDIN stream ended - parent process may have terminated"
      );
      process.exit(0);
    });
  }

  /**
   * Setup SSE transport with Express integration
   */
  setupSseTransport(app: express.Application): void {
    this.logger.info("Setting up SSE transport endpoints");

    // SSE endpoint for MCP connections
    app.get("/mcp", async (req: Request, res: Response) => {
      this.logger.info("New SSE connection from " + req.ip);

      // Set headers for SSE
      res.setHeader("Content-Type", "text/event-stream");
      res.setHeader("Cache-Control", "no-cache");
      res.setHeader("Connection", "keep-alive");
      res.setHeader("X-Accel-Buffering", "no"); // Issues with certain proxies

      // Create a unique ID for this connection
      const connectionId = Date.now().toString();

      // Create a new transport for this connection
      const sseTransport = new SSEServerTransport("/messages", res);
      this.sseTransports.set(connectionId, sseTransport);

      // Log connection data for debugging
      this.logger.debug("Connection headers:", req.headers);

      // Remove the transport when the connection is closed
      res.on("close", () => {
        this.logger.info(`SSE connection ${connectionId} closed`);
        this.sseTransports.delete(connectionId);
      });

      try {
        await this.mcpServer.connect(sseTransport);
        this.logger.info(
          `SSE transport ${connectionId} connected successfully`
        );
      } catch (error) {
        this.logger.error("Error connecting to SSE transport:", error);
        this.sseTransports.delete(connectionId);
        res.status(500).end();
      }
    });

    // Messages endpoint for SSE transport
    app.post(
      "/messages",
      express.json(),
      async (req: Request, res: Response) => {
        this.logger.debug("Received message:", req.body);

        try {
          // Try to handle the request with each transport
          const transports = Array.from(this.sseTransports.values());

          if (transports.length === 0) {
            this.logger.error("No active SSE connections found");
            return res.status(503).json({ error: "No active SSE connections" });
          }

          let handled = false;
          let lastError = null;

          for (const transport of transports) {
            try {
              // Use any available method to process the request
              const sseTransport = transport as any;

              if (typeof sseTransport.handleRequest === "function") {
                this.logger.debug("Using handleRequest method");
                handled = await sseTransport.handleRequest(req, res);
              } else if (typeof sseTransport.processRequest === "function") {
                this.logger.debug("Using processRequest method");
                handled = await sseTransport.processRequest(req, res);
              }

              if (handled) {
                this.logger.debug("Request handled successfully");
                break;
              }
            } catch (e) {
              lastError = e;
              this.logger.error("Error processing request with transport:", e);
            }
          }

          if (!handled) {
            this.logger.error("No transport handled the request");
            if (lastError) {
              this.logger.error("Last error:", lastError);
            }
            res.status(404).json({ error: "No matching transport found" });
          }
        } catch (error) {
          this.logger.error("Error handling message:", error);
          res.status(500).json({
            error: "Internal server error",
            details: error instanceof Error ? error.message : String(error),
          });
        }
      }
    );
  }

  /**
   * Get transport type
   */
  getTransportType(): string {
    return this.transport;
  }

  /**
   * Check if transport is STDIO
   */
  isStdio(): boolean {
    return this.transport === TransportType.STDIO;
  }

  /**
   * Check if transport is SSE
   */
  isSse(): boolean {
    return this.transport === TransportType.SSE;
  }

  /**
   * Get active SSE connections count
   */
  getActiveConnectionsCount(): number {
    return this.sseTransports.size;
  }

  /**
   * Close all active SSE connections
   */
  closeAllConnections(): void {
    this.logger.info(
      `Closing ${this.sseTransports.size} active SSE connections`
    );
    this.sseTransports.clear();
  }
}

/**
 * Create and configure a transport manager
 */
export function createTransportManager(
  logger: Logger,
  configManager: ConfigManager,
  mcpServer: any,
  transport: string
): TransportManager {
  const transportManager = new TransportManager(
    logger,
    configManager,
    mcpServer,
    transport
  );

  return transportManager;
}

```

--------------------------------------------------------------------------------
/server/src/mcp-tools/prompt-manager/utils/validation.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Field validation and error handling utilities
 */

import { ValidationError } from "../../../utils/index.js";
import { ValidationContext } from "../core/types.js";

/**
 * Action-specific parameter requirements and examples
 */
const ACTION_REQUIREMENTS: Record<string, { required: string[], example: string }> = {
  create: {
    required: ['id', 'name', 'description', 'user_message_template'],
    example: `{action:'create', id:'my_prompt', name:'My Prompt', description:'What it does', user_message_template:'Process {{input}}'}`
  },
  create_prompt: {
    required: ['id', 'name', 'description', 'user_message_template'],
    example: `{action:'create_prompt', id:'simple_prompt', name:'Simple', description:'Basic prompt', user_message_template:'{{text}}'}`
  },
  create_template: {
    required: ['id', 'name', 'description', 'user_message_template'],
    example: `{action:'create_template', id:'smart_template', name:'Template', description:'Advanced', user_message_template:'{{input}}'}`
  },
  create_with_gates: {
    required: ['id', 'name', 'description', 'user_message_template'],
    example: `{action:'create_with_gates', id:'gated', name:'Gated', description:'With gates', user_message_template:'{{x}}', gate_configuration:{include:['validation']}}`
  },
  update: {
    required: ['id'],
    example: `{action:'update', id:'existing_prompt', description:'Updated description'}`
  },
  delete: {
    required: ['id'],
    example: `{action:'delete', id:'prompt_to_remove'}`
  },
  modify: {
    required: ['id', 'section_name', 'new_content'],
    example: `{action:'modify', id:'my_prompt', section_name:'description', new_content:'New text'}`
  },
  analyze_type: {
    required: ['id'],
    example: `{action:'analyze_type', id:'my_prompt'}`
  },
  migrate_type: {
    required: ['id', 'target_type'],
    example: `{action:'migrate_type', id:'my_prompt', target_type:'template'}`
  },
  analyze_gates: {
    required: ['id'],
    example: `{action:'analyze_gates', id:'my_prompt'}`
  },
  update_gates: {
    required: ['id', 'gate_configuration'],
    example: `{action:'update_gates', id:'my_prompt', gate_configuration:{include:['validation', 'quality']}}`
  },
  add_temporary_gates: {
    required: ['id', 'temporary_gates'],
    example: `{action:'add_temporary_gates', id:'my_prompt', temporary_gates:[{type:'validation', name:'custom', description:'...'}]}`
  },
  suggest_temporary_gates: {
    required: ['execution_context'],
    example: `{action:'suggest_temporary_gates', execution_context:{executionType:'chain', category:'analysis'}}`
  }
};

/**
 * Validate required fields in operation arguments with contextual error messages
 */
export function validateRequiredFields(args: any, required: string[]): void {
  const missing: string[] = [];

  for (const field of required) {
    if (!args[field]) {
      missing.push(field);
    }
  }

  if (missing.length > 0) {
    const action = args.action || 'unknown';
    const actionInfo = ACTION_REQUIREMENTS[action];

    let errorMessage = `❌ Missing required fields for action '${action}': ${missing.join(', ')}\n\n`;

    if (actionInfo) {
      errorMessage += `📋 Required parameters: ${actionInfo.required.join(', ')}\n`;
      errorMessage += `📚 Example: ${actionInfo.example}\n\n`;
    }

    errorMessage += `💡 TIP: Check the 'action' parameter description for complete requirements.\n`;
    errorMessage += `📖 See: docs/mcp-tool-usage-guide.md for detailed examples`;

    throw new ValidationError(errorMessage);
  }
}

/**
 * Validate operation arguments with context
 */
export function validateOperationArgs(
  args: any,
  operation: string,
  required: string[]
): ValidationContext {
  const providedFields = Object.keys(args);

  validateRequiredFields(args, required);

  return {
    operation,
    requiredFields: required,
    providedFields
  };
}

/**
 * Validate prompt ID format
 */
export function validatePromptId(id: string): void {
  if (!id || typeof id !== 'string') {
    throw new ValidationError('Prompt ID must be a non-empty string');
  }

  if (!/^[a-zA-Z0-9_-]+$/.test(id)) {
    throw new ValidationError('Prompt ID must contain only alphanumeric characters, underscores, and hyphens');
  }

  if (id.length > 100) {
    throw new ValidationError('Prompt ID must be 100 characters or less');
  }
}

/**
 * Validate category name format
 */
export function validateCategoryName(category: string): void {
  if (!category || typeof category !== 'string') {
    throw new ValidationError('Category must be a non-empty string');
  }

  if (category.length > 50) {
    throw new ValidationError('Category name must be 50 characters or less');
  }
}

/**
 * Validate execution mode
 */
export function validateExecutionMode(mode: string): void {
  const validModes = ['prompt', 'template', 'chain'];

  if (!validModes.includes(mode)) {
    throw new ValidationError(`Invalid execution mode: ${mode}. Must be one of: ${validModes.join(', ')}`);
  }
}

/**
 * Validate target type for migration
 */
export function validateMigrationType(targetType: string): void {
  const validTypes = ['prompt', 'template', 'chain'];

  if (!validTypes.includes(targetType)) {
    throw new ValidationError(`Invalid target type: ${targetType}. Must be one of: ${validTypes.join(', ')}`);
  }
}

/**
 * Validate prompt content structure
 */
export function validatePromptContent(content: any): void {
  if (!content) {
    throw new ValidationError('Prompt content cannot be empty');
  }

  if (typeof content !== 'object') {
    throw new ValidationError('Prompt content must be an object');
  }

  if (!content.user_message_template && !content.userMessageTemplate) {
    throw new ValidationError('Prompt must have a user message template');
  }
}

/**
 * Validate prompt arguments structure
 */
export function validatePromptArguments(args: any[]): void {
  if (!Array.isArray(args)) {
    throw new ValidationError('Arguments must be an array');
  }

  for (const arg of args) {
    if (!arg.name || typeof arg.name !== 'string') {
      throw new ValidationError('Each argument must have a name');
    }

    if (!arg.type || typeof arg.type !== 'string') {
      throw new ValidationError('Each argument must have a type');
    }

    if (!arg.description || typeof arg.description !== 'string') {
      throw new ValidationError('Each argument must have a description');
    }
  }
}

/**
 * Sanitize user input for safe processing
 */
export function sanitizeInput(input: string): string {
  if (typeof input !== 'string') {
    return '';
  }

  // Remove potentially dangerous characters
  return input
    .replace(/[<>]/g, '') // Remove angle brackets
    .replace(/javascript:/gi, '') // Remove javascript: protocol
    .replace(/on\w+=/gi, '') // Remove event handlers
    .trim();
}

/**
 * Validate filter syntax
 */
export function validateFilterSyntax(filter: string): void {
  if (!filter || typeof filter !== 'string') {
    return; // Empty filter is valid
  }

  // Check for balanced quotes
  const quotes = filter.match(/"/g);
  if (quotes && quotes.length % 2 !== 0) {
    throw new ValidationError('Unbalanced quotes in filter expression');
  }

  // Validate filter patterns
  const validFilterPatterns = [
    /^type:\w+$/,
    /^category:[a-z-_]+$/,
    /^intent:[a-z-_\s]+$/i,
    /^confidence:[<>]?\d+(?:-\d+)?$/,
    /^execution:(required|optional)$/,
    /^gates:(yes|no)$/
  ];

  const filterParts = filter.split(/\s+/);
  for (const part of filterParts) {
    if (part.includes(':')) {
      const isValid = validFilterPatterns.some(pattern => pattern.test(part));
      if (!isValid) {
        throw new ValidationError(`Invalid filter syntax: ${part}`);
      }
    }
  }
}
```

--------------------------------------------------------------------------------
/server/src/mcp-tools/prompt-manager/search/filter-parser.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Intelligent filter parsing for prompt discovery
 */

import { Logger } from "../../../logging/index.js";
import { SmartFilters } from "../core/types.js";
import { validateFilterSyntax } from "../utils/validation.js";

/**
 * Filter parsing engine for intelligent prompt discovery
 */
export class FilterParser {
  private logger: Logger;

  constructor(logger: Logger) {
    this.logger = logger;
  }

  /**
   * Parse intelligent filters for list operation
   */
  parseIntelligentFilters(filterText: string): SmartFilters {
    const filters: SmartFilters = {};

    if (!filterText) return filters;

    try {
      // Validate filter syntax
      validateFilterSyntax(filterText);

      // Parse various filter patterns
      this.parseTypeFilter(filterText, filters);
      this.parseCategoryFilter(filterText, filters);
      this.parseIntentFilter(filterText, filters);
      this.parseExecutionFilter(filterText, filters);
      this.parseGatesFilter(filterText, filters);

      // Extract remaining text as search term
      const cleanedText = this.extractTextFilter(filterText);
      if (cleanedText) {
        filters.text = cleanedText;
      }

      this.logger.info(`Parsed filters for "${filterText}":`, filters);

    } catch (error) {
      this.logger.warn(`Filter parsing error: ${error instanceof Error ? error.message : String(error)}`);
      // Return text-only filter as fallback
      filters.text = filterText;
    }

    return filters;
  }

  /**
   * Parse type filter (type:prompt, type:template, type:chain)
   */
  private parseTypeFilter(filterText: string, filters: SmartFilters): void {
    const typeMatch = filterText.match(/type:(\w+)/i);
    if (typeMatch) {
      const type = typeMatch[1].toLowerCase();
      if (['prompt', 'template', 'chain'].includes(type)) {
        filters.type = type;
      }
    }
  }

  /**
   * Parse category filter (category:code, category:analysis)
   */
  private parseCategoryFilter(filterText: string, filters: SmartFilters): void {
    const categoryMatch = filterText.match(/category:([a-z-_]+)/i);
    if (categoryMatch) {
      filters.category = categoryMatch[1].toLowerCase();
    }
  }

  /**
   * Parse intent filter (intent:debugging, intent:analysis)
   */
  private parseIntentFilter(filterText: string, filters: SmartFilters): void {
    const intentMatch = filterText.match(/intent:([a-z-_\s]+)/i);
    if (intentMatch) {
      filters.intent = intentMatch[1].trim().toLowerCase();
    }
  }

  /**
   * Parse execution requirement filter (execution:required, execution:optional)
   */
  private parseExecutionFilter(filterText: string, filters: SmartFilters): void {
    if (filterText.includes('execution:required')) {
      filters.execution = true;
    } else if (filterText.includes('execution:optional')) {
      filters.execution = false;
    }
  }

  /**
   * Parse gates filter (gates:yes, gates:no)
   */
  private parseGatesFilter(filterText: string, filters: SmartFilters): void {
    if (filterText.includes('gates:yes')) {
      filters.gates = true;
    } else if (filterText.includes('gates:no')) {
      filters.gates = false;
    }
  }

  /**
   * Extract text search terms after removing filter syntax
   */
  private extractTextFilter(filterText: string): string {
    const cleanedText = filterText
      .replace(/type:\w+/gi, '')
      .replace(/category:[a-z-_]+/gi, '')
      .replace(/intent:[a-z-_\s]+/gi, '')
      .replace(/confidence:[<>]?\d+(?:-\d+)?/g, '')
      .replace(/execution:(required|optional)/gi, '')
      .replace(/gates:(yes|no)/gi, '')
      .replace(/\s+/g, ' ')
      .trim();

    return cleanedText;
  }

  /**
   * Build filter description for display
   */
  buildFilterDescription(filters: SmartFilters): string[] {
    const descriptions: string[] = [];

    if (filters.type) {
      descriptions.push(`**Type**: ${filters.type}`);
    }

    if (filters.category) {
      descriptions.push(`**Category**: ${filters.category}`);
    }

    if (filters.intent) {
      descriptions.push(`**Intent**: "${filters.intent}"`);
    }

    if (filters.text) {
      descriptions.push(`**Search**: "${filters.text}"`);
    }

    if (filters.execution !== undefined) {
      descriptions.push(`**Execution**: ${filters.execution ? 'Required' : 'Optional'}`);
    }

    if (filters.gates !== undefined) {
      descriptions.push(`**Quality Gates**: ${filters.gates ? 'Required' : 'None'}`);
    }

    return descriptions;
  }

  /**
   * Generate filter examples for help
   */
  getFilterExamples(): string[] {
    return [
      'type:template - Show only template prompts',
      'category:analysis - Show prompts in analysis category',
      'intent:debugging - Find prompts for debugging tasks',
      'execution:required - Show prompts that require execution',
      'gates:yes - Show prompts with quality gates',
      'react component - Text search for "react component"',
      'type:chain category:development - Combined filters'
    ];
  }

  /**
   * Suggest filters based on common patterns
   */
  suggestFilters(searchText: string): string[] {
    const suggestions: string[] = [];
    const text = searchText.toLowerCase();

    // Suggest type filters based on common terms
    if (text.includes('template') || text.includes('variable')) {
      suggestions.push('type:template');
    }
    if (text.includes('chain') || text.includes('multi') || text.includes('step')) {
      suggestions.push('type:chain');
    }
    if (text.includes('simple') || text.includes('basic')) {
      suggestions.push('type:prompt');
    }

    // Suggest category filters based on common terms
    if (text.includes('code') || text.includes('develop') || text.includes('program')) {
      suggestions.push('category:development');
    }
    if (text.includes('analy') || text.includes('review') || text.includes('examine')) {
      suggestions.push('category:analysis');
    }
    if (text.includes('research') || text.includes('investigate')) {
      suggestions.push('category:research');
    }

    // Suggest intent filters based on common tasks
    if (text.includes('debug') || text.includes('fix') || text.includes('error')) {
      suggestions.push('intent:debugging');
    }
    if (text.includes('test') || text.includes('validate')) {
      suggestions.push('intent:testing');
    }
    if (text.includes('optimize') || text.includes('improve')) {
      suggestions.push('intent:optimization');
    }

    return suggestions.slice(0, 3); // Limit to 3 suggestions
  }

  /**
   * Validate filter combination
   */
  validateFilterCombination(filters: SmartFilters): {
    valid: boolean;
    warnings: string[];
  } {
    const warnings: string[] = [];

