trinity-method-sdk 2.0.8 → 2.1.0

package/dist/templates/.claude/commands/maintenance/trinity-docs.md.template

@@ -0,0 +1,2828 @@
+# Trinity Documentation Generator (Orchestration Architecture)
+
+**Command:** `/execution:trinity-docs`
+**Purpose:** Generate comprehensive project documentation using multi-agent orchestration
+**Architecture:** JUNO audit → Parallel APO execution → Verification
+**Trinity Version:** 2.1.0
+**Last Updated:** 2026-01-21
+
+---
+
+## Overview
+
+This command uses **agent orchestration** to generate documentation:
+
+1. **JUNO** audits codebase and creates documentation checklist report
+2. **Three APO instances** execute in parallel, each handling one section:
+   - APO-1: Architecture diagrams
+   - APO-2: API documentation and guides
+   - APO-3: Configuration files
+3. **Verification** ensures all items from checklist were completed
+
+**Key Benefits:**
+- Each agent has clean, focused context (<100 lines of instructions)
+- Parallel execution (3x faster)
+- Quality gate upfront (JUNO validates before generation)
+- No single agent reads massive command (prevents context fatigue)
+
+---
+
+## Phase 0: Preparation
+
+Before invoking agents, set up the environment:
+
+```javascript
+// Global state tracking
+global.trinity_docs_session = {
+  started: new Date().toISOString(),
+  audit_report: null,
+  juno_incomplete: false,
+  juno_issues: [],
+  apo_results: {
+    diagrams: null,
+    docs: null,
+    config: null
+  },
+  verification: null,
+  performance_metrics: {
+    juno_start: null,
+    juno_end: null,
+    apo_start: null,
+    apo_end: null,
+    verification_start: null,
+    verification_end: null,
+    total_start: Date.now(),
+    total_end: null
+  }
+};
+
+LOG: "";
+LOG: "╔════════════════════════════════════════════════════════════╗";
+LOG: "║     TRINITY DOCUMENTATION GENERATOR v2.0.9                 ║";
+LOG: "║     Architecture: Multi-Agent Orchestration                ║";
+LOG: "╚════════════════════════════════════════════════════════════╝";
+LOG: "";
+LOG: "📋 Documentation generation process:";
+LOG: "   1. JUNO audits codebase (READ-ONLY)";
+LOG: "   2. Three APO instances generate docs (PARALLEL)";
+LOG: "   3. Verification ensures completeness and quality";
+LOG: "";
+```
+
+---
+
+## Phase 0.2: Template Validation (Rec 18 - Optional)
+
+**Purpose:** Validate template files before APO execution (optional quality check)
+
+```javascript
+// Optional: Enable template validation (default: disabled for performance)
+const VALIDATE_TEMPLATES = false; // Set to true to enable template validation
+
+if (VALIDATE_TEMPLATES) {
+  LOG: "";
+  LOG: "=== PHASE 0.2: TEMPLATE VALIDATION ===";
+  LOG: "";
+  LOG: "Validating template files for correct variable syntax...";
+  LOG: "";
+
+  // Template paths - See trinity/templates/documentation/configuration/documentation-structure.md
+  const template_base = "trinity/templates/documentation";
+  const template_paths = [
+    `${template_base}/mermaid-diagrams/*.md`,
+    `${template_base}/guides/*.md`,
+    `${template_base}/api/README.md`,
+    `${template_base}/configuration/*.md`
+  ];
+
+  const template_issues = [];
+  let templates_validated = 0;
+  let templates_skipped = 0;
+
+  for (const path of template_paths) {
+    if (!exists(path)) {
+      templates_skipped++;
+      LOG: \`  ⏭️ Skipped: \${path} (not found)\`;
+      continue;
+    }
+
+    const content = Read(path);
+    templates_validated++;
+
+    // Check 1: Valid variable syntax (only {{UPPERCASE_UNDERSCORE}})
+    const variable_pattern = /\{\{([^}]+)\}\}/g;
+    const variables = content.match(variable_pattern);
+
+    if (variables) {
+      for (const variable of variables) {
+        const var_name = variable.replace(/[{}]/g, '');
+
+        // Valid: {{DATABASE_TYPE}}, {{API_BASE_PATH}}
+        // Invalid: {{databaseType}}, {{Database Type}}, {{123}}
+        if (!/^[A-Z][A-Z0-9_]*$/.test(var_name)) {
+          template_issues.push({
+            file: path,
+            variable: variable,
+            reason: "Invalid variable name (must be UPPERCASE_UNDERSCORE)"
+          });
+        }
+      }
+    }
+
+    // Check 2: Ensure no nested variables ({{VAR_{{NESTED}}}})