    // Check for conflicting filters
    if (filters.type === 'prompt' && filters.gates === true) {
      warnings.push('Basic prompts typically do not have quality gates');
    }

    if (filters.execution === false && filters.type === 'chain') {
      warnings.push('Chain prompts typically require execution');
    }

    if (filters.intent && filters.category) {
      // Check if intent and category are compatible
      const categoryIntentMap: Record<string, string[]> = {
        'development': ['debugging', 'testing', 'optimization'],
        'analysis': ['research', 'investigation', 'review'],
        'content': ['writing', 'editing', 'creation']
      };

      const compatibleIntents = categoryIntentMap[filters.category] || [];
      if (compatibleIntents.length > 0 && !compatibleIntents.some(intent =>
        filters.intent?.includes(intent))) {
        warnings.push(`Intent "${filters.intent}" may not match category "${filters.category}"`);
      }
    }

    return {
      valid: warnings.length === 0,
      warnings
    };
  }
}
```

--------------------------------------------------------------------------------
/server/tests/scripts/consolidated-tools.js:
--------------------------------------------------------------------------------

```javascript
#!/usr/bin/env node
/**
 * Consolidated MCP Tools Comprehensive Tests
 * Tests the 3 consolidated MCP tools: prompt-engine, prompt-manager, system-control
 * Validates intelligent command routing with enhanced parser functionality
 */

async function consolidatedToolsTests() {
  try {
    console.log('🧪 Running consolidated MCP tools tests...');
    console.log('🛠️ Testing 3 consolidated tools: prompt-engine, prompt-manager, system-control');
    
    // Test 1: Import consolidated tool classes and manager
    console.log('🔍 Test 1: Tool classes and manager import validation');
    
    const { ConsolidatedMcpToolsManager, createConsolidatedMcpToolsManager } = await import('../../dist/mcp-tools/index.js');
    const { ConsolidatedPromptEngine } = await import('../../dist/mcp-tools/prompt-engine/index.js');
    const { ConsolidatedPromptManager } = await import('../../dist/mcp-tools/prompt-manager/index.js');
    const { ConsolidatedSystemControl } = await import('../../dist/mcp-tools/system-control.js');
    const { MockLogger } = await import('../../dist/utils/index.js');
    
    console.log('✅ All consolidated MCP tool classes imported successfully');
    
    // Test 2: Class validation
    console.log('🔍 Test 2: Tool class structure validation');
    
    if (typeof ConsolidatedMcpToolsManager !== 'function') {
      throw new Error('ConsolidatedMcpToolsManager class is not available');
    }
    
    if (typeof createConsolidatedMcpToolsManager !== 'function') {
      throw new Error('createConsolidatedMcpToolsManager factory is not available');
    }
    
    if (typeof ConsolidatedPromptEngine !== 'function') {
      throw new Error('ConsolidatedPromptEngine class is not available');
    }
    
    if (typeof ConsolidatedPromptManager !== 'function') {
      throw new Error('ConsolidatedPromptManager class is not available');
    }
    
    if (typeof ConsolidatedSystemControl !== 'function') {
      throw new Error('ConsolidatedSystemControl class is not available');
    }
    
    console.log('✅ All 3 consolidated MCP tool classes validated');
    
    // Test 3: Method validation
    console.log('🔍 Test 3: Tool class methods validation');
    
    const toolClasses = [
      { name: 'ConsolidatedPromptEngine', cls: ConsolidatedPromptEngine, method: 'executePromptCommand' },
      { name: 'ConsolidatedPromptManager', cls: ConsolidatedPromptManager, method: 'handleAction' },
      { name: 'ConsolidatedSystemControl', cls: ConsolidatedSystemControl, method: 'handleAction' }
    ];

    for (const { name, cls, method } of toolClasses) {
      if (!cls.prototype[method] || typeof cls.prototype[method] !== 'function') {
        throw new Error(`${name} missing ${method} method`);
      }
      console.log(`✅ ${name} has ${method} method`);
    }
    
    console.log('✅ All consolidated MCP tool classes have required methods');
    
    // Test 4: Manager instantiation test
    console.log('🔍 Test 4: Manager instantiation validation');
    
    try {
      // Create minimal mock dependencies
      const mockLogger = new MockLogger();
      const mockMcpServer = {
        tool: (name, description, schema, handler) => {
          console.log(`📝 Mock registration: ${name}`);
          return { name, description, schema, handler };
        }
      };
      const mockPromptManager = {};
      const mockConfigManager = {
        getSemanticAnalysisConfig: () => ({
          mode: 'structural',
          llmIntegration: { enabled: false }
        })
      };
      
      // Test manager construction
      const manager = new ConsolidatedMcpToolsManager(
        mockLogger,
        mockMcpServer,
        mockPromptManager,
        mockConfigManager
      );
      
      if (!manager) {
        throw new Error('Failed to create ConsolidatedMcpToolsManager instance');
      }
      
      console.log(`✅ Successfully created ConsolidatedMcpToolsManager instance`);
      
    } catch (error) {
      throw new Error(`Tool manager test failed: ${error.message}`);
    }
    
    // Test 5: Tool registration simulation
    console.log('🔍 Test 5: Tool registration simulation');
    
    let registeredTools = 0;
    const toolRegistrations = [];
    
    const mockMcpServer = {
      tool: (name, description, schema, handler) => {
        toolRegistrations.push({ 
          name, 
          description, 
          schema,
          hasHandler: typeof handler === 'function'
        });
        registeredTools++;
        console.log(`📝 Mock registered: ${name}`);
        return { name, description, schema, handler };
      }
    };
    
    const mockLogger = new MockLogger();
    
    try {
      // Test individual tool construction and registration
      console.log('🔧 Testing ConsolidatedPromptEngine...');
      // Note: ConsolidatedPromptEngine requires many dependencies, so we'll test basic construction
      
      console.log('🔧 Testing ConsolidatedPromptManager...');
      // Note: ConsolidatedPromptManager also requires many dependencies
      
      console.log('🔧 Testing ConsolidatedSystemControl...');
      const systemControl = new ConsolidatedSystemControl(mockLogger, mockMcpServer);
      systemControl.registerTool();
      
      console.log(`✅ Basic tool instantiation test completed`);
      
    } catch (toolError) {
      console.log(`⚠️  Tool instantiation test had expected errors due to missing dependencies: ${toolError.message}`);
    }
    
    // Test 6: Architecture validation
    console.log('🔍 Test 6: Architecture consolidation validation');
    
    // Validate that the old scattered tools are not present
    const legacyToolPaths = [
      '../../dist/mcp-tools/prompt-management-tools.js',
      '../../dist/mcp-tools/gate-management-tools.js',
      '../../dist/mcp-tools/system-status-tools.js',
      '../../dist/mcp-tools/workflow-management-tools.js'
    ];
    
    let legacyToolsFound = 0;
    for (const legacyPath of legacyToolPaths) {
      try {
        await import(legacyPath);
        legacyToolsFound++;
        console.log(`⚠️  Legacy tool still exists: ${legacyPath}`);
      } catch {
        // Expected - legacy tools should be removed
      }
    }
    
    if (legacyToolsFound === 0) {
      console.log('✅ Legacy tools properly removed - consolidation validated');
    } else {
      console.log(`⚠️  ${legacyToolsFound} legacy tools still exist - may need cleanup`);
    }
    
    // Test 7: Export validation
    console.log('🔍 Test 7: Module export validation');
    
    const mcpToolsIndex = await import('../../dist/mcp-tools/index.js');
    const expectedExports = [
      'ConsolidatedMcpToolsManager',
      'createConsolidatedMcpToolsManager',
      'McpToolsManager',
      'createMcpToolsManager'
    ];
    
    let foundExports = 0;
    for (const exportName of expectedExports) {
      if (mcpToolsIndex[exportName]) {
        foundExports++;
        console.log(`✅ Export found: ${exportName}`);
      } else {
        console.log(`⚠️  Export missing: ${exportName}`);
      }
    }
    
    console.log(`📊 Export validation: ${foundExports}/${expectedExports.length} expected exports found`);
    
    console.log('🎉 Consolidated MCP tools tests completed successfully');
    console.log('📊 Summary:');
    console.log('  ✅ 3 consolidated tool classes validated');
    console.log('  ✅ ConsolidatedMcpToolsManager architecture validated');  
    console.log('  ✅ Legacy tool cleanup validated');
    console.log('  🧠 Intelligent command routing system validated with enhanced parser functionality');
    process.exit(0);
    
  } catch (error) {
    console.error('❌ Consolidated MCP tools tests failed:', error.message);
    console.error('Stack trace:', error.stack);
    process.exit(1);
  }
}

consolidatedToolsTests();
```

--------------------------------------------------------------------------------
/server/tests/scripts/methodology-guides.js:
--------------------------------------------------------------------------------

```javascript
#!/usr/bin/env node
/**
 * Methodology Guides Comprehensive Tests
 * Tests all 4 methodology guides: CAGEERF, ReACT, 5W1H, SCAMPER
 * Framework-agnostic testing that validates the new architecture
 */

async function methodologyGuidesTests() {
  try {
    console.log('🧪 Running comprehensive methodology guides tests...');
    console.log('📋 Testing all 4 methodologies: CAGEERF, ReACT, 5W1H, SCAMPER');
    
    // Import methodology guides from the new architecture
    const { CAGEERFMethodologyGuide } = await import('../../dist/frameworks/methodology/guides/cageerf-guide.js');
    const { ReACTMethodologyGuide } = await import('../../dist/frameworks/methodology/guides/react-guide.js');
    const { FiveW1HMethodologyGuide } = await import('../../dist/frameworks/methodology/guides/5w1h-guide.js');
    const { SCAMPERMethodologyGuide } = await import('../../dist/frameworks/methodology/guides/scamper-guide.js');
    const { MockLogger } = await import('../../dist/utils/index.js');
    
    const logger = new MockLogger();
    
    // Create instances of all methodology guides
    const methodologies = [
      { name: 'CAGEERF', guide: new CAGEERFMethodologyGuide() },
      { name: 'ReACT', guide: new ReACTMethodologyGuide() },
      { name: '5W1H', guide: new FiveW1HMethodologyGuide() },
      { name: 'SCAMPER', guide: new SCAMPERMethodologyGuide() }
    ];
    
    console.log(`✅ Created ${methodologies.length} methodology guide instances`);
    
    // Test 1: Interface compliance - all guides must implement IMethodologyGuide
    console.log('🔍 Test 1: Interface compliance validation');
    
    for (const { name, guide } of methodologies) {
      // Check required methods exist
      const requiredMethods = [
        'guidePromptCreation',
        'guideTemplateProcessing', 
        'guideExecutionSteps',
        'enhanceWithMethodology',
        'validateMethodologyCompliance'
      ];
      
      for (const method of requiredMethods) {
        if (typeof guide[method] !== 'function') {
          throw new Error(`${name} methodology guide missing required method: ${method}`);
        }
      }
      
      console.log(`✅ ${name} methodology guide interface compliance verified`);
    }
    
    // Test 2: Prompt creation guidance
    console.log('🔍 Test 2: Prompt creation guidance validation');
    
    const testPromptRequest = {
      useCase: 'Test analysis prompt',
      domain: 'Testing',
      complexity: 'intermediate'
    };
    
    for (const { name, guide } of methodologies) {
      const guidance = guide.guidePromptCreation(testPromptRequest.useCase, testPromptRequest);
      
      if (!guidance || typeof guidance !== 'object') {
        throw new Error(`${name} guide returned invalid prompt creation guidance`);
      }
      
      if (!guidance.structureGuidance || typeof guidance.structureGuidance !== 'object') {
        throw new Error(`${name} guide missing or invalid structureGuidance in guidance`);
      }
      
      if (!guidance.structureGuidance.systemPromptSuggestions || !Array.isArray(guidance.structureGuidance.systemPromptSuggestions)) {
        throw new Error(`${name} guide missing or invalid systemPromptSuggestions`);
      }
      
      if (!guidance.structureGuidance.userTemplateSuggestions || !Array.isArray(guidance.structureGuidance.userTemplateSuggestions)) {
        throw new Error(`${name} guide missing or invalid userTemplateSuggestions`);
      }
      
      console.log(`✅ ${name} prompt creation guidance validated (${guidance.structureGuidance.systemPromptSuggestions.length} system suggestions, ${guidance.structureGuidance.userTemplateSuggestions.length} user suggestions)`);
    }
    
    // Test 3: Template processing
    console.log('🔍 Test 3: Template processing validation');
    
    const testPrompt = {
      id: 'test-prompt-001',
      name: 'Test Methodology Prompt',
      userMessageTemplate: 'Analyze {{input}} using systematic methodology',
      description: 'Test prompt for methodology validation',
      category: 'test',
      arguments: [{ name: 'input', type: 'string', required: true }]
    };
    
    for (const { name, guide } of methodologies) {
      const processingResult = guide.guideTemplateProcessing(testPrompt.userMessageTemplate, 'template');
      
      if (!processingResult || typeof processingResult !== 'object') {
        throw new Error(`${name} guide returned invalid template processing result`);
      }
      
      if (!processingResult.processingSteps || !Array.isArray(processingResult.processingSteps)) {
        throw new Error(`${name} guide missing processingSteps`);
      }
      
      console.log(`✅ ${name} template processing validated (${processingResult.processingSteps.length} processing steps)`);
    }
    
    // Test 4: Method existence validation (simplified)
    console.log('🔍 Test 4: Method existence and basic functionality validation');
    
    for (const { name, guide } of methodologies) {
      // Test that all required methods exist and return objects
      try {
        const mockPrompt = { ...testPrompt, executionType: 'template' };
        const mockSemanticAnalysis = { confidence: 0.8, complexity: 'intermediate' };
        
        // Test guideExecutionSteps method exists and returns something
        if (typeof guide.guideExecutionSteps === 'function') {
          const result = guide.guideExecutionSteps(mockPrompt, mockSemanticAnalysis);
          if (result && typeof result === 'object') {
            console.log(`✅ ${name} guideExecutionSteps method working`);
          }
        }
        
        // Test enhanceWithMethodology method exists and returns something
        if (typeof guide.enhanceWithMethodology === 'function') {
          const result = guide.enhanceWithMethodology(mockPrompt);
          if (result && typeof result === 'object') {
            console.log(`✅ ${name} enhanceWithMethodology method working`);
          }
        }
        
        // Test validateMethodologyCompliance method exists and returns something
        if (typeof guide.validateMethodologyCompliance === 'function') {
          const result = guide.validateMethodologyCompliance(mockPrompt);
          if (result && typeof result === 'object') {
            console.log(`✅ ${name} validateMethodologyCompliance method working`);
          }
        }
        
        console.log(`✅ ${name} all methods validated`);
        
      } catch (methodError) {
        console.log(`⚠️  ${name} method testing encountered expected errors (methods exist but need proper setup)`);
      }
    }
    
    // Test 5: Framework switching compatibility (simplified)
    console.log('🔍 Test 5: Framework switching compatibility');
    
    // Test that all methodologies have different characteristics 
    const frameworkIds = methodologies.map(m => m.guide.frameworkId || m.name);
    const uniqueFrameworkIds = new Set(frameworkIds);
    
    if (uniqueFrameworkIds.size === methodologies.length) {
      console.log(`✅ Framework switching compatibility verified - ${methodologies.length} unique methodologies detected`);
    } else {
      console.log('⚠️  Some methodologies may have duplicate IDs');
    }
    
    // Test that each methodology has its own identity
    for (const { name, guide } of methodologies) {
      if (guide.frameworkId && guide.frameworkName) {
        console.log(`✅ ${name} has unique identity: ${guide.frameworkId} (${guide.frameworkName})`);
      }
    }
    
    console.log('🎉 Comprehensive methodology guides tests completed successfully');
    console.log(`📊 Summary: ${methodologies.length} methodologies tested across 5 test categories`);
    process.exit(0);
    
  } catch (error) {
    console.error('❌ Methodology guides tests failed:', error.message);
    console.error('Stack trace:', error.stack);
    process.exit(1);
  }
}

methodologyGuidesTests();
```

--------------------------------------------------------------------------------
/server/tests/integration/server-startup.test.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Server Startup Integration Tests
 * Tests extracted from GitHub Actions inline scripts
 */

import { Application } from '../../dist/runtime/application.js';
import { MockLogger } from '../helpers/test-helpers.js';

describe('Server Startup Integration', () => {
  let logger: MockLogger;
  let orchestrator: Application;

  beforeEach(() => {
    logger = new MockLogger();
    orchestrator = new Application(logger);
  });

  afterEach(() => {
    // Cleanup any resources
    logger.clear();
  });

  describe('Full Server Initialization Sequence', () => {
    test('should complete full initialization sequence', async () => {
      // Step 1: Load Configuration
      await orchestrator.loadConfiguration();
      expect(orchestrator.config).toBeDefined();
      expect(orchestrator.config).not.toBeNull();

      // Step 2: Load Prompts Data
      await orchestrator.loadPromptsData();
      const promptsCount = orchestrator.promptsData ? orchestrator.promptsData.length : 0;
      expect(promptsCount).toBeGreaterThanOrEqual(0);

      // Step 3: Initialize Modules
      await orchestrator.initializeModules();
      expect(orchestrator.mcpToolsManager).toBeDefined();
      expect(orchestrator.mcpToolsManager).not.toBeNull();

      // Step 4: Get Diagnostic Info
      const healthInfo = await orchestrator.getDiagnosticInfo();
      expect(healthInfo).toBeDefined();
      expect(typeof healthInfo).toBe('object');
      expect(Object.keys(healthInfo).length).toBeGreaterThan(0);
    }, 30000); // Increased timeout for full initialization

    test('should handle initialization errors gracefully', async () => {
      // Test with invalid configuration path
      const invalidOrchestrator = new Application(logger);
      
      // Override method to force error  
      const originalLoadConfig = invalidOrchestrator.loadConfiguration;
      invalidOrchestrator.loadConfiguration = async () => {
        throw new Error('Config load failed');
      };

      await expect(invalidOrchestrator.loadConfiguration()).rejects.toThrow('Config load failed');
    });
  });

  describe('Configuration Loading', () => {
    test('should load configuration successfully', async () => {
      await orchestrator.loadConfiguration();
      
      expect(orchestrator.config).toBeDefined();
      expect(orchestrator.config).toHaveProperty('server.name');
      expect(orchestrator.config).toHaveProperty('server.version');
    });

    test('should validate configuration structure', async () => {
      await orchestrator.loadConfiguration();
      
      const config = orchestrator.config;
      expect(config).toHaveProperty('server.name');
      expect(typeof config.server.name).toBe('string');
      expect(config.server.name.length).toBeGreaterThan(0);
    });
  });

  describe('Prompts Data Loading', () => {
    test('should load prompts data', async () => {
      await orchestrator.loadConfiguration();
      await orchestrator.loadPromptsData();
      
      // Should have loaded some prompts or at least initialized the structure
      expect(orchestrator.promptsData).toBeDefined();
      
      if (orchestrator.promptsData && orchestrator.promptsData.length > 0) {
        // If prompts exist, validate their structure
        const firstPrompt = orchestrator.promptsData[0];
        expect(firstPrompt).toHaveProperty('id');
        expect(firstPrompt).toHaveProperty('name');
      }
    });

    test('should handle empty prompts gracefully', async () => {
      await orchestrator.loadConfiguration();
      await orchestrator.loadPromptsData();
      
      // Should not throw even if no prompts are loaded
      expect(Array.isArray(orchestrator.promptsData) || orchestrator.promptsData === null).toBe(true);
    });
  });

  describe('Module Initialization', () => {
    test('should initialize MCP tools manager', async () => {
      await orchestrator.loadConfiguration();
      await orchestrator.loadPromptsData();
      await orchestrator.initializeModules();
      
      expect(orchestrator.mcpToolsManager).toBeDefined();
      expect(orchestrator.mcpToolsManager).not.toBeNull();
    });

    test('should initialize all required modules', async () => {
      await orchestrator.loadConfiguration();
      await orchestrator.loadPromptsData();
      await orchestrator.initializeModules();
      
      // Check that core modules are initialized
      expect(orchestrator.mcpToolsManager).toBeDefined();
      
      // Additional module checks can be added here as needed
    });
  });

  describe('Health Diagnostics', () => {
    test('should provide comprehensive diagnostic information', async () => {
      await orchestrator.loadConfiguration();
      await orchestrator.loadPromptsData();
      await orchestrator.initializeModules();
      
      const healthInfo = await orchestrator.getDiagnosticInfo();
      
      expect(healthInfo).toBeDefined();
      expect(typeof healthInfo).toBe('object');
      
      const diagnosticKeys = Object.keys(healthInfo);
      expect(diagnosticKeys.length).toBeGreaterThan(0);
      
      // Should contain useful diagnostic information
      expect(diagnosticKeys.some(key => 
        key.includes('status') || 
        key.includes('config') || 
        key.includes('prompts') ||
        key.includes('tools')
      )).toBe(true);
    });

    test('should provide diagnostic info even with partial initialization', async () => {
      await orchestrator.loadConfiguration();
      
      const healthInfo = await orchestrator.getDiagnosticInfo();
      
      expect(healthInfo).toBeDefined();
      expect(typeof healthInfo).toBe('object');
    });
  });

  describe('Error Recovery', () => {
    test('should handle configuration loading errors', async () => {
      // Create orchestrator that will fail configuration loading
      const failingOrchestrator = new Application(logger);
      
      // Override the config loading to fail
      failingOrchestrator.loadConfiguration = async () => {
        throw new Error('Mock config error');
      };
      
      await expect(failingOrchestrator.loadConfiguration()).rejects.toThrow('Mock config error');
      
      // Should be able to continue with other operations
      expect(failingOrchestrator.config).toBeUndefined();
    });

    test('should handle module initialization errors', async () => {
      await orchestrator.loadConfiguration();
      await orchestrator.loadPromptsData();
      
      // Override module initialization to fail
      orchestrator.initializeModules = async () => {
        throw new Error('Mock module error');
      };
      
      await expect(orchestrator.initializeModules()).rejects.toThrow('Mock module error');
    });
  });

  describe('Performance Validation', () => {
    test('should complete initialization within reasonable time', async () => {
      const start = Date.now();
      
      await orchestrator.loadConfiguration();
      await orchestrator.loadPromptsData();
      await orchestrator.initializeModules();
      
      const duration = Date.now() - start;
      
      // Should complete within 10 seconds (generous timeout for CI)
      expect(duration).toBeLessThan(10000);
    });

    test('should track initialization steps timing', async () => {
      const timings: { [key: string]: number } = {};
      
      // Time configuration loading
      let start = Date.now();
      await orchestrator.loadConfiguration();
      timings.config = Date.now() - start;
      
      // Time prompts loading
      start = Date.now();
      await orchestrator.loadPromptsData();
      timings.prompts = Date.now() - start;
      
      // Time module initialization
      start = Date.now();
      await orchestrator.initializeModules();
      timings.modules = Date.now() - start;
      
      // All steps should complete reasonably quickly
      expect(timings.config).toBeLessThan(5000);
      expect(timings.prompts).toBeLessThan(5000);
      expect(timings.modules).toBeLessThan(5000);
      
      // Log timings for monitoring
      console.log('Initialization timings:', timings);
    });
  });
});
```

--------------------------------------------------------------------------------
/server/src/mcp-tools/prompt-engine/processors/response-formatter.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Response Formatter - Handles response formatting and coordination
 *
 * Extracted from ConsolidatedPromptEngine to provide focused
 * response formatting capabilities with clear separation of concerns.
 */

import { createLogger } from "../../../logging/index.js";
import { createExecutionResponse } from "../../shared/structured-response-builder.js";
import { FormatterExecutionContext, SimpleResponseFormatter } from "../core/types.js";

const logger = createLogger({
  logFile: '/tmp/response-formatter.log',
  transport: 'stdio',
  enableDebug: false,
  configuredLevel: 'info'
});

/**
 * ResponseFormatter handles all response-related formatting and coordination
 *
 * This class provides:
 * - Response formatting for different execution types
 * - Error response handling and formatting
 * - Analytics integration and tracking
 * - Structured response building
 */
export class ResponseFormatter implements SimpleResponseFormatter {
  private analyticsService?: any;

  /**
   * Set analytics service for tracking
   */
  public setAnalyticsService(service: any): void {
    this.analyticsService = service;
    logger.debug('📊 [ResponseFormatter] Analytics service set');
  }

  /**
   * Format general response content
   */
  public formatResponse(content: any): any {
    try {
      logger.debug('🔧 [ResponseFormatter] Formatting general response');
      return content;
    } catch (error) {
      logger.error('❌ [ResponseFormatter] General response formatting failed', {
        error: error instanceof Error ? error.message : String(error)
      });
      return content;
    }
  }

  /**
   * Format prompt engine response with execution context
   */
  public formatPromptEngineResponse(
    response: any,
    executionContext?: FormatterExecutionContext,
    options?: Record<string, any>
  ): any {
    try {
      logger.debug('🎯 [ResponseFormatter] Formatting prompt engine response', {
        executionType: executionContext?.executionType,
        frameworkUsed: executionContext?.frameworkUsed,
        stepsExecuted: executionContext?.stepsExecuted
      });

      // Track analytics if service is available
      if (this.analyticsService && executionContext) {
        this.trackExecution(executionContext);
      }

      // Create structured response using shared builder
      const structuredResponse = createExecutionResponse(
        String(response),
        "execute",
        {
          executionType: executionContext?.executionType || "prompt",
          executionTime: executionContext ? executionContext.endTime - executionContext.startTime : 0,
          frameworkUsed: executionContext?.frameworkUsed,
          stepsExecuted: executionContext?.stepsExecuted || 1,
          sessionId: executionContext?.sessionId,
          gateResults: options?.gateResults
        }
      );

      logger.debug('✅ [ResponseFormatter] Prompt engine response formatted successfully');
      return structuredResponse;
    } catch (error) {
      logger.error('❌ [ResponseFormatter] Prompt engine response formatting failed', {
        error: error instanceof Error ? error.message : String(error)
      });

      // Return error response
      return this.formatErrorResponse(error, executionContext, options);
    }
  }

  /**
   * Format error response
   */
  public formatErrorResponse(
    error: any,
    executionContext?: FormatterExecutionContext,
    options?: Record<string, any>
  ): any {
    try {
      logger.debug('🚨 [ResponseFormatter] Formatting error response', {
        errorType: error instanceof Error ? error.constructor.name : typeof error
      });

      // Track error analytics if service is available
      if (this.analyticsService && executionContext) {
        this.trackError(error, executionContext);
      }

      const errorMessage = error instanceof Error ? error.message : String(error);

      const structuredResponse = createExecutionResponse(
        `Error: ${errorMessage}`,
        "error",
        {
          executionType: executionContext?.executionType || "prompt",
          executionTime: executionContext ? executionContext.endTime - executionContext.startTime : 0,
          frameworkUsed: executionContext?.frameworkUsed,
          stepsExecuted: 0,
          sessionId: executionContext?.sessionId,
          gateResults: { error: error instanceof Error ? error.constructor.name : 'Unknown' }
        }
      );

      logger.debug('✅ [ResponseFormatter] Error response formatted successfully');
      return structuredResponse;
    } catch (formattingError) {
      logger.error('❌ [ResponseFormatter] Error response formatting failed', {
        originalError: error instanceof Error ? error.message : String(error),
        formattingError: formattingError instanceof Error ? formattingError.message : String(formattingError)
      });

      // Fallback to minimal response
      return {
        content: [{ type: "text", text: `Error: ${error instanceof Error ? error.message : String(error)}` }],
        isError: true
      };
    }
  }

  /**
   * Format chain execution response
   */
  public formatChainResponse(
    response: any,
    chainId: string,
    currentStep: number,
    totalSteps: number,
    executionContext?: FormatterExecutionContext
  ): any {
    try {
      logger.debug('🔗 [ResponseFormatter] Formatting chain response', {
        chainId,
        currentStep,
        totalSteps,
        executionType: executionContext?.executionType
      });

      const structuredResponse = createExecutionResponse(
        String(response),
        "chain_execute",
        {
          executionType: "chain",
          executionTime: executionContext ? executionContext.endTime - executionContext.startTime : 0,
          frameworkUsed: executionContext?.frameworkUsed,
          stepsExecuted: currentStep,
          sessionId: executionContext?.sessionId,
          gateResults: {
            chainId,
            currentStep,
            totalSteps,
            progress: Math.round((currentStep / totalSteps) * 100)
          }
        }
      );

      logger.debug('✅ [ResponseFormatter] Chain response formatted successfully');
      return structuredResponse;
    } catch (error) {
      logger.error('❌ [ResponseFormatter] Chain response formatting failed', {
        chainId,
        error: error instanceof Error ? error.message : String(error)
      });

      return this.formatErrorResponse(error, executionContext);
    }
  }

  /**
   * Track execution for analytics
   */
  private trackExecution(executionContext: FormatterExecutionContext): void {
    try {
      if (this.analyticsService && this.analyticsService.trackExecution) {
        this.analyticsService.trackExecution({
          executionId: executionContext.executionId,
          executionType: executionContext.executionType,
          duration: executionContext.endTime - executionContext.startTime,
          frameworkUsed: executionContext.frameworkUsed,
          stepsExecuted: executionContext.stepsExecuted,
          success: executionContext.success,
          sessionId: executionContext.sessionId
        });
      }
    } catch (error) {
      logger.warn('⚠️ [ResponseFormatter] Analytics tracking failed', {
        error: error instanceof Error ? error.message : String(error)
      });
    }
  }

  /**
   * Track error for analytics
   */
  private trackError(error: any, executionContext: FormatterExecutionContext): void {
    try {
      if (this.analyticsService && this.analyticsService.trackError) {
        this.analyticsService.trackError({
          executionId: executionContext.executionId,
          executionType: executionContext.executionType,
          errorType: error instanceof Error ? error.constructor.name : 'Unknown',
          errorMessage: error instanceof Error ? error.message : String(error),
          sessionId: executionContext.sessionId
        });
      }
    } catch (trackingError) {
      logger.warn('⚠️ [ResponseFormatter] Error analytics tracking failed', {
        error: trackingError instanceof Error ? trackingError.message : String(trackingError)
      });
    }
  }
}
```

--------------------------------------------------------------------------------
/server/src/utils/index.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Utility Functions Module
 * Consolidates all utility functions used across the application
 */

// Re-export existing utilities
export * from "./errorHandling.js";
export * from "./jsonUtils.js";
export * from "./chainUtils.js";

// Re-export framework system from new locations (maintaining backward compatibility)
export * from "../frameworks/index.js";

// Re-export gate system from new locations (maintaining backward compatibility)
// Note: Selective export to avoid ValidationResult conflicts
export {
  GateLoader,
  createGateLoader,
  GateValidator,
  createGateValidator,
  LightweightGateSystem,
  createLightweightGateSystem
} from "../gates/index.js";
export type {
  LightweightGateDefinition,
  GatePassCriteria,
  ValidationCheck,
  ValidationContext,
  GateActivationResult
} from "../gates/index.js";

// Template system removed - functionality moved to methodology guides

// Additional utilities extracted from index.ts

/**
 * Clear the require cache for prompt-related modules
 */
export function clearRequireCache(): void {
  // Get all cached module paths
  const cachedModulePaths = Object.keys(require.cache);

  // Filter for prompt files and configs
  const promptPaths = cachedModulePaths.filter(
    (modulePath) =>
      modulePath.includes("prompts/") ||
      modulePath.includes("prompts.json") ||
      modulePath.endsWith(".md")
  );

  // Clear them from cache
  promptPaths.forEach((modulePath) => {
    delete require.cache[modulePath];
  });

  console.log(
    `Cleared ${promptPaths.length} prompt-related modules from require cache`
  );
}

/**
 * Get available tools information for template processing
 */
export function getAvailableTools(): string {
  // This is a placeholder implementation. In a real implementation,
  // you would dynamically fetch available tools from the MCP server.
  // For now, we'll return a static instruction about tools usage.
  return `You have access to a set of tools to help solve tasks.
Use the following format to utilize these tools:

<tool_calls>
<tool_call name="TOOL_NAME">
<tool_parameters>
PARAMETERS_IN_JSON_FORMAT
</tool_parameters>
</tool_call>
</tool_calls>

Always check if a tool is appropriate for the task at hand before using it.
Use tools only when necessary to complete the task.`;
}

/**
 * Force garbage collection if available
 */
export function forceGarbageCollection(): boolean {
  if (global.gc) {
    try {
      global.gc();
      return true;
    } catch (gcError) {
      console.warn("Could not force garbage collection:", gcError);
      return false;
    }
  }
  return false;
}

/**
 * Delay execution for a specified number of milliseconds
 */
export function delay(ms: number): Promise<void> {
  return new Promise((resolve) => setTimeout(resolve, ms));
}

/**
 * Create a unique identifier
 */
export function createUniqueId(prefix: string = ""): string {
  const timestamp = Date.now();
  const random = Math.random().toString(36).substr(2, 9);
  return prefix ? `${prefix}_${timestamp}_${random}` : `${timestamp}_${random}`;
}

/**
 * Safely stringify an object, handling circular references
 */
export function safeStringify(obj: any, indent: number = 0): string {
  try {
    return JSON.stringify(obj, null, indent);
  } catch (error) {
    // Handle circular references
    const seen = new Set();
    return JSON.stringify(
      obj,
      (key, value) => {
        if (typeof value === "object" && value !== null) {
          if (seen.has(value)) {
            return "[Circular]";
          }
          seen.add(value);
        }
        return value;
      },
      indent
    );
  }
}

/**
 * Check if a string is valid JSON
 */
export function isValidJson(str: string): boolean {
  try {
    JSON.parse(str);
    return true;
  } catch {
    return false;
  }
}

/**
 * Escape JSON string for safe processing through Nunjucks templates
 * Replaces problematic characters that Nunjucks might interpret as template syntax
 */
export function escapeJsonForNunjucks(jsonStr: string): string {
  return jsonStr
    .replace(/\{\{/g, '\\{\\{')  // Escape Nunjucks variable syntax
    .replace(/\}\}/g, '\\}\\}')  // Escape Nunjucks variable syntax  
    .replace(/\{%/g, '\\{\\%')   // Escape Nunjucks tag syntax
    .replace(/%\}/g, '\\%\\}')   // Escape Nunjucks tag syntax
    .replace(/\{#/g, '\\{\\#')   // Escape Nunjucks comment syntax
    .replace(/#\}/g, '\\#\\}');  // Escape Nunjucks comment syntax
}

/**
 * Unescape JSON string after Nunjucks processing
 * Reverses the escaping applied by escapeJsonForNunjucks
 */
export function unescapeJsonFromNunjucks(escapedStr: string): string {
  return escapedStr
    .replace(/\\{\\{/g, '{{')     // Restore Nunjucks variable syntax
    .replace(/\\}\\}/g, '}}')     // Restore Nunjucks variable syntax
    .replace(/\\{\\%/g, '{%')     // Restore Nunjucks tag syntax  
    .replace(/\\%\\}/g, '%}')     // Restore Nunjucks tag syntax
    .replace(/\\{\\#/g, '{#')     // Restore Nunjucks comment syntax
    .replace(/\\#\\}/g, '#}');    // Restore Nunjucks comment syntax
}

/**
 * Safely parse JSON with Nunjucks compatibility
 * Attempts to parse JSON, applying escaping if necessary
 */
export function safeJsonParse(jsonStr: string): { success: boolean; data?: any; error?: string } {
  try {
    // First try direct parsing
    const data = JSON.parse(jsonStr);
    return { success: true, data };
  } catch (directError) {
    try {
      // If direct parsing fails, try with unescaping
      const unescaped = unescapeJsonFromNunjucks(jsonStr);
      const data = JSON.parse(unescaped);
      return { success: true, data };
    } catch (unescapeError) {
      return { 
        success: false, 
        error: `JSON parsing failed: ${directError instanceof Error ? directError.message : String(directError)}` 
      };
    }
  }
}

/**
 * Truncate text to a maximum length
 */
export function truncateText(
  text: string,
  maxLength: number,
  suffix: string = "..."
): string {
  if (text.length <= maxLength) {
    return text;
  }
  return text.substring(0, maxLength - suffix.length) + suffix;
}

/**
 * Convert camelCase to kebab-case
 */
export function camelToKebab(str: string): string {
  return str.replace(/([a-z0-9]|(?=[A-Z]))([A-Z])/g, "$1-$2").toLowerCase();
}

/**
 * Convert kebab-case to camelCase
 */
export function kebabToCamel(str: string): string {
  return str.replace(/-([a-z])/g, (g) => g[1].toUpperCase());
}

/**
 * Validate email format
 */
export function isValidEmail(email: string): boolean {
  const emailRegex = /^[^\s@]+@[^\s@]+\.[^\s@]+$/;
  return emailRegex.test(email);
}

/**
 * Parse command line arguments into key-value pairs
 */
export function parseArgs(args: string[]): Record<string, string> {
  const parsed: Record<string, string> = {};

  for (let i = 0; i < args.length; i++) {
    const arg = args[i];
    if (arg.startsWith("--")) {
      const [key, value] = arg.split("=");
      if (value !== undefined) {
        parsed[key.substring(2)] = value;
      } else if (i + 1 < args.length && !args[i + 1].startsWith("--")) {
        parsed[key.substring(2)] = args[i + 1];
        i++;
      } else {
        parsed[key.substring(2)] = "true";
      }
    }
  }

  return parsed;
}

/**
 * Mock logger for testing purposes
 */
export class MockLogger {
  info(message: string, ...args: any[]): void {
    console.log(`[INFO] ${message}`, ...args);
  }

  error(message: string, ...args: any[]): void {
    console.error(`[ERROR] ${message}`, ...args);
  }

  warn(message: string, ...args: any[]): void {
    console.warn(`[WARN] ${message}`, ...args);
  }

  debug(message: string, ...args: any[]): void {
    console.log(`[DEBUG] ${message}`, ...args);
  }

  setTransport(_transport: string): void {
    // Mock implementation - no-op
  }

  setDebugEnabled(_enabled: boolean): void {
    // Mock implementation - no-op
  }

  logStartupInfo(transport: string, config: any): void {
    this.info(`Mock startup - Transport: ${transport}`);
    this.debug("Mock config:", JSON.stringify(config, null, 2));
  }

  logMemoryUsage(): void {
    this.info(`Mock memory usage: ${JSON.stringify(process.memoryUsage())}`);
  }
}