+    if (/\{\{[^}]*\{\{/.test(content)) {
+      template_issues.push({
+        file: path,
+        variable: "N/A",
+        reason: "Nested variables detected (not supported)"
+      });
+    }
+
+    // Check 3: Balanced braces
+    const open_braces = (content.match(/\{\{/g) || []).length;
+    const close_braces = (content.match(/\}\}/g) || []).length;
+
+    if (open_braces !== close_braces) {
+      template_issues.push({
+        file: path,
+        variable: "N/A",
+        reason: \`Unbalanced braces (\${open_braces} open, \${close_braces} close)\`
+      });
+    }
+
+    if (template_issues.filter(i => i.file === path).length === 0) {
+      LOG: \`  ✅ Valid: \${path}\`;
+    } else {
+      WARNING: \`  ⚠️ Issues: \${path}\`;
+    }
+  }
+
+  LOG: "";
+  LOG: \`Template Validation Summary:\`;
+  LOG: \`  Validated: \${templates_validated}\`;
+  LOG: \`  Skipped: \${templates_skipped} (not found)\`;
+  LOG: \`  Issues: \${template_issues.length}\`;
+  LOG: "";
+
+  if (template_issues.length > 0) {
+    WARNING: "";
+    WARNING: "⚠️ Template validation warnings (non-blocking):";
+    for (const issue of template_issues) {
+      WARNING: \`   \${issue.file}\`;
+      WARNING: \`     Variable: \${issue.variable}\`;
+      WARNING: \`     Issue: \${issue.reason}\`;
+    }
+    WARNING: "";
+    WARNING: "These issues may cause APO variable replacement failures.";
+    WARNING: "Consider fixing templates before production use.";
+    WARNING: "";
+  } else if (templates_validated > 0) {
+    LOG: "✅ All templates have valid syntax";
+    LOG: "";
+  }
+}
+```
+
+---
+
+## Phase 0.25: Retry Mechanism (Rec 21)
+
+**Purpose:** Handle transient failures gracefully (filesystem delays, race conditions)
+
+```javascript
+// Rec 21: Retry mechanism for operations that may have transient failures
+function retry_operation(operation_name, operation_func, max_attempts = 3, delay_ms = 500) {
+  LOG: `Executing: ${operation_name} (max ${max_attempts} attempts)`;
+
+  for (let attempt = 1; attempt <= max_attempts; attempt++) {
+    try {
+      LOG: `  Attempt ${attempt}/${max_attempts}...`;
+
+      const result = operation_func();
+
+      LOG: `  ✅ ${operation_name} succeeded on attempt ${attempt}`;
+      return {
+        success: true,
+        result: result,
+        attempts: attempt
+      };
+    } catch (error) {
+      if (attempt < max_attempts) {
+        WARNING: `  ⚠️ Attempt ${attempt} failed: ${error.message}`;
+        WARNING: `  Retrying in ${delay_ms}ms...`;
+
+        // Wait before retry
+        const start = Date.now();
+        while (Date.now() - start < delay_ms) {
+          // Busy wait
+        }
+      } else {
+        // Final attempt failed
+        ERROR: `  ❌ ${operation_name} failed after ${max_attempts} attempts`;
+        ERROR: `  Final error: ${error.message}`;
+
+        return {
+          success: false,
+          error: error,
+          attempts: attempt
+        };
+      }
+    }
+  }
+}
+
+// Example usage patterns:
+
+// Pattern 1: File read with retry (handles filesystem delays)
+const file_read_result = retry_operation(
+  "Read JUNO report",
+  () => Read("trinity/reports/DOCS-AUDIT-*.md"),
+  3,
+  500
+);
+
+if (!file_read_result.success) {
+  ERROR: "Failed to read JUNO report after retries";
+  ABORT_COMMAND();
+}
+
+const audit_report_content = file_read_result.result;
+
+// Pattern 2: Glob with retry (handles race conditions in parallel execution)
+const file_discovery_result = retry_operation(
+  "Discover documentation files",
+  () => {
+    const files = {
+      diagrams: Glob({pattern: "docs/images/*.md"}),
+      guides: Glob({pattern: "docs/guides/*.md"}),
+      api: Glob({pattern: "docs/api/*.md"})
+    };
+
+    const total = files.diagrams.length + files.guides.length + files.api.length;
+
+    if (total === 0) {
+      throw new Error("No files discovered - may be transient filesystem delay");
+    }
+
+    return files;
+  },
+  3,
+  1000 // Longer delay for file discovery
+);
+
+if (!file_discovery_result.success) {
+  ERROR: "Failed to discover files after retries - generation likely failed";
+  ABORT_COMMAND();
+}
+
+// Pattern 3: File existence check with retry