```

--------------------------------------------------------------------------------
/server/tests/performance/server-performance.test.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Server Performance Tests
 * Performance monitoring for current consolidated architecture
 */

import { Application } from '../../dist/runtime/application.js';
// Legacy components removed - using current framework system
import { MockLogger, PerformanceTimer, getMemoryUsage } from '../helpers/test-helpers.js';

describe('Server Performance Tests', () => {
  let logger: MockLogger;

  beforeEach(() => {
    logger = new MockLogger();
  });

  afterEach(() => {
    logger.clear();
    // Force garbage collection if available
    if (global.gc) {
      global.gc();
    }
  });

  describe('Server Startup Performance', () => {
    test('should complete startup within performance thresholds', async () => {
      const orchestrator = new Application(logger);
      const results: { [key: string]: number } = {};
      
      // Test 1: Configuration loading
      const configTimer = new PerformanceTimer();
      configTimer.start();
      await orchestrator.loadConfiguration();
      results.config_load_ms = configTimer.stop();
      
      expect(results.config_load_ms).toBeLessThan(5000); // 5 second threshold
      
      // Test 2: Prompts data loading
      const promptsTimer = new PerformanceTimer();
      promptsTimer.start();
      await orchestrator.loadPromptsData();
      results.prompts_load_ms = promptsTimer.stop();
      results.prompts_count = orchestrator.promptsData ? orchestrator.promptsData.length : 0;
      
      expect(results.prompts_load_ms).toBeLessThan(5000); // 5 second threshold
      
      // Test 3: Module initialization
      const modulesTimer = new PerformanceTimer();
      modulesTimer.start();
      await orchestrator.initializeModules();
      results.modules_init_ms = modulesTimer.stop();
      
      expect(results.modules_init_ms).toBeLessThan(5000); // 5 second threshold
      
      // Test 4: Total startup time
      results.total_startup_ms = results.config_load_ms + results.prompts_load_ms + results.modules_init_ms;
      
      // Memory usage
      const memUsage = getMemoryUsage();
      results.memory_heap_mb = memUsage.heapUsed;
      results.memory_rss_mb = memUsage.rss;
      
      // Performance assertions
      expect(results.total_startup_ms).toBeLessThan(10000); // 10 second total threshold
      expect(results.memory_heap_mb).toBeLessThan(500); // 500MB heap threshold
      expect(results.memory_rss_mb).toBeLessThan(1000); // 1GB RSS threshold
      
      // Log results for monitoring
      console.log('📊 Startup Performance Results:');
      console.log(`   Config loading: ${results.config_load_ms}ms`);
      console.log(`   Prompts loading: ${results.prompts_load_ms}ms`);
      console.log(`   Modules init: ${results.modules_init_ms}ms`);
      console.log(`   Total startup: ${results.total_startup_ms}ms`);
      console.log(`   Prompts loaded: ${results.prompts_count}`);
      console.log(`   Memory (heap): ${results.memory_heap_mb}MB`);
      console.log(`   Memory (RSS): ${results.memory_rss_mb}MB`);
    }, 30000); // 30 second timeout

    test('should maintain consistent performance across multiple startups', async () => {
      const startupTimes: number[] = [];
      
      for (let i = 0; i < 3; i++) {
        const orchestrator = new Application(logger);
        const timer = new PerformanceTimer();
        
        timer.start();
        await orchestrator.loadConfiguration();
        await orchestrator.loadPromptsData();
        await orchestrator.initializeModules();
        const duration = timer.stop();
        
        startupTimes.push(duration);
        
        // Allow some cleanup time between runs
        await new Promise(resolve => setTimeout(resolve, 100));
      }
      
      // Calculate average and variance
      const average = startupTimes.reduce((a, b) => a + b, 0) / startupTimes.length;
      const variance = startupTimes.reduce((acc, time) => acc + Math.pow(time - average, 2), 0) / startupTimes.length;
      const standardDeviation = Math.sqrt(variance);
      
      console.log(`Startup times: ${startupTimes.join(', ')}ms`);
      console.log(`Average: ${average.toFixed(2)}ms, StdDev: ${standardDeviation.toFixed(2)}ms`);
      
      // Performance should be consistent (low variance)
      expect(standardDeviation).toBeLessThan(average * 0.5); // StdDev should be less than 50% of average
      expect(average).toBeLessThan(10000); // Average should be under 10 seconds
    }, 60000); // 60 second timeout for multiple runs
  });

  describe('Framework System Performance', () => {
    test('should handle framework operations efficiently', () => {
      // Test current framework system performance instead of legacy CAGEERF analyzer
      const timer = new PerformanceTimer();

      timer.start();
      // Framework operations would be tested here for current system
      // This is a placeholder for framework performance testing
      const duration = timer.stop();

      console.log(`📊 Framework System Performance: ${duration}ms`);

      // Should complete very quickly since we removed legacy analyzer
      expect(duration).toBeLessThan(100);
    });
  });

  describe('Memory Usage Tests', () => {
    test('should not have significant memory leaks', async () => {
      // Test current system memory usage without legacy components
      const initialMemory = getMemoryUsage();
      console.log(`Initial memory: ${initialMemory.heapUsed}MB heap, ${initialMemory.rss}MB RSS`);

      // Perform multiple operations with current system
      for (let i = 0; i < 100; i++) {
        // Test memory usage with actual system operations
        const testData = { operation: `memory_test_${i}` };
        // This represents operations in the current system
      }

      // Force garbage collection if available
      if (global.gc) {
        global.gc();
      }

      // Wait a bit for cleanup
      await new Promise(resolve => setTimeout(resolve, 1000));

      const finalMemory = getMemoryUsage();
      const memoryIncrease = finalMemory.heapUsed - initialMemory.heapUsed;

      console.log(`Final memory: ${finalMemory.heapUsed}MB heap, ${finalMemory.rss}MB RSS`);
      console.log(`Memory increase: ${memoryIncrease.toFixed(2)}MB for 100 operations`);

      // Memory leak threshold: should not increase by more than 25MB for 100 operations
      if (memoryIncrease > 25) {
        console.warn(`⚠️  Potential memory leak: ${memoryIncrease.toFixed(2)}MB increase`);
      } else {
        console.log(`✅ Memory usage acceptable: ${memoryIncrease.toFixed(2)}MB increase for 100 operations`);
      }

      expect(memoryIncrease).toBeLessThan(100); // Hard limit: less than 100MB increase
    }, 30000); // 30 second timeout

    test('should maintain stable memory usage under load', async () => {
      const measurements: number[] = [];

      // Take memory measurements during sustained load
      for (let i = 0; i < 10; i++) {
        // Perform batch of operations with current system
        for (let j = 0; j < 10; j++) {
          // Simulate operations in current system
          const operationData = { batch: i, operation: j };
        }

        // Force garbage collection if available
        if (global.gc) {
          global.gc();
        }
        
        // Measure memory
        const memory = getMemoryUsage();
        measurements.push(memory.heapUsed);
        
        // Brief pause between batches
        await new Promise(resolve => setTimeout(resolve, 100));
      }
      
      // Analyze memory stability
      const maxMemory = Math.max(...measurements);
      const minMemory = Math.min(...measurements);
      const memoryRange = maxMemory - minMemory;
      const averageMemory = measurements.reduce((a, b) => a + b, 0) / measurements.length;
      
      console.log(`Memory range: ${minMemory.toFixed(2)} - ${maxMemory.toFixed(2)}MB (range: ${memoryRange.toFixed(2)}MB)`);
      console.log(`Average memory: ${averageMemory.toFixed(2)}MB`);
      
      // Memory should remain relatively stable (range < 50MB)
      expect(memoryRange).toBeLessThan(50);
      expect(maxMemory).toBeLessThan(200); // Should not exceed 200MB under normal load
    }, 30000); // 30 second timeout
  });
});
```

--------------------------------------------------------------------------------
/server/src/text-references/index.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Text Reference System Module
 * Handles storage and retrieval of text references for template processing
 */

import { Logger } from "../logging/index.js";
import { TextReference, TextReferenceStore } from "../types/index.js";

/**
 * Text Reference Manager class
 */
export class TextReferenceManager {
  private store: TextReferenceStore;
  private logger: Logger;

  // Chain step results storage - single source of truth for step content
  private chainStepResults: Record<string, Record<number, {
    content: string;
    timestamp: number;
    metadata?: any;
  }>> = {};

  constructor(
    logger: Logger,
    maxAge: number = 24 * 60 * 60 * 1000,
    maxSize: number = 1000
  ) {
    this.store = {
      references: [],
      maxAge,
      maxSize,
    };
    this.logger = logger;
  }

  /**
   * Generate a title for a text using Claude (placeholder implementation)
   */
  private async generateTextTitle(text: string): Promise<string> {
    try {
      // For now, create a simple title from the first 50 characters
      // In the future, this could call Claude directly for better titles
      const title = text.substring(0, 50).trim();
      return title || `Text_${Date.now()}`;
    } catch (error) {
      this.logger.error("Error generating title:", error);
      return `Text_${Date.now()}`;
    }
  }

  /**
   * Store a text reference and return its reference ID
   */
  async storeTextReference(text: string): Promise<string> {
    try {
      const title = await this.generateTextTitle(text);
      const id = `ref_${Date.now()}_${Math.random().toString(36).substr(2, 9)}`;

      const reference: TextReference = {
        id,
        title,
        content: text,
        createdAt: Date.now(),
        lastUsed: Date.now(),
      };

      this.store.references.push(reference);

      // Clean up old references if we exceed maxSize
      if (this.store.references.length > this.store.maxSize) {
        this.cleanupOldReferences();
      }

      return `{{ref:${id}}}`;
    } catch (error) {
      this.logger.error("Error storing text reference:", error);
      throw new Error(
        `Failed to store text reference: ${
          error instanceof Error ? error.message : String(error)
        }`
      );
    }
  }

  /**
   * Retrieve a text reference by ID
   */
  getTextReference(refId: string): string | null {
    const reference = this.store.references.find((ref) => ref.id === refId);
    if (reference) {
      reference.lastUsed = Date.now();
      return reference.content;
    }
    return null;
  }

  /**
   * Clean up old references
   */
  private cleanupOldReferences(): void {
    const now = Date.now();
    this.store.references = this.store.references
      .filter((ref) => now - ref.lastUsed < this.store.maxAge)
      .sort((a, b) => b.lastUsed - a.lastUsed)
      .slice(0, this.store.maxSize);
  }

  /**
   * List available references
   */
  listTextReferences(): Array<{
    id: string;
    title: string;
    createdAt: number;
  }> {
    return this.store.references.map((ref) => ({
      id: ref.id,
      title: ref.title,
      createdAt: ref.createdAt,
    }));
  }

  /**
   * Process template text references by replacing reference placeholders with content
   */
  processTemplateReferences(template: string): string {
    return template.replace(/{{ref:([^}]+)}}/g, (match, refId) => {
      const content = this.getTextReference(refId);
      return content || match; // Keep the reference placeholder if content not found
    });
  }

  /**
   * Get statistics about the reference store
   */
  getStats(): {
    totalReferences: number;
    oldestReference: number | null;
    newestReference: number | null;
  } {
    const references = this.store.references;

    if (references.length === 0) {
      return {
        totalReferences: 0,
        oldestReference: null,
        newestReference: null,
      };
    }

    const oldest = Math.min(...references.map((ref) => ref.createdAt));
    const newest = Math.max(...references.map((ref) => ref.createdAt));

    return {
      totalReferences: references.length,
      oldestReference: oldest,
      newestReference: newest,
    };
  }

  /**
   * Clear all references (useful for testing or memory management)
   */
  clearAllReferences(): void {
    this.store.references = [];
    this.chainStepResults = {};
    this.logger.info("Cleared all text references and chain step results");
  }

  /**
   * Set new limits for the reference store
   */
  setLimits(maxAge: number, maxSize: number): void {
    this.store.maxAge = maxAge;
    this.store.maxSize = maxSize;

    // Clean up if current size exceeds new limit
    if (this.store.references.length > maxSize) {
      this.cleanupOldReferences();
    }

    this.logger.info(
      `Updated text reference limits: maxAge=${maxAge}ms, maxSize=${maxSize}`
    );
  }

  // ===== CHAIN STEP MANAGEMENT METHODS =====
  // Single source of truth for chain step content storage

  /**
   * Store a chain step result
   */
  storeChainStepResult(chainId: string, stepNumber: number, content: string, metadata?: any): void {
    if (!this.chainStepResults[chainId]) {
      this.chainStepResults[chainId] = {};
    }

    this.chainStepResults[chainId][stepNumber] = {
      content,
      timestamp: Date.now(),
      metadata
    };

    this.logger.debug(`Stored step ${stepNumber} result for chain ${chainId} (${content.length} chars)`);
  }

  /**
   * Get all step results for a specific chain
   */
  getChainStepResults(chainId: string): Record<number, string> {
    const chainResults = this.chainStepResults[chainId] || {};
    const results: Record<number, string> = {};

    Object.entries(chainResults).forEach(([stepNum, stepData]) => {
      results[parseInt(stepNum)] = stepData.content;
    });

    return results;
  }

  /**
   * Get a specific step result
   */
  getChainStepResult(chainId: string, stepNumber: number): string | null {
    const stepData = this.chainStepResults[chainId]?.[stepNumber];
    return stepData ? stepData.content : null;
  }

  /**
   * Build template variables for chain step interpolation
   * Creates variables like {{step1_result}}, {{step2_result}}, etc.
   */
  buildChainVariables(chainId: string): Record<string, any> {
    const stepResults = this.getChainStepResults(chainId);
    const variables: Record<string, any> = {};

    // Build step-specific variables
    Object.entries(stepResults).forEach(([stepNum, content]) => {
      const stepNumber = parseInt(stepNum);
      variables[`step${stepNumber + 1}_result`] = content; // 1-based naming for user-friendliness
      variables[`previous_step_result`] = content; // Always contains the latest result
    });

    // Add chain metadata
    variables[`chain_id`] = chainId;
    variables[`step_results`] = stepResults; // Raw step results for advanced access

    return variables;
  }

  /**
   * Get chain step metadata
   */
  getChainStepMetadata(chainId: string, stepNumber: number): any | null {
    return this.chainStepResults[chainId]?.[stepNumber]?.metadata || null;
  }

  /**
   * Clear all step results for a specific chain
   */
  clearChainStepResults(chainId: string): void {
    delete this.chainStepResults[chainId];
    this.logger.debug(`Cleared all step results for chain ${chainId}`);
  }

  /**
   * Get statistics about chain step storage
   */
  getChainStats(): {
    totalChains: number;
    totalSteps: number;
    chainsWithSteps: string[];
  } {
    const chainIds = Object.keys(this.chainStepResults);
    let totalSteps = 0;

    chainIds.forEach(chainId => {
      totalSteps += Object.keys(this.chainStepResults[chainId]).length;
    });

    return {
      totalChains: chainIds.length,
      totalSteps,
      chainsWithSteps: chainIds
    };
  }

  /**
   * Check if a chain has any step results
   */
  hasChainStepResults(chainId: string): boolean {
    return !!this.chainStepResults[chainId] && Object.keys(this.chainStepResults[chainId]).length > 0;
  }
}

/**
 * Create a text reference manager instance
 */
export function createTextReferenceManager(
  logger: Logger,
  maxAge: number = 24 * 60 * 60 * 1000,
  maxSize: number = 1000
): TextReferenceManager {
  return new TextReferenceManager(logger, maxAge, maxSize);
}

```

--------------------------------------------------------------------------------
/server/tests/scripts/functional-mcp-validation.js:
--------------------------------------------------------------------------------

```javascript
#!/usr/bin/env node
/**
 * Functional MCP Validation Tests
 *
 * Replaces abstract file existence checks with actual functionality validation.
 * Tests intelligent command routing, MCP tool functionality, and framework system.
 */

async function functionalMcpValidation() {
  try {
    console.log('🧪 Running Functional MCP Validation Tests...');
    console.log('🎯 Testing actual functionality instead of file existence\n');

    const results = {
      mcpTools: false,
      commandRouting: false,
      frameworkSystem: false,
      transportLayer: false,
      totalTests: 0,
      passedTests: 0
    };

    // Test 1: MCP Tools Functional Validation
    console.log('🔧 Test 1: MCP Tools Functionality');
    results.totalTests++;

    try {
      // Test that MCP tools can be imported correctly
      const promptEngineModule = await import('../../dist/mcp-tools/prompt-engine/index.js');
      const promptManagerModule = await import('../../dist/mcp-tools/prompt-manager/index.js');
      const systemControlModule = await import('../../dist/mcp-tools/system-control.js');

      // Check that the expected exports exist
      const hasPromptEngine = typeof promptEngineModule.createConsolidatedPromptEngine === 'function';
      const hasPromptManager = typeof promptManagerModule.createConsolidatedPromptManager === 'function';
      const hasSystemControl = typeof systemControlModule.createConsolidatedSystemControl === 'function';

      if (hasPromptEngine && hasPromptManager && hasSystemControl) {
        console.log('   ✅ All 3 MCP tools modules import correctly');
        console.log('   ✅ Factory functions are available for tool creation');
        results.mcpTools = true;
        results.passedTests++;
      } else {
        console.log('   ❌ MCP tool modules missing expected exports');
        console.log(`     Prompt Engine: ${hasPromptEngine ? '✅' : '❌'}`);
        console.log(`     Prompt Manager: ${hasPromptManager ? '✅' : '❌'}`);
        console.log(`     System Control: ${hasSystemControl ? '✅' : '❌'}`);
      }
    } catch (error) {
      console.log(`   ❌ MCP tools functionality test failed: ${error.message}`);
    }

    // Test 2: Command Routing Detection
    console.log('\n🧠 Test 2: Intelligent Command Routing');
    results.totalTests++;

    try {
      const { UnifiedCommandParser } = await import('../../dist/execution/parsers/unified-command-parser.js');

      const mockLogger = { debug: () => {}, info: () => {}, warn: () => {}, error: () => {} };
      const parser = new UnifiedCommandParser(mockLogger);

      // Test routing pattern detection
      const testCommands = [
        { command: '>>listprompts', expectedRoute: 'prompt_manager' },
        { command: '>>help', expectedRoute: 'system_control' },
        { command: '>>status', expectedRoute: 'system_control' },
        { command: '>>some_prompt', expectedRoute: null }
      ];

      let routingPassed = 0;
      let totalRoutingTime = 0;

      for (const test of testCommands) {
        try {
          const start = performance.now();
          const result = await parser.parseCommand(test.command, []); // Empty prompts array for testing
          const duration = performance.now() - start;
          totalRoutingTime += duration;

          if (result && result.metadata) {
            routingPassed++;
          }
        } catch (error) {
          // Expected for some test cases
        }
      }

      const avgRoutingTime = totalRoutingTime / testCommands.length;

      // Routing system performance baselines from CLAUDE.md
      const ROUTING_BASELINES = {
        detection: 1,    // <1ms command routing detection
        parsing: 500,    // <500ms parser strategy selection
        recognition: 100 // <100ms built-in command recognition
      };

      console.log(`   📊 Routing Performance: ${avgRoutingTime.toFixed(2)}ms average`);

      if (routingPassed >= 3 && avgRoutingTime <= ROUTING_BASELINES.detection) {
        console.log(`   ✅ Command routing detection working (${routingPassed}/4 tests, ${avgRoutingTime.toFixed(2)}ms < ${ROUTING_BASELINES.detection}ms baseline)`);
        results.commandRouting = true;
        results.passedTests++;
      } else {
        console.log(`   ❌ Command routing failed (${routingPassed}/4 tests, ${avgRoutingTime.toFixed(2)}ms routing time)`);
      }
    } catch (error) {
      console.log(`   ❌ Command routing test failed: ${error.message}`);
    }

    // Test 3: Framework System Functionality
    console.log('\n🔄 Test 3: Framework System');
    results.totalTests++;

    try {
      const { FrameworkManager } = await import('../../dist/frameworks/framework-manager.js');
      const { FrameworkStateManager } = await import('../../dist/frameworks/framework-state-manager.js');

      const mockLogger = { debug: () => {}, info: () => {}, warn: () => {}, error: () => {} };
      const frameworkManager = new FrameworkManager(mockLogger);
      const stateManager = new FrameworkStateManager(mockLogger);

      // Test framework loading
      await frameworkManager.initialize();
      const frameworks = frameworkManager.listFrameworks();

      if (frameworks && frameworks.length >= 4) {
        console.log(`   ✅ Framework system loaded ${frameworks.length} methodologies`);

        // Test framework switching (initialize state manager first)
        await stateManager.initialize();
        const switchResult = await stateManager.switchFramework('CAGEERF', 'Test switch');
        if (switchResult && switchResult.success) {
          console.log('   ✅ Framework switching functionality working');
          results.frameworkSystem = true;
          results.passedTests++;
        } else {
          console.log('   ❌ Framework switching failed');
        }
      } else {
        console.log(`   ❌ Framework system failed to load methodologies (found: ${frameworks?.length || 0})`);
      }
    } catch (error) {
      console.log(`   ❌ Framework system test failed: ${error.message}`);
    }

    // Test 4: Transport Layer Compatibility
    console.log('\n🚀 Test 4: Transport Layer');
    results.totalTests++;

    try {
      const { Application } = await import('../../dist/runtime/application.js');
      const mockLogger = { debug: () => {}, info: () => {}, warn: () => {}, error: () => {} };

      const application = new Application(mockLogger);
      await application.loadConfiguration();

      // Test that the application can initialize without starting server
      const config = application.config;
      const transport = config?.transports?.default || 'stdio';
      if (config && (transport === 'stdio' || transport === 'sse')) {
        console.log(`   ✅ Transport layer configured for ${transport}`);
        results.transportLayer = true;
        results.passedTests++;
      } else {
        console.log('   ❌ Transport layer configuration invalid');
      }
    } catch (error) {
      console.log(`   ❌ Transport layer test failed: ${error.message}`);
    }

    // Results Summary
    console.log('\n📊 Functional Validation Results:');
    console.log(`   Tests Passed: ${results.passedTests}/${results.totalTests}`);
    console.log(`   MCP Tools: ${results.mcpTools ? '✅' : '❌'}`);
    console.log(`   Command Routing: ${results.commandRouting ? '✅' : '❌'}`);
    console.log(`   Framework System: ${results.frameworkSystem ? '✅' : '❌'}`);
    console.log(`   Transport Layer: ${results.transportLayer ? '✅' : '❌'}`);

    const successRate = (results.passedTests / results.totalTests) * 100;

    if (successRate >= 75) {
      console.log(`\n🎉 Functional validation passed! (${successRate.toFixed(1)}% success rate)`);
      console.log('   All critical MCP functionality is working correctly.');
      process.exit(0);
    } else {
      console.log(`\n❌ Functional validation failed! (${successRate.toFixed(1)}% success rate)`);
      console.log('   Critical functionality issues detected.');
      process.exit(1);
    }

  } catch (error) {
    console.error('❌ Functional MCP validation failed:', error.message);
    console.error('Stack trace:', error.stack);
    process.exit(1);
  }
}

// Only run if this script is executed directly
if (import.meta.url === `file://${process.argv[1]}`) {
  functionalMcpValidation();
}

export { functionalMcpValidation };
```

--------------------------------------------------------------------------------
/server/src/mcp-tools/prompt-engine/utils/classification.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Prompt Classifier - Handles prompt classification and analysis
 *
 * Extracted from ConsolidatedPromptEngine to provide focused
 * classification capabilities with clear separation of concerns.
 */

import { createLogger } from "../../../logging/index.js";
import { ContentAnalyzer } from "../../../semantic/configurable-semantic-analyzer.js";
import { PromptClassification } from "../core/types.js";
import { ConvertedPrompt } from "../../../types/index.js";
import { isChainPrompt } from "../../../utils/chainUtils.js";

const logger = createLogger({
  logFile: '/tmp/prompt-classifier.log',
  transport: 'stdio',
  enableDebug: false,
  configuredLevel: 'info'
});

/**
 * PromptClassifier handles all prompt classification and analysis
 *
 * This class provides:
 * - Prompt type detection (prompt, template, chain)
 * - Execution strategy recommendation
 * - Confidence scoring and reasoning
 * - Gate recommendation based on complexity
 * - Framework suggestion for execution
 */
export class PromptClassifier {
  private semanticAnalyzer: ContentAnalyzer;

  constructor(semanticAnalyzer: ContentAnalyzer) {
    this.semanticAnalyzer = semanticAnalyzer;
  }

  /**
   * Classify prompt and determine execution strategy
   */
  public classifyPrompt(
    convertedPrompt: ConvertedPrompt,
    promptArgs: Record<string, any> = {}
  ): PromptClassification {
    try {
      logger.debug('🔍 [PromptClassifier] Classifying prompt', {
        promptId: convertedPrompt.id,
        hasArgs: Object.keys(promptArgs).length > 0
      });

      const classification = this.performClassification(convertedPrompt, promptArgs);

      logger.debug('✅ [PromptClassifier] Prompt classified successfully', {
        promptId: convertedPrompt.id,
        executionType: classification.executionType,
        confidence: classification.confidence,
        framework: classification.framework
      });

      return classification;
    } catch (error) {
      logger.error('❌ [PromptClassifier] Prompt classification failed', {
        promptId: convertedPrompt.id,
        error: error instanceof Error ? error.message : String(error)
      });

      // Return fallback classification
      return {
        executionType: "prompt",
        requiresExecution: true,
        confidence: 50,
        reasoning: [`Classification failed: ${error instanceof Error ? error.message : String(error)}`],
        suggestedGates: [],
        framework: undefined
      };
    }
  }

  /**
   * Perform the actual classification logic
   */
  private performClassification(
    convertedPrompt: ConvertedPrompt,
    promptArgs: Record<string, any>
  ): PromptClassification {
    const reasoning: string[] = [];
    let confidence = 100;
    let executionType: "prompt" | "template" | "chain" = "prompt";
    let requiresExecution = true;
    const suggestedGates: string[] = [];
    let framework: string | undefined;

    // Check if it's a chain prompt
    if (isChainPrompt(convertedPrompt)) {
      executionType = "chain";
      reasoning.push("Detected chain structure in prompt content");
      suggestedGates.push("chain_validation", "step_validation");
      confidence = 95;
    }
    // Check if it has template variables
    else if (this.hasTemplateVariables(convertedPrompt.userMessageTemplate)) {
      executionType = "template";
      reasoning.push("Detected template variables in content");
      if (Object.keys(promptArgs).length === 0) {
        requiresExecution = false;
        reasoning.push("No arguments provided for template");
        confidence = 80;
      }
    }
    // Default to prompt
    else {
      executionType = "prompt";
      reasoning.push("Standard prompt execution");
      confidence = 90;
    }

    // Determine framework based on content analysis
    framework = this.suggestFramework(convertedPrompt);
    if (framework) {
      reasoning.push(`Suggested framework: ${framework}`);
    }

    // Add complexity-based gates
    const complexity = this.assessComplexity(convertedPrompt);
    if (complexity > 0.7) {
      suggestedGates.push("complexity_validation");
      reasoning.push("High complexity detected, added validation gates");
    }

    // Use semantic analyzer if available
    if (this.semanticAnalyzer) {
      try {
        // Note: ContentAnalyzer interface may not have analyzeContent method
        // Using basic analysis instead of complex semantic analysis
        const semanticResult = { confidence: 0.8 };
        if (semanticResult && semanticResult.confidence > confidence) {
          confidence = Math.min(confidence, semanticResult.confidence * 100);
          reasoning.push("Semantic analysis applied");
        }
      } catch (error) {
        logger.warn('⚠️ [PromptClassifier] Semantic analysis failed', {
          error: error instanceof Error ? error.message : String(error)
        });
      }
    }

    return {
      executionType,
      requiresExecution,
      confidence,
      reasoning,
      suggestedGates,
      framework
    };
  }

  /**
   * Check if content has template variables
   */
  private hasTemplateVariables(content: string): boolean {
    // Check for common template patterns
    const patterns = [
      /\{\{\s*\w+\s*\}\}/, // Nunjucks/Jinja style {{variable}}
      /\$\{\w+\}/, // Shell style ${variable}
      /\{\w+\}/, // Simple {variable}
    ];

    return patterns.some(pattern => pattern.test(content));
  }

  /**
   * Suggest framework based on content
   */
  private suggestFramework(convertedPrompt: ConvertedPrompt): string | undefined {
    const content = convertedPrompt.userMessageTemplate.toLowerCase();

    // Look for methodology keywords
    if (content.includes('context') && content.includes('analysis') && content.includes('goal')) {
      return 'CAGEERF';
    }

    if (content.includes('reasoning') && content.includes('action')) {
      return 'ReACT';
    }

    if (content.includes('who') && content.includes('what') && content.includes('when')) {
      return '5W1H';
    }

    if (content.includes('substitute') || content.includes('combine') || content.includes('adapt')) {
      return 'SCAMPER';
    }

    return undefined;
  }

  /**
   * Assess prompt complexity
   */
  private assessComplexity(convertedPrompt: ConvertedPrompt): number {
    let complexity = 0;

    // Content length factor
    const contentLength = convertedPrompt.userMessageTemplate.length;
    complexity += Math.min(contentLength / 1000, 0.3);

    // Argument complexity
    if (convertedPrompt.arguments) {
      complexity += convertedPrompt.arguments.length * 0.1;
    }

    // Template complexity
    const templateVars = this.countTemplateVariables(convertedPrompt.userMessageTemplate);
    complexity += templateVars * 0.05;

    // Chain complexity
    if (isChainPrompt(convertedPrompt)) {
      complexity += 0.4;
    }

    // Conditional logic complexity
    const conditionals = (convertedPrompt.userMessageTemplate.match(/\{%\s*(if|for|while)\s/g) || []).length;
    complexity += conditionals * 0.1;

    return Math.min(complexity, 1.0);
  }

  /**
   * Count template variables in content
   */
  private countTemplateVariables(content: string): number {
    const matches = content.match(/\{\{\s*\w+\s*\}\}/g);
    return matches ? matches.length : 0;
  }

  /**
   * Get execution recommendations based on classification
   */
  public getExecutionRecommendations(classification: PromptClassification): {
    strategy: string;
    timeout: number;
    retries: number;
    enableGates: boolean;
  } {
    const recommendations = {
      strategy: classification.executionType,
      timeout: 30000, // 30 seconds default
      retries: 1,
      enableGates: classification.suggestedGates.length > 0
    };

    // Adjust based on execution type
    switch (classification.executionType) {
      case "chain":
        recommendations.timeout = 120000; // 2 minutes for chains
        recommendations.retries = 2;
        break;
      case "template":
        recommendations.timeout = 15000; // 15 seconds for templates
        recommendations.retries = 0;
        break;
      default:
        // Keep defaults for prompts
        break;
    }

    // Adjust based on confidence
    if (classification.confidence < 70) {
      recommendations.enableGates = true;
      recommendations.retries += 1;
    }

    return recommendations;
  }
}
```

--------------------------------------------------------------------------------
/docs/TODO.md:
--------------------------------------------------------------------------------

```markdown
# Roadmap & TODO

This document outlines planned features, improvements, and enhancements for the Claude Prompts MCP Server. Items are organized by priority and development phases.

## 🎯 High Priority Features

### 🌐 Web UI for Prompt Management

**Status**: Planned
**Priority**: High
**Estimated Effort**: 4-6 weeks

Transform prompt management from file-based configuration to an intuitive web interface.

**Key Features**:

- **Visual Prompt Builder**: Drag-and-drop interface for creating prompts with live preview
- **Category Management**: Create, edit, and organize categories through the UI
- **Template Editor**: Rich text editor with syntax highlighting for Nunjucks templates
- **Argument Designer**: Visual form builder for defining prompt arguments with validation
- **Chain Designer**: Visual flowchart interface for building prompt chains
- **Import/Export**: Backup and share prompt collections
- **Search & Discovery**: Full-text search across prompts with filtering
- **Preview & Testing**: Test prompts directly in the UI before deployment

**Technical Considerations**:

- Modern React/Vue.js frontend with responsive design
- Real-time updates using WebSocket connection to server
- Integration with existing hot-reload system
- Authentication and user management for multi-user environments
- Dark/light theme support matching Claude Desktop aesthetic

### ⚡ Simplified Installation & Configuration

**Status**: Planned
**Priority**: High
**Estimated Effort**: 2-3 weeks

Streamline the setup process and consolidate configuration files.

**Installation Improvements**:

- **One-Command Setup**: `npx claude-prompts-mcp@latest setup`
- **Interactive CLI Installer**: Guided setup with environment detection
- **Docker Container**: Pre-configured container with all dependencies
- **Auto-Detection**: Automatically find and configure Claude Desktop

**Configuration Consolidation**:

```typescript
// Single unified config.json
interface UnifiedConfig {
  server: {
    name: string;
    version: string;
    port: number;
    host: string;
  };

  features: {
    webUI: boolean;
    contextMemory: boolean;
    autoFormatting: boolean;
  };

  prompts: {
    categories: Category[];
    defaultCategory: string;
    autoReload: boolean;
  };

  storage: {
    type: "file" | "sqlite" | "postgresql" | "mongodb";
    connectionString?: string;
    backupEnabled: boolean;
  };

  integrations: {
    claudeDesktop: boolean;
    cursorWindsurf: boolean;
    customClients: ClientConfig[];
  };
}
```

**Migration Tools**:

- Automatic migration from legacy config files
- Validation and error reporting
- Backup creation before migration

### 🤖 Intelligent Query Formatting

**Status**: Planned
**Priority**: Medium-High
**Estimated Effort**: 2-3 weeks

Automatically format user input to match expected prompt templates.

**Smart Formatting Features**:

- **Input Analysis**: Detect user intent and suggest appropriate prompts
- **Parameter Extraction**: Parse natural language input to extract prompt arguments
- **Template Suggestion**: Recommend which prompt to use based on user query
- **Auto-Completion**: Suggest missing required arguments
- **Format Conversion**: Convert between different input formats (JSON, natural language, structured)

**Technical Approach**:

```typescript
interface QueryFormatter {
  analyzeIntent(input: string): IntentAnalysis;
  extractParameters(input: string, template: PromptTemplate): ParameterMap;
  suggestPrompts(input: string): PromptSuggestion[];
  formatQuery(input: string, targetPrompt: string): FormattedQuery;
}

interface IntentAnalysis {
  confidence: number;
  detectedPrompts: string[];
  extractedEntities: Entity[];
  suggestedAction: "execute" | "clarify" | "suggest";
}
```

**LLM Integration Options**:

- **Local Models**: Use lightweight models for privacy-sensitive environments
- **Cloud APIs**: Integration with OpenAI, Anthropic, or other providers
- **Hybrid Approach**: Local processing with cloud fallback
- **Custom Training**: Fine-tuned models for domain-specific formatting

## 🚀 Medium Priority Features

### 📊 Advanced Analytics & Insights

**Status**: Planned
**Priority**: Medium
**Estimated Effort**: 2-3 weeks

Provide detailed analytics on prompt usage and performance.

**Analytics Features**:

- **Usage Statistics**: Track which prompts are used most frequently
- **Performance Metrics**: Response times, error rates, success rates
- **User Behavior**: Common usage patterns and process analysis
- **A/B Testing**: Compare different prompt versions
- **Export Reports**: Generate usage reports for analysis

### 🔌 Enhanced Integration Ecosystem

**Status**: Planned
**Priority**: Medium
**Estimated Effort**: 3-4 weeks

Expand integration capabilities with popular development tools.

**Planned Integrations**:

- **VS Code Extension**: Manage prompts directly from the editor
- **Slack/Discord Bots**: Access prompts through team chat
- **Zapier/n8n**: Process automation integration
- **REST API Client Libraries**: SDKs for popular languages
- **Claude Desktop Plugins**: Enhanced Claude Desktop integration

## 🔮 Future Considerations

### 🤝 Collaborative Features

**Status**: Research
**Priority**: Low-Medium
**Estimated Effort**: 4-6 weeks

Enable team collaboration on prompt development.

**Potential Features**:

- **Version Control**: Git-like versioning for prompts
- **Team Workspaces**: Shared prompt libraries
- **Review Process**: Peer review for prompt changes
- **Comments & Discussions**: Collaborative feedback system

### 🧪 Advanced Prompt Techniques

**Status**: Research
**Priority**: Low-Medium
**Estimated Effort**: 3-5 weeks

Implement cutting-edge prompt engineering techniques.

**Research Areas**:

- **Few-Shot Learning**: Dynamic example selection
- **Chain-of-Thought**: Automated reasoning prompts
- **Tree of Thoughts**: Complex decision-making processes
- **Meta-Prompting**: Prompts that generate other prompts
- **Prompt Optimization**: Automated prompt improvement

### 🔐 Enterprise Security Features

**Status**: Research
**Priority**: Low
**Estimated Effort**: 4-6 weeks

Advanced security features for enterprise deployments.

**Security Enhancements**:

- **Authentication**: Multi-factor authentication
- **Authorization**: Role-based access control
- **Audit Logging**: Comprehensive activity logging
- **Encryption**: End-to-end encryption for sensitive prompts
- **Compliance**: SOC2, GDPR compliance features

## 🛠️ Technical Debt & Improvements

### Code Quality & Architecture

- **TypeScript Strictness**: Enable strict mode across all modules
- **Test Coverage**: Achieve 90%+ test coverage
- **Error Handling**: Comprehensive error handling and recovery

### Developer Experience

- **Debugging Tools**: Enhanced debugging capabilities
- **Development Scripts**: Improved npm scripts and tooling
- **Documentation**: More comprehensive developer documentation

## 📅 Implementation Timeline

### Phase 1: Foundation (Months 1-2)

- Simplified Installation & Configuration
- Enhanced Context & Memory Management
- Basic Web UI prototype

### Phase 2: Core Features (Months 3-4)

- Complete Web UI for Prompt Management
- Intelligent Query Formatting
- Advanced Analytics foundation

### Phase 3: Integration & Polish (Months 5-6)

- Enhanced Integration Ecosystem
- Multi-Language Support
- Performance optimizations

### Phase 4: Advanced Features (Months 7+)

- Collaborative Features
- Advanced Prompt Techniques
- Enterprise Security Features

## 🤝 Contributing to the Roadmap

We welcome community input on this roadmap! Here's how you can contribute:

- **Feature Requests**: [Open an issue](https://github.com/minipuft/claude-prompts-mcp/issues) with the `enhancement` label
- **Discussion**: Join conversations in [GitHub Discussions](https://github.com/minipuft/claude-prompts-mcp/discussions)
- **Implementation**: Pick up items from this TODO and submit PRs
- **Feedback**: Share your thoughts on priorities and implementation approaches

## 📊 Progress Tracking

This document will be updated regularly to reflect:

- ✅ Completed features
- 🚧 In-progress work
- 🔄 Changed priorities
- 💡 New ideas and community suggestions

Last updated: [Date will be maintained as features are implemented]

---

**Note**: This roadmap is living document and priorities may shift based on community feedback, technical discoveries, and changing requirements. All estimated timeframes are approximate and subject to change.

```

--------------------------------------------------------------------------------
/server/src/server/index.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Server Management Module
 * Handles HTTP server lifecycle, process management, and orchestration
 */

import { createServer, Server } from "http";
import { ApiManager } from "../api/index.js";
import { ConfigManager } from "../config/index.js";
import { Logger } from "../logging/index.js";
import {
  TransportManager,
  createTransportManager,
  TransportType
} from "./transport/index.js";

// Re-export transport types and utilities for external consumers
export { TransportManager, createTransportManager, TransportType };

/**
 * Server Manager class
 */
export class ServerManager {
  private logger: Logger;
  private configManager: ConfigManager;
  private transportManager: TransportManager;
  private apiManager?: ApiManager;
  private httpServer?: Server;
  private port: number;

  constructor(
    logger: Logger,
    configManager: ConfigManager,
    transportManager: TransportManager,
    apiManager?: ApiManager
  ) {
    this.logger = logger;
    this.configManager = configManager;
    this.transportManager = transportManager;
    this.apiManager = apiManager;
    this.port = configManager.getPort();
  }

  /**
   * Start the server based on transport type
   */
  async startServer(): Promise<void> {
    try {
      this.logger.info(
        `Starting server with ${this.transportManager.getTransportType()} transport`
      );

      // Setup process event handlers
      this.setupProcessEventHandlers();

      if (this.transportManager.isStdio()) {
        await this.startStdioServer();
      } else if (this.transportManager.isSse()) {
        await this.startSseServer();
      } else {
        throw new Error(
          `Unsupported transport type: ${this.transportManager.getTransportType()}`
        );
      }

      this.logger.info("Server started successfully");
    } catch (error) {
      this.logger.error("Error starting server:", error);
      throw error;
    }
  }

  /**
   * Start server with STDIO transport
   */
  private async startStdioServer(): Promise<void> {
    // For STDIO, we don't need an HTTP server
    await this.transportManager.setupStdioTransport();
  }

  /**
   * Start server with SSE transport
   */
  private async startSseServer(): Promise<void> {
    if (!this.apiManager) {
      throw new Error("API Manager is required for SSE transport");
    }

    // Create Express app
    const app = this.apiManager.createApp();

    // Setup SSE transport endpoints
    this.transportManager.setupSseTransport(app);

    // Create HTTP server
    this.httpServer = createServer(app);

    // Setup HTTP server event handlers
    this.setupHttpServerEventHandlers();

    // Start listening
    await new Promise<void>((resolve, reject) => {
      this.httpServer!.listen(this.port, () => {
        this.logger.info(
          `MCP Prompts Server running on http://localhost:${this.port}`
        );
        this.logger.info(
          `Connect to http://localhost:${this.port}/mcp for MCP connections`
        );
        resolve();
      });

      this.httpServer!.on("error", (error: any) => {
        if (error.code === "EADDRINUSE") {
          this.logger.error(
            `Port ${this.port} is already in use. Please choose a different port or stop the other service.`
          );
        } else {
          this.logger.error("Server error:", error);
        }
        reject(error);
      });
    });
  }

  /**
   * Setup HTTP server event handlers
   */
  private setupHttpServerEventHandlers(): void {
    if (!this.httpServer) return;

    this.httpServer.on("error", (error: any) => {
      if (error.code === "EADDRINUSE") {
        this.logger.error(
          `Port ${this.port} is already in use. Please choose a different port or stop the other service.`
        );
      } else {
        this.logger.error("Server error:", error);
      }
      process.exit(1);
    });

    this.httpServer.on("close", () => {
      this.logger.info("HTTP server closed");
    });
  }

  /**
   * Setup process event handlers
   */
  private setupProcessEventHandlers(): void {
    // Handle graceful shutdown
    process.on("SIGINT", () => {
      this.logger.info("Received SIGINT, shutting down server...");
      this.shutdown();
    });

    process.on("SIGTERM", () => {
      this.logger.info("Received SIGTERM, shutting down server...");
      this.shutdown();
    });

    // Handle uncaught exceptions
    process.on("uncaughtException", (error) => {
      this.logger.error("Uncaught exception:", error);
      this.shutdown(1);
    });

    // Handle unhandled promise rejections
    process.on("unhandledRejection", (reason, promise) => {
      this.logger.error("Unhandled Rejection at:", promise, "reason:", reason);
      this.shutdown(1);
    });

    // Log system info for debugging
    this.logSystemInfo();
  }

  /**
   * Log system information
   */
  private logSystemInfo(): void {
    this.logger.info(
      `Server process memory usage: ${JSON.stringify(process.memoryUsage())}`
    );
    this.logger.info(`Process ID: ${process.pid}`);
    this.logger.info(`Node version: ${process.version}`);
    this.logger.info(`Working directory: ${process.cwd()}`);
  }

  /**
   * Graceful shutdown
   */
  shutdown(exitCode: number = 0): void {
    this.logger.info("Initiating graceful shutdown...");

    // Close HTTP server if running
    if (this.httpServer) {
      this.httpServer.close((error) => {
        if (error) {
          this.logger.error("Error closing HTTP server:", error);
        } else {
          this.logger.info("HTTP server closed successfully");
        }
        this.finalizeShutdown(exitCode);
      });
    } else {
      this.finalizeShutdown(exitCode);
    }
  }

  /**
   * Finalize shutdown process
   */
  private finalizeShutdown(exitCode: number): void {
    // Close transport connections
    if (this.transportManager.isSse()) {
      this.transportManager.closeAllConnections();
    }

    this.logger.info("Server shutdown complete");
    process.exit(exitCode);
  }

  /**
   * Restart the server
   */
  async restart(reason: string = "Manual restart"): Promise<void> {
    this.logger.info(`Restarting server: ${reason}`);

    try {
      // Shutdown current server
      if (this.httpServer) {
        await new Promise<void>((resolve) => {
          this.httpServer!.close(() => {
            this.logger.info("Server closed for restart");
            resolve();
          });
        });
      }

      // Wait a moment before restarting
      await new Promise((resolve) => setTimeout(resolve, 1000));

      // Start server again
      await this.startServer();

      this.logger.info("Server restarted successfully");
    } catch (error) {
      this.logger.error("Error during server restart:", error);
      throw error;
    }
  }

  /**
   * Check if server is running
   */
  isRunning(): boolean {
    if (this.transportManager.isStdio()) {
      // For STDIO, we consider it running if the process is alive
      return true;
    } else {
      // For SSE, check if HTTP server is listening
      return this.httpServer?.listening || false;
    }
  }

  /**
   * Get server status information
   */
  getStatus(): {
    running: boolean;
    transport: string;
    port?: number;
    connections?: number;
    uptime: number;
  } {
    return {
      running: this.isRunning(),
      transport: this.transportManager.getTransportType(),
      port: this.transportManager.isSse() ? this.port : undefined,
      connections: this.transportManager.isSse()
        ? this.transportManager.getActiveConnectionsCount()
        : undefined,
      uptime: process.uptime(),
    };
  }

  /**
   * Get the HTTP server instance (for SSE transport)
   */
  getHttpServer(): Server | undefined {
    return this.httpServer;
  }

  /**
   * Get the port number
   */
  getPort(): number {
    return this.port;
  }
}

/**
 * Create and configure a server manager
 */
export function createServerManager(
  logger: Logger,
  configManager: ConfigManager,
  transportManager: TransportManager,
  apiManager?: ApiManager
): ServerManager {
  return new ServerManager(logger, configManager, transportManager, apiManager);
}

/**
 * Server startup helper function
 */
export async function startMcpServer(
  logger: Logger,
  configManager: ConfigManager,
  transportManager: TransportManager,
  apiManager?: ApiManager
): Promise<ServerManager> {
  const serverManager = createServerManager(
    logger,
    configManager,
    transportManager,
    apiManager
  );

  await serverManager.startServer();
  return serverManager;
}

```

--------------------------------------------------------------------------------
/server/tests/enhanced-validation/lifecycle-validation/process-lifecycle-validator.js:
--------------------------------------------------------------------------------

```javascript
/**
 * Process Lifecycle Validation System
 *
 * Eliminates the need for emergency process.exit() calls by ensuring proper
 * application shutdown and resource cleanup validation.
 */

/**
 * Process Lifecycle Validator
 *
 * Validates clean application shutdown and resource management
 */
export class ProcessLifecycleValidator {
  constructor(logger) {
    this.logger = logger;
    this.trackedResources = new Set();
    this.shutdownCallbacks = [];
  }

  /**
   * Validate that an Application instance shuts down cleanly
   */
  async validateCleanShutdown(applicationInstance, maxShutdownTime = 5000) {
    this.logger.debug('[LIFECYCLE VALIDATOR] Starting clean shutdown validation');

    const startTime = Date.now();
    const initialMemory = this.getMemorySnapshot();

    try {
      // Test that shutdown method exists
      if (typeof applicationInstance.shutdown !== 'function') {
        return {
          success: false,
          error: 'Application instance missing shutdown method',
          shutdownTime: 0,
          resourcesCleared: false,
          memoryReclaimed: false
        };
      }

      // Test shutdown with timeout
      const shutdownPromise = applicationInstance.shutdown();
      const timeoutPromise = new Promise((_, reject) =>
        setTimeout(() => reject(new Error('Shutdown timeout')), maxShutdownTime)
      );

      await Promise.race([shutdownPromise, timeoutPromise]);

      const shutdownTime = Date.now() - startTime;

      // Allow brief time for cleanup to complete
      await new Promise(resolve => setTimeout(resolve, 100));

      const finalMemory = this.getMemorySnapshot();
      const resourcesCleared = await this.validateResourceCleanup();

      this.logger.debug('[LIFECYCLE VALIDATOR] Clean shutdown validation completed', {
        shutdownTime,
        resourcesCleared,
        memoryDelta: finalMemory.heapUsed - initialMemory.heapUsed
      });

      return {
        success: true,
        shutdownTime,
        resourcesCleared,
        memoryReclaimed: finalMemory.heapUsed <= initialMemory.heapUsed * 1.1, // Allow 10% tolerance
        initialMemory: initialMemory.heapUsed,
        finalMemory: finalMemory.heapUsed
      };

    } catch (error) {
      const shutdownTime = Date.now() - startTime;

      return {
        success: false,
        error: error.message,
        shutdownTime,
        resourcesCleared: false,
        memoryReclaimed: false
      };
    }
  }

  /**
   * Detect resource leaks by monitoring active handles
   */
  async detectResourceLeaks() {
    const activeHandles = process._getActiveHandles();
    const activeRequests = process._getActiveRequests();

    // Filter out expected system handles
    const userHandles = activeHandles.filter(handle => {
      // Keep common system handles but filter out test-related ones
      const handleType = handle.constructor?.name || 'unknown';
      return !['TTYWrap', 'SignalWrap', 'Process'].includes(handleType);
    });

    const leakReport = {
      hasLeaks: userHandles.length > 0 || activeRequests.length > 0,
      activeHandles: userHandles.length,
      activeRequests: activeRequests.length,
      handleTypes: userHandles.map(h => h.constructor?.name || 'unknown'),
      recommendations: []
    };

    if (leakReport.hasLeaks) {
      leakReport.recommendations.push('Clear all timers and intervals before test completion');
      leakReport.recommendations.push('Close all open connections and streams');
      leakReport.recommendations.push('Remove all event listeners');
    }

    this.logger.debug('[LIFECYCLE VALIDATOR] Resource leak detection completed', leakReport);

    return leakReport;
  }

  /**
   * Validate global resource cleanup using existing tracker
   */
  async validateResourceCleanup() {
    try {
      // Try to import and use the existing global resource tracker
      const { globalResourceTracker } = await import('../../../dist/utils/global-resource-tracker.js');

      const trackedResources = globalResourceTracker.getAllResources();
      const hasTrackedResources = trackedResources.length > 0;

      if (hasTrackedResources) {
        this.logger.debug(`[LIFECYCLE VALIDATOR] Found ${trackedResources.length} tracked resources`);

        // Trigger cleanup and see how many are cleared
        const clearedCount = globalResourceTracker.emergencyCleanup();

        return {
          hadTrackedResources: true,
          clearedResources: clearedCount,
          allResourcesCleared: clearedCount === trackedResources.length
        };
      }

      return {
        hadTrackedResources: false,
        clearedResources: 0,
        allResourcesCleared: true
      };

    } catch (error) {
      // If global resource tracker is not available, do basic validation
      this.logger.debug('[LIFECYCLE VALIDATOR] Global resource tracker not available, using basic validation');

      const leakReport = await this.detectResourceLeaks();
      return {
        hadTrackedResources: false,
        clearedResources: 0,
        allResourcesCleared: !leakReport.hasLeaks
      };
    }
  }

  /**
   * Enforce timeout compliance - test should complete without process.exit()
   */
  async enforceTimeoutCompliance(testFunction, maxTime = 30000) {
    const startTime = Date.now();
    let completed = false;
    let forceExitUsed = false;

    // Monitor for process.exit calls
    const originalExit = process.exit;
    process.exit = function(code) {
      forceExitUsed = true;
      completed = true;

      // Restore original exit
      process.exit = originalExit;

      throw new Error(`Test used process.exit(${code}) - should complete naturally`);
    };

    try {
      const timeoutPromise = new Promise((_, reject) =>
        setTimeout(() => reject(new Error('Test timeout - should complete faster')), maxTime)
      );

      const testPromise = testFunction();

      await Promise.race([testPromise, timeoutPromise]);

      const duration = Date.now() - startTime;
      completed = true;

      // Restore original exit
      process.exit = originalExit;

      return {
        success: true,
        duration,
        forceExitUsed: false,
        completedNaturally: true
      };

    } catch (error) {
      const duration = Date.now() - startTime;

      // Restore original exit
      process.exit = originalExit;

      return {
        success: false,
        duration,
        forceExitUsed,
        completedNaturally: completed && !forceExitUsed,
        error: error.message
      };
    }
  }

  /**
   * Register cleanup callback for test teardown
   */
  registerCleanupCallback(callback) {
    this.shutdownCallbacks.push(callback);
  }

  /**
   * Execute all cleanup callbacks
   */
  async executeCleanup() {
    const results = [];

    for (const callback of this.shutdownCallbacks) {
      try {
        await callback();
        results.push({ success: true });
      } catch (error) {
        results.push({ success: false, error: error.message });
      }
    }

    return results;
  }

  /**
   * Get memory usage snapshot
   */
  getMemorySnapshot() {
    const usage = process.memoryUsage();
    return {
      heapUsed: Math.round(usage.heapUsed / 1024 / 1024 * 100) / 100, // MB
      heapTotal: Math.round(usage.heapTotal / 1024 / 1024 * 100) / 100, // MB
      rss: Math.round(usage.rss / 1024 / 1024 * 100) / 100, // MB
      external: Math.round(usage.external / 1024 / 1024 * 100) / 100 // MB
    };
  }

  /**
   * Comprehensive lifecycle validation report
   */
  async generateLifecycleReport(applicationInstance) {
    const startTime = Date.now();

    const shutdownResult = await this.validateCleanShutdown(applicationInstance);
    const leakReport = await this.detectResourceLeaks();
    const resourceCleanup = await this.validateResourceCleanup();

    const totalTime = Date.now() - startTime;

    return {
      timestamp: new Date(),
      totalValidationTime: totalTime,
      shutdown: shutdownResult,
      resourceLeaks: leakReport,
      resourceCleanup,
      overallSuccess: shutdownResult.success && !leakReport.hasLeaks && resourceCleanup.allResourcesCleared,
      recommendations: [
        ...leakReport.recommendations,
        ...(shutdownResult.success ? [] : ['Implement proper shutdown method']),
        ...(resourceCleanup.allResourcesCleared ? [] : ['Ensure all resources are tracked and cleaned'])
      ]
    };
  }
}

/**
 * Factory function for creating validator instance
 */
export function createProcessLifecycleValidator(logger) {
  return new ProcessLifecycleValidator(logger);
}
```

--------------------------------------------------------------------------------
/server/src/semantic/integrations/index.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Semantic Integrations Module
 *
 * Central module for creating and managing semantic integrations
 * Handles LLM clients for content analysis
 */

import { Logger } from "../../logging/index.js";
import { SemanticAnalysisConfig } from "../../types/index.js";
import {
  ContentAnalyzer,
  createContentAnalyzer
} from "../configurable-semantic-analyzer.js";
import { 
  LLMClientFactory,
  loadLLMConfigFromEnv 
} from "./llm-clients.js";

/**
 * Integration factory for content analyzer
 */
export class SemanticIntegrationFactory {
  private logger: Logger;

  constructor(logger: Logger) {
    this.logger = logger;
  }

  /**
   * Create fully configured semantic analyzer with all integrations
   */
  async createConfiguredAnalyzer(config: SemanticAnalysisConfig): Promise<ContentAnalyzer> {
    const analyzer = createContentAnalyzer(this.logger, config);
    
    // Setup LLM integration if enabled
    if (config.llmIntegration.enabled && config.llmIntegration.endpoint) {
      try {
        const llmClient = LLMClientFactory.create(this.logger, config.llmIntegration);
        analyzer.setLLMClient(llmClient);
        // Auto-detect provider from endpoint
        const provider = config.llmIntegration.endpoint?.includes('api.openai.com') ? 'openai' :
                        config.llmIntegration.endpoint?.includes('api.anthropic.com') ? 'anthropic' : 'custom';
        this.logger.info(`LLM integration configured: ${provider} (auto-detected from ${config.llmIntegration.endpoint})`);
        
        // Test the client
        const testResult = await LLMClientFactory.testClient(this.logger, config.llmIntegration);
        if (!testResult) {
          this.logger.warn("LLM client test failed - integration may not work correctly");
        }
      } catch (error) {
        this.logger.error("Failed to setup LLM integration:", error);
        if (config.mode === 'semantic') {
          this.logger.warn("Semantic mode requested but LLM integration failed");
        }
      }
    }


    return analyzer;
  }

  /**
   * Create analyzer with environment variable overrides
   */
  async createFromEnvironment(baseConfig: SemanticAnalysisConfig): Promise<ContentAnalyzer> {
    // Merge with environment variables
    const envLLMConfig = loadLLMConfigFromEnv();
    
    const mergedConfig: SemanticAnalysisConfig = {
      ...baseConfig,
      llmIntegration: {
        ...baseConfig.llmIntegration,
        ...envLLMConfig
      }
    };

    // Override mode if environment variable is set
    if (process.env.MCP_ANALYSIS_MODE) {
      const mode = process.env.MCP_ANALYSIS_MODE as any;
      if (['structural', 'semantic'].includes(mode)) {
        mergedConfig.mode = mode;
        this.logger.info(`Analysis mode overridden by environment: ${mode}`);
      }
    }

    return this.createConfiguredAnalyzer(mergedConfig);
  }

  /**
   * Validate configuration and provide recommendations
   */
  validateConfiguration(config: SemanticAnalysisConfig): {
    isValid: boolean;
    warnings: string[];
    recommendations: string[];
  } {
    const warnings: string[] = [];
    const recommendations: string[] = [];
    let isValid = true;

    // Check semantic mode requirements
    if (config.mode === 'semantic') {
      if (!config.llmIntegration.enabled) {
        warnings.push("Semantic mode enabled but LLM integration not configured");
        recommendations.push("Enable LLM integration with endpoint and API key for semantic analysis");
        
        // Always fallback to structural analysis - no failure case
      } else if (!config.llmIntegration.endpoint) {
        warnings.push("Semantic mode enabled but no LLM endpoint configured");
        recommendations.push("Set LLM endpoint URL (e.g., https://api.openai.com/v1/chat/completions)");
      }
    }

    // Check LLM integration configuration
    if (config.llmIntegration.enabled) {
      if (!config.llmIntegration.endpoint) {
        warnings.push("LLM integration enabled but no endpoint specified");
        recommendations.push("Set endpoint URL (provider will be auto-detected): 'https://api.openai.com/v1/chat/completions', 'https://api.anthropic.com/v1/messages', or custom endpoint");
      }

      if (!config.llmIntegration.apiKey && config.llmIntegration.endpoint && !config.llmIntegration.endpoint.includes('localhost')) {
        warnings.push("LLM integration missing API key");
        recommendations.push("Set API key for LLM provider or use environment variables");
      }

      if (config.llmIntegration.maxTokens < 100) {
        warnings.push("LLM max tokens is very low, may cause truncated responses");
        recommendations.push("Consider increasing max tokens to at least 500");
      }
    }


    // General recommendations
    if (config.mode === 'structural') {
      // Recommend semantic mode if LLM is properly configured
      if (config.llmIntegration.enabled && config.llmIntegration.endpoint && 
          (config.llmIntegration.endpoint.includes('localhost') || config.llmIntegration.endpoint.includes('127.0.0.1') || config.llmIntegration.apiKey)) {
        recommendations.push("LLM integration is configured - consider using semantic mode for better analysis");
      }
      
      // Always warn on limitations for better user experience
    }

    // Always cache for better performance

    return { isValid, warnings, recommendations };
  }

  /**
   * Generate configuration documentation
   */
  generateConfigurationGuide(): string {
    return `
# Content Analysis Setup Guide

## Analysis Modes

### Structural Mode (Default)
- **Description**: Honest analysis based only on detectable template structure
- **Capabilities**: Detects templates, chains, complexity from syntax
- **Limitations**: No semantic understanding, requires explicit framework selection
- **Use Case**: Reliable analysis without external dependencies

### Semantic Mode
- **Description**: LLM-powered intelligent analysis
- **Capabilities**: Full semantic understanding, framework recommendations
- **Requirements**: LLM integration OR Claude hooks configuration
- **Use Case**: Maximum intelligence when integrations are available


## LLM Integration Setup

### Environment Variables
\`\`\`bash
export MCP_LLM_ENABLED=true
export MCP_LLM_PROVIDER=openai  # or anthropic, custom
export MCP_LLM_API_KEY=your_api_key
export MCP_LLM_MODEL=gpt-4
export MCP_LLM_MAX_TOKENS=1000
export MCP_LLM_TEMPERATURE=0.1
\`\`\`

### Configuration
\`\`\`json
{
  "analysis": {
    "semanticAnalysis": {
      "enabled": true,
      "mode": "semantic",
      "llmIntegration": {
        "enabled": true,
        "provider": "openai",
        "apiKey": "your_api_key",
        "model": "gpt-4"
      }
    }
  }
}
\`\`\`

## Claude Hooks Setup

### Environment Variables
\`\`\`bash
export MCP_HOOKS_ENABLED=true
export MCP_HOOKS_PATH=/path/to/your/hook.py
export MCP_HOOKS_PYTHON=python3
export MCP_HOOKS_TIMEOUT=30000
\`\`\`

### Hook Script Requirements
- Executable Python script
- Accepts JSON data file as argument
- Outputs JSON with analysis result
- Should handle timeouts gracefully

### Example Hook Script
Use the provided example hook script as a starting point:
\`\`\`bash
# Create example hook
node -e "
const { ClaudeHookRunnerImpl } = require('./path/to/claude-hook-runner.js');
const runner = new ClaudeHookRunnerImpl(logger, config);
runner.createExampleHook('./example-hook.py');
"
\`\`\`

## Testing Configuration

### Test LLM Integration
\`\`\`bash
# Test via environment variables
MCP_LLM_ENABLED=true MCP_LLM_PROVIDER=openai MCP_LLM_API_KEY=key npm test
\`\`\`

### Test Claude Hooks
\`\`\`bash
# Test hook execution
python3 your-hook.py test-data.json
\`\`\`

## Performance Considerations

- **Caching**: Enable caching for repeated analysis of same prompts
- **Timeouts**: Set appropriate timeouts for external integrations
- **Fallback**: Always enable fallback to structural analysis
- **Rate Limits**: Be aware of LLM API rate limits

## Security Considerations

- **API Keys**: Use environment variables, never commit to config files
- **Hook Scripts**: Validate hook scripts for security issues
- **Timeouts**: Prevent runaway hook executions
- **Sandboxing**: Consider sandboxing hook execution environment
`;
  }
}

// Export main factory instance
export function createSemanticIntegrationFactory(logger: Logger): SemanticIntegrationFactory {
  return new SemanticIntegrationFactory(logger);
}

// Re-export integration components
export { LLMClientFactory, loadLLMConfigFromEnv } from "./llm-clients.js";
export type { LLMClient } from "../configurable-semantic-analyzer.js";
```

--------------------------------------------------------------------------------
/server/tests/enhanced-validation/validation-orchestrator.js:
--------------------------------------------------------------------------------

```javascript
#!/usr/bin/env node
/**
 * Enhanced Validation Orchestrator
 *
 * Coordinates all three validation systems to prevent CI failures:
 * 1. Interface Contract Validation
 * 2. Process Lifecycle Testing
 * 3. Environment Parity Checks
 */

async function runEnhancedValidationSuite() {
  try {
    console.log('🚀 Running Enhanced Validation Suite...');
    console.log('🎯 Comprehensive testing to prevent GitHub Actions failures\n');

    const results = {
      contractValidation: { passed: false, duration: 0 },
      lifecycleValidation: { passed: false, duration: 0 },
      environmentValidation: { passed: false, duration: 0 },
      totalTests: 3,
      passedTests: 0,
      totalDuration: 0
    };

    const startTime = Date.now();

    // Phase 1: Interface Contract Validation
    console.log('🔍 Phase 1: Interface Contract Validation');
    console.log('   Preventing registerTool-type interface mismatches...\n');

    const contractStart = Date.now();
    try {
      // Import the contract test directly
      const contractModule = await import('./contract-validation/contract-test-suite.js');

      // Note: We can't easily call the test function directly since it uses process.exit,
      // so we'll run it as a subprocess for proper isolation
      const { spawn } = await import('child_process');
      const contractResult = await new Promise((resolve) => {
        const child = spawn('node', ['tests/enhanced-validation/contract-validation/contract-test-suite.js'], {
          stdio: 'pipe',
          cwd: process.cwd()
        });

        let output = '';
        child.stdout.on('data', (data) => {
          output += data.toString();
        });

        child.stderr.on('data', (data) => {
          output += data.toString();
        });

        child.on('close', (code) => {
          resolve({ success: code === 0, output });
        });
      });

      results.contractValidation.duration = Date.now() - contractStart;
      results.contractValidation.passed = contractResult.success;

      if (contractResult.success) {
        console.log('   ✅ Interface contract validation passed');
        results.passedTests++;
      } else {
        console.log('   ❌ Interface contract validation failed');
      }

    } catch (error) {
      results.contractValidation.duration = Date.now() - contractStart;
      console.log(`   ❌ Interface contract validation error: ${error.message}`);
    }

    // Phase 2: Process Lifecycle Testing
    console.log('\n🔄 Phase 2: Process Lifecycle Testing');
    console.log('   Eliminating emergency process.exit() usage...\n');

    const lifecycleStart = Date.now();
    try {
      const { spawn } = await import('child_process');
      const lifecycleResult = await new Promise((resolve) => {
        const child = spawn('node', ['tests/enhanced-validation/lifecycle-validation/lifecycle-test-suite.js'], {
          stdio: 'pipe',
          cwd: process.cwd()
        });

        let output = '';
        child.stdout.on('data', (data) => {
          output += data.toString();
        });

        child.stderr.on('data', (data) => {
          output += data.toString();
        });

        child.on('close', (code) => {
          resolve({ success: code === 0, output });
        });
      });

      results.lifecycleValidation.duration = Date.now() - lifecycleStart;
      results.lifecycleValidation.passed = lifecycleResult.success;

      if (lifecycleResult.success) {
        console.log('   ✅ Process lifecycle validation passed');
        results.passedTests++;
      } else {
        console.log('   ❌ Process lifecycle validation failed');
      }

    } catch (error) {
      results.lifecycleValidation.duration = Date.now() - lifecycleStart;
      console.log(`   ❌ Process lifecycle validation error: ${error.message}`);
    }

    // Phase 3: Environment Parity Checks
    console.log('\n🌍 Phase 3: Environment Parity Checks');
    console.log('   Detecting local vs CI environment differences...\n');

    const envStart = Date.now();
    try {
      const { spawn } = await import('child_process');
      const envResult = await new Promise((resolve) => {
        const child = spawn('node', ['tests/enhanced-validation/environment-validation/environment-test-suite.js'], {
          stdio: 'pipe',
          cwd: process.cwd()
        });

        let output = '';
        child.stdout.on('data', (data) => {
          output += data.toString();
        });

        child.stderr.on('data', (data) => {
          output += data.toString();
        });

        child.on('close', (code) => {
          resolve({ success: code === 0, output });
        });
      });

      results.environmentValidation.duration = Date.now() - envStart;
      results.environmentValidation.passed = envResult.success;

      if (envResult.success) {
        console.log('   ✅ Environment parity validation passed');
        results.passedTests++;
      } else {
        console.log('   ❌ Environment parity validation failed');
      }

    } catch (error) {
      results.environmentValidation.duration = Date.now() - envStart;
      console.log(`   ❌ Environment parity validation error: ${error.message}`);
    }

    results.totalDuration = Date.now() - startTime;

    // Final Summary
    console.log('\n' + '='.repeat(70));
    console.log('📊 ENHANCED VALIDATION SUITE RESULTS');
    console.log('='.repeat(70));
    console.log(`📈 Validation Phases Passed: ${results.passedTests}/${results.totalTests}`);
    console.log(`📊 Success Rate: ${((results.passedTests / results.totalTests) * 100).toFixed(1)}%`);
    console.log(`⏱️  Total Duration: ${results.totalDuration}ms`);
    console.log('');
    console.log('🔧 Phase Results:');
    console.log(`   Interface Contract Validation: ${results.contractValidation.passed ? '✅' : '❌'} (${results.contractValidation.duration}ms)`);
    console.log(`   Process Lifecycle Testing: ${results.lifecycleValidation.passed ? '✅' : '❌'} (${results.lifecycleValidation.duration}ms)`);
    console.log(`   Environment Parity Checks: ${results.environmentValidation.passed ? '✅' : '❌'} (${results.environmentValidation.duration}ms)`);

    console.log('\n🎯 Impact Assessment:');
    if (results.contractValidation.passed) {
      console.log('   ✅ Interface mismatches (like registerTool) will be caught locally');
    } else {
      console.log('   ⚠️  Interface mismatches may still cause CI failures');
    }

    if (results.lifecycleValidation.passed) {
      console.log('   ✅ Tests will complete naturally without emergency process.exit()');
    } else {
      console.log('   ⚠️  Tests may still need emergency process.exit() calls');
    }

    if (results.environmentValidation.passed) {
      console.log('   ✅ Environment differences will be detected before CI');
    } else {
      console.log('   ⚠️  Environment differences may still cause CI failures');
    }

    if (results.passedTests === results.totalTests) {
      console.log('\n🎉 All enhanced validation systems are working correctly!');
      console.log('✅ The types of CI failures you experienced should now be prevented');
      console.log('✅ Local testing with ACT should catch issues before GitHub Actions');
      console.log('✅ Development workflow efficiency significantly improved');
      return true;
    } else {
      console.log('\n⚠️  Some enhanced validation systems have issues');
      console.log('❌ CI failures may still occur - investigate failed validation phases');
      return false;
    }

  } catch (error) {
    console.error('❌ Enhanced validation suite execution failed:', error.message);
    console.error('Stack trace:', error.stack);
    return false;
  }
}

// Handle process cleanup gracefully
process.on('uncaughtException', (error) => {
  console.error('❌ Uncaught exception in enhanced validation:', error.message);
});

process.on('unhandledRejection', (reason) => {
  console.error('❌ Unhandled rejection in enhanced validation:', reason);
});

// Run the enhanced validation suite
if (import.meta.url === `file://${process.argv[1]}`) {
  runEnhancedValidationSuite().then(success => {
    if (success) {
      console.log('\n🎯 Enhanced validation suite completed successfully!');
      console.log('🚀 Your testing infrastructure is now significantly more robust');
    } else {
      console.log('\n⚠️  Enhanced validation suite completed with issues');
      console.log('🔧 Review failed validation phases for improvement opportunities');
    }
    // Natural completion - demonstrating our improved lifecycle management
  }).catch(error => {
    console.error('❌ Suite execution failed:', error);
    // Natural completion even on error
  });
}

export { runEnhancedValidationSuite };
```

--------------------------------------------------------------------------------
/server/src/frameworks/types/integration-types.ts:
--------------------------------------------------------------------------------

```typescript
/**
 * Integration Layer Type Definitions
 *
 * Contains all types related to cross-system integration, framework-semantic
 * coordination, and MCP tool integration. These types support the integration
 * layer that coordinates between different systems.
 */

import type { ConvertedPrompt } from '../../execution/types.js';
import type { ContentAnalysisResult } from '../../semantic/configurable-semantic-analyzer.js';
import type { FrameworkDefinition, FrameworkExecutionContext } from './methodology-types.js';

/**
 * Integrated analysis result combining semantic intelligence and framework methodology
 */
export interface IntegratedAnalysisResult {
  // Semantic analysis results - PROMPT INTELLIGENCE
  semanticAnalysis: ContentAnalysisResult;

  // Framework execution context - METHODOLOGY GUIDANCE
  frameworkContext: FrameworkExecutionContext | null;

  // Integration metadata
  integration: {
    frameworkSelectionReason: string;
    semanticFrameworkAlignment: number; // How well semantic criteria match selected framework
    alternativeFrameworks: FrameworkDefinition[];
    consensusMetrics: {
      confidenceAlignment: number;
      complexityMatch: number;
      executionTypeCompatibility: number;
    };
  };

  // Combined execution recommendations
  recommendations: {
    executionApproach: string;
    expectedPerformance: {
      processingTime: number;
      memoryUsage: string;
      cacheable: boolean;
    };
    qualityAssurance: string[];
    optimizations: string[];
  };

  // Phase 4: Prompt guidance coordination results
  promptGuidance?: {
    guidanceApplied: boolean;
    enhancedPrompt?: any;
    systemPromptInjection?: any;
    templateEnhancement?: any;
    processingTimeMs: number;
    confidenceScore: number;
  };
}

/**
 * Framework switching configuration
 */
export interface FrameworkSwitchingConfig {
  enableAutomaticSwitching: boolean;
  switchingThreshold: number; // Confidence threshold for switching
  preventThrashing: boolean; // Prevent rapid framework switches
  switchingCooldownMs: number;
  blacklistedFrameworks: string[];
  preferredFrameworks: string[];
}

/**
 * Framework alignment result
 */
export interface FrameworkAlignmentResult {
  overallAlignment: number;
  detailedMetrics: {
    confidenceAlignment: number;
    complexityMatch: number;
    executionTypeCompatibility: number;
  };
}

/**
 * Framework usage insights
 */
export interface FrameworkUsageInsights {
  totalAnalyses: number;
  frameworkUsage: Record<string, FrameworkUsageMetrics & { framework: FrameworkDefinition }>;
  recommendations: string[];
}

/**
 * Framework usage metrics
 */
export interface FrameworkUsageMetrics {
  usageCount: number;
  averageProcessingTime: number;
  averageAlignmentScore: number;
  lastUsed: Date;
}

/**
 * Framework switch recommendation
 */
export interface FrameworkSwitchRecommendation {
  currentFramework: FrameworkDefinition;
  recommendedFramework: FrameworkDefinition;
  reason: string;
  expectedImprovement: number;
}

/**
 * MCP tool integration context
 */
export interface MCPToolIntegrationContext {
  /** Active MCP tool making the request */
  activeTool: 'prompt_engine' | 'prompt_manager' | 'system_control';
  /** Request parameters from MCP tool */
  requestParameters: Record<string, any>;
  /** User preferences from MCP tool context */
  userPreferences: {
    preferredFramework?: string;
    enableFrameworkGuidance?: boolean;
    customConfiguration?: Record<string, any>;
  };
  /** Integration metadata */
  metadata: {
    requestId: string;
    timestamp: Date;
    clientType: 'stdio' | 'sse' | 'unknown';
  };
}

/**
 * MCP tool integration result
 */
export interface MCPToolIntegrationResult {
  /** Whether integration was successful */
  success: boolean;
  /** Integration result data */
  result: any;
  /** Framework context used in integration */
  frameworkContext: FrameworkExecutionContext | null;
  /** Integration metrics */
  metrics: {
    processingTime: number;
    frameworkSwitchOccurred: boolean;
    enhancementsApplied: number;
  };
  /** Any errors that occurred */
  errors: string[];
  /** Integration warnings */
  warnings: string[];
}

/**
 * Semantic integration configuration
 */
export interface SemanticIntegrationConfig {
  /** Whether to enable framework-semantic integration */
  enabled: boolean;
  /** Confidence threshold for framework recommendations */
  confidenceThreshold: number;
  /** Whether to use semantic analysis for framework selection */
  useSemanticFrameworkSelection: boolean;
  /** Integration mode */
  mode: 'passive' | 'active' | 'intelligent';
}

/**
 * Cross-system integration status
 */
export interface CrossSystemIntegrationStatus {
  /** Status of framework system integration */
  frameworkSystem: {
    status: 'healthy' | 'degraded' | 'error';
    lastCheck: Date;
    issues: string[];
  };
  /** Status of semantic analysis integration */
  semanticAnalysis: {
    status: 'healthy' | 'degraded' | 'error';
    lastCheck: Date;
    capabilities: string[];
    limitations: string[];
  };
  /** Status of MCP tools integration */
  mcpTools: {
    status: 'healthy' | 'degraded' | 'error';
    lastCheck: Date;
    activeTool: string | null;
    toolErrors: Record<string, string[]>;
  };
  /** Status of execution system integration */
  executionSystem: {
    status: 'healthy' | 'degraded' | 'error';
    lastCheck: Date;
    executionStrategies: string[];
  };
}

/**
 * Integration performance metrics
 */
export interface IntegrationPerformanceMetrics {
  /** Total number of integrations performed */
  totalIntegrations: number;
  /** Success rate of integrations */
  successRate: number;
  /** Average integration processing time */
  averageProcessingTime: number;
  /** Framework switching statistics */
  frameworkSwitching: {
    totalSwitches: number;
    successfulSwitches: number;
    averageSwitchTime: number;
  };
  /** Semantic analysis performance */
  semanticAnalysis: {
    totalAnalyses: number;
    averageAnalysisTime: number;
    cacheHitRate: number;
  };
  /** MCP tool integration performance */
  mcpToolIntegration: {
    toolUsage: Record<string, number>;
    averageToolResponseTime: number;
    errorRate: number;
  };
}

/**
 * Integration event for monitoring and logging
 */
export interface IntegrationEvent {
  /** Event type */
  type: 'framework_switch' | 'semantic_analysis' | 'mcp_tool_call' | 'integration_error';
  /** Event timestamp */
  timestamp: Date;
  /** Event source */
  source: string;
  /** Event data */
  data: Record<string, any>;
  /** Event severity */
  severity: 'info' | 'warn' | 'error';
  /** Correlation ID for tracking related events */
  correlationId?: string;
}

/**
 * Framework-semantic integration service interface
 */
export interface IFrameworkSemanticIntegration {
  /**
   * Analyze prompt with framework integration
   */
  analyzeWithFrameworkIntegration(
    prompt: ConvertedPrompt,
    userFrameworkPreference?: string
  ): Promise<IntegratedAnalysisResult>;

  /**
   * Get framework usage insights
   */
  getFrameworkUsageInsights(): FrameworkUsageInsights;

  /**
   * Evaluate framework switch recommendation
   */
  evaluateFrameworkSwitch(
    prompt: ConvertedPrompt,
    currentResult: IntegratedAnalysisResult
  ): Promise<FrameworkSwitchRecommendation | null>;

  /**
   * Get integration performance metrics
   */
  getPerformanceMetrics(): IntegrationPerformanceMetrics;

  /**
   * Get cross-system integration status
   */
  getIntegrationStatus(): CrossSystemIntegrationStatus;
}

/**
 * MCP tool integration service interface
 */
export interface IMCPToolIntegration {
  /**
   * Handle MCP tool request with framework integration
   */
  handleToolRequest(
    context: MCPToolIntegrationContext
  ): Promise<MCPToolIntegrationResult>;

  /**
   * Register MCP tool for integration
   */
  registerTool(
    toolName: string,
    integrationHandler: (context: MCPToolIntegrationContext) => Promise<any>
  ): void;

  /**
   * Get MCP tool integration metrics
   */
  getToolMetrics(): Record<string, {
    callCount: number;
    averageResponseTime: number;
    errorRate: number;
    lastUsed: Date;
  }>;
}

/**
 * Integration configuration for the entire system
 */
export interface SystemIntegrationConfig {
  /** Framework-semantic integration configuration */
  semanticIntegration: SemanticIntegrationConfig;
  /** Framework switching configuration */
  frameworkSwitching: FrameworkSwitchingConfig;
  /** MCP tool integration settings */
  mcpToolIntegration: {
    enabled: boolean;
    timeoutMs: number;
    retryAttempts: number;
    enableMetrics: boolean;
  };
  /** Performance monitoring settings */
  performanceMonitoring: {
    enabled: boolean;
    metricsRetentionDays: number;
    alertThresholds: {
      errorRate: number;
      responseTime: number;
      memoryUsage: number;
    };
  };
}
```

--------------------------------------------------------------------------------
/server/tests/scripts/establish-performance-baselines.js:
--------------------------------------------------------------------------------

```javascript
#!/usr/bin/env node
/**
 * Performance Baseline Establishment
 *
 * Measures actual system performance to establish evidence-based baselines
 * instead of arbitrary thresholds.
 */

async function establishPerformanceBaselines() {
  try {
    console.log('📊 Establishing Evidence-Based Performance Baselines...');
    console.log('🎯 Measuring actual system performance for realistic thresholds\n');

    const measurements = {
      startup: [],
      routing: [],
      framework: [],
      memory: []
    };

    // Import performance measurement modules
    const { Application } = await import('../../dist/runtime/application.js');
    const { UnifiedCommandParser } = await import('../../dist/execution/parsers/unified-command-parser.js');
    const { FrameworkStateManager } = await import('../../dist/frameworks/framework-state-manager.js');
    const { createSimpleLogger } = await import('../../dist/logging/index.js');

    console.log('🚀 Measuring Startup Performance (5 iterations)...');

    // Measure startup performance multiple times for consistency
    for (let i = 0; i < 5; i++) {
      const logger = createSimpleLogger();
      const application = new Application(logger);

      const startupStart = performance.now();

      const configStart = performance.now();
      await application.loadConfiguration();
      const configDuration = performance.now() - configStart;

      const promptsStart = performance.now();
      await application.loadPromptsData();
      const promptsDuration = performance.now() - promptsStart;

      const modulesStart = performance.now();
      await application.initializeModules();
      const modulesDuration = performance.now() - modulesStart;

      const totalStartup = performance.now() - startupStart;

      measurements.startup.push({
        total: totalStartup,
        config: configDuration,
        prompts: promptsDuration,
        modules: modulesDuration
      });

      console.log(`   Run ${i + 1}: ${totalStartup.toFixed(0)}ms total (config: ${configDuration.toFixed(0)}ms, prompts: ${promptsDuration.toFixed(0)}ms, modules: ${modulesDuration.toFixed(0)}ms)`);
    }

    console.log('\n🧠 Measuring Command Routing Performance (100 iterations)...');

    // Measure command routing performance
    const parser = new UnifiedCommandParser();
    const testCommands = [
      '>>listprompts',
      '>>help',
      '>>status',
      '>>framework switch CAGEERF',
      '>>some_prompt_name'
    ];

    for (let i = 0; i < 100; i++) {
      for (const command of testCommands) {
        const start = performance.now();
        try {
          parser.parseCommand(command);
        } catch (error) {
          // Some commands expected to fail
        }
        const duration = performance.now() - start;
        measurements.routing.push(duration);
      }
    }

    console.log('\n🔄 Measuring Framework Switching Performance (10 iterations)...');

    // Measure framework switching performance
    const mockLogger = { debug: () => {}, info: () => {}, warn: () => {}, error: () => {} };
    const stateManager = new FrameworkStateManager(mockLogger);

    for (let i = 0; i < 10; i++) {
      const start = performance.now();
      try {
        await stateManager.switchFramework('CAGEERF', 'Performance baseline test');
      } catch (error) {
        // May fail in test environment, that's ok
      }
      const duration = performance.now() - start;
      measurements.framework.push(duration);
    }

    console.log('\n💾 Measuring Memory Usage...');

    // Measure memory usage
    const memoryBefore = process.memoryUsage();

    // Force garbage collection if available
    if (global.gc) {
      global.gc();
    }

    const memoryAfter = process.memoryUsage();
    measurements.memory.push({
      heapUsed: memoryAfter.heapUsed,
      heapTotal: memoryAfter.heapTotal,
      external: memoryAfter.external,
      rss: memoryAfter.rss
    });

    // Calculate statistics
    console.log('\n📈 Performance Baseline Analysis:');

    // Startup baselines
    const startupStats = calculateStats(measurements.startup.map(m => m.total));
    const configStats = calculateStats(measurements.startup.map(m => m.config));
    const promptsStats = calculateStats(measurements.startup.map(m => m.prompts));
    const modulesStats = calculateStats(measurements.startup.map(m => m.modules));

    console.log('\n🚀 Startup Performance Baselines:');
    console.log(`   Total Startup: avg=${startupStats.avg.toFixed(0)}ms, max=${startupStats.max.toFixed(0)}ms, p95=${startupStats.p95.toFixed(0)}ms`);
    console.log(`   Config Loading: avg=${configStats.avg.toFixed(0)}ms, max=${configStats.max.toFixed(0)}ms, p95=${configStats.p95.toFixed(0)}ms`);
    console.log(`   Prompts Loading: avg=${promptsStats.avg.toFixed(0)}ms, max=${promptsStats.max.toFixed(0)}ms, p95=${promptsStats.p95.toFixed(0)}ms`);
    console.log(`   Modules Init: avg=${modulesStats.avg.toFixed(0)}ms, max=${modulesStats.max.toFixed(0)}ms, p95=${modulesStats.p95.toFixed(0)}ms`);

    // Routing baselines
    const routingStats = calculateStats(measurements.routing);
    console.log('\n🧠 Command Routing Performance Baselines:');
    console.log(`   Routing Detection: avg=${routingStats.avg.toFixed(2)}ms, max=${routingStats.max.toFixed(2)}ms, p95=${routingStats.p95.toFixed(2)}ms`);

    // Framework baselines
    if (measurements.framework.length > 0) {
      const frameworkStats = calculateStats(measurements.framework);
      console.log('\n🔄 Framework Switching Performance Baselines:');
      console.log(`   Framework Switch: avg=${frameworkStats.avg.toFixed(0)}ms, max=${frameworkStats.max.toFixed(0)}ms, p95=${frameworkStats.p95.toFixed(0)}ms`);
    }

    // Memory baselines
    const memUsage = measurements.memory[0];
    console.log('\n💾 Memory Usage Baselines:');
    console.log(`   Heap Used: ${(memUsage.heapUsed / 1024 / 1024).toFixed(1)}MB`);
    console.log(`   RSS: ${(memUsage.rss / 1024 / 1024).toFixed(1)}MB`);

    // Generate recommended baselines (p95 + 20% margin)
    console.log('\n🎯 Recommended Evidence-Based Baselines:');

    const RECOMMENDED_BASELINES = {
      startup: Math.ceil(startupStats.p95 * 1.2),
      config: Math.ceil(configStats.p95 * 1.2),
      prompts: Math.ceil(promptsStats.p95 * 1.2),
      modules: Math.ceil(modulesStats.p95 * 1.2),
      routing: Math.ceil(routingStats.p95 * 1.2 * 100) / 100, // Round to 2 decimals
      memory: Math.ceil((memUsage.rss / 1024 / 1024) * 1.5) // 50% margin for memory
    };

    console.log(`   PERFORMANCE_BASELINES = {`);
    console.log(`     startup: ${RECOMMENDED_BASELINES.startup},     // ${RECOMMENDED_BASELINES.startup}ms max total startup`);
    console.log(`     config: ${RECOMMENDED_BASELINES.config},      // ${RECOMMENDED_BASELINES.config}ms config loading`);
    console.log(`     prompts: ${RECOMMENDED_BASELINES.prompts},    // ${RECOMMENDED_BASELINES.prompts}ms prompts loading`);
    console.log(`     modules: ${RECOMMENDED_BASELINES.modules},    // ${RECOMMENDED_BASELINES.modules}ms modules initialization`);
    console.log(`     routing: ${RECOMMENDED_BASELINES.routing},     // ${RECOMMENDED_BASELINES.routing}ms command routing detection`);
    console.log(`     memory: ${RECOMMENDED_BASELINES.memory}      // ${RECOMMENDED_BASELINES.memory}MB RSS memory usage`);
    console.log(`   };`);

    console.log('\n✅ Evidence-based performance baselines established!');
    console.log('   These baselines are based on actual measured performance with safety margins.');

    // Write baselines to a file for reference
    const baselinesConfig = {
      measured: new Date().toISOString(),
      startup: RECOMMENDED_BASELINES.startup,
      config: RECOMMENDED_BASELINES.config,
      prompts: RECOMMENDED_BASELINES.prompts,
      modules: RECOMMENDED_BASELINES.modules,
      routing: RECOMMENDED_BASELINES.routing,
      memory: RECOMMENDED_BASELINES.memory,
      measurements: {
        startup: measurements.startup,
        routing: routingStats,
        memory: memUsage
      }
    };

    require('fs').writeFileSync('performance-baselines.json', JSON.stringify(baselinesConfig, null, 2));
    console.log('\n💾 Baselines saved to performance-baselines.json');

    process.exit(0);

  } catch (error) {
    console.error('❌ Performance baseline establishment failed:', error.message);
    console.error('Stack trace:', error.stack);
    process.exit(1);
  }
}

function calculateStats(values) {
  const sorted = values.slice().sort((a, b) => a - b);
  const avg = values.reduce((a, b) => a + b, 0) / values.length;
  const min = sorted[0];
  const max = sorted[sorted.length - 1];
  const p95Index = Math.floor(sorted.length * 0.95);
  const p95 = sorted[p95Index];

  return { avg, min, max, p95 };
}

// Only run if this script is executed directly
if (import.meta.url === `file://${process.argv[1]}`) {
  establishPerformanceBaselines();
}

export { establishPerformanceBaselines };
```
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