+const file_exists_result = retry_operation(
+  "Check file existence",
+  () => {
+    if (!exists("expected/file/path.md")) {
+      throw new Error("File not found");
+    }
+    return true;
+  },
+  3,
+  500
+);
+```
+
+**When to Use Retry Mechanism:**
+
+1. **File Operations After Parallel Execution:**
+   - Reading files created by parallel APO instances
+   - Glob operations immediately after APO completion
+   - File existence checks in verification phase
+
+2. **Transient Error Indicators:**
+   - "File not found" (immediately after known file creation)
+   - Empty Glob results (when files should exist)
+   - "Permission denied" (temporary lock)
+   - "Resource temporarily unavailable"
+
+3. **DO NOT Use For:**
+   - Permanent errors (syntax errors, logic errors)
+   - User input errors
+   - Configuration errors
+   - Business logic failures
+
+**Integration Points:**
+
+- Phase 1: Reading JUNO report after generation
+- Phase 2: APO synchronization barrier (file availability check)
+- Phase 2: APO-3 README link validation (file existence)
+- Phase 3: Verification file discovery
+- Phase 3: Reading generated files for quality checks
+
+---
+
+## Phase 0.5: Success Criteria Definition
+
+**Purpose:** Define objective quality standards for documentation generation
+
+### Tier 1: Completion (REQUIRED - 40 points)
+
+**File Creation:**
+- All expected files created (based on JUNO report)
+- Correct directory structure (docs/images/, docs/guides/, docs/api/)
+- No missing files from checklist
+
+**Threshold:** 100% completion required (0 points if any file missing)
+
+### Tier 2: Content Quality (REQUIRED - 40 points)
+
+**Template Placeholders (10 points):**
+- ABORT: Any {{VARIABLE}} syntax remaining in output files
+- Expected: 0 placeholders in all documentation
+
+**Internal Link Validation (15 points):**
+- ABORT: Any broken internal links (file references that don't exist)
+- Expected: 0 broken links in all documentation
+
+**Mermaid Syntax Validation (15 points):**
+- ABORT: Invalid Mermaid syntax in diagram files
+- Expected: All diagrams have valid Mermaid code blocks with proper diagram types
+
+**Threshold:** Must pass all checks (100%) - any failure causes ABORT
+
+### Tier 3: Content Accuracy (WARNING - 15 points)
+
+**Documentation vs. Reality (15 points):**
+- WARN: API endpoint counts differ by >±1
+- WARN: Component counts differ by >±2
+- WARN: Testing framework mentioned incorrectly (e.g., Jest when using Vitest)
+- WARN: Non-existent components referenced in diagrams
+
+**Threshold:** Warnings logged but do not cause ABORT
+
+### Tier 4: Excellence (OPTIONAL - 5 points)
+
+**Best Practices:**
+- Comprehensive code examples in guides
+- Clear architecture explanations
+- Helpful deployment instructions
+- Complete API documentation with examples
+
+### Scoring Formula
+
+```
+Total Score = Tier1_Points + Tier2_Points + Tier3_Points + Tier4_Points
+
+Grade Scale:
+- 95-100: Excellent (Production Ready)
+- 85-94: Good (Minor improvements recommended)
+- 70-84: Acceptable (Requires review and fixes)
+- <70: Poor (Significant issues, re-generation recommended)
+```
+
+**Quality Gates:**
+- Tier 1 failure: ABORT immediately
+- Tier 2 failure: ABORT immediately
+- Tier 3 issues: LOG warnings, continue
+- Tier 4 issues: LOG suggestions, continue
+
+---
+
+## Phase 1: JUNO Documentation Audit
+
+**Purpose:** Analyze codebase and create comprehensive documentation checklist
+
+### Step 1.1: Invoke JUNO for Codebase Audit
+
+```javascript
+// ============================================================
+// PHASE 0: TEMPLATE VALIDATION (PRE-EXECUTION GATE)
+// WO-003: Pre-execution gate ensures all required templates exist
+// ============================================================
+
+LOG: "";
+LOG: "=== PHASE 0: TEMPLATE VALIDATION ===";
+LOG: "Verifying all required templates exist before execution...";
+LOG: "";
+
+const required_templates = [
+  // Mermaid diagrams (WO-1.8) - deployed without .template suffix
+  "trinity/templates/documentation/mermaid-diagrams/mvc-flow.md",
+  "trinity/templates/documentation/mermaid-diagrams/database-er.md",
+  "trinity/templates/documentation/mermaid-diagrams/api-endpoint-map.md",
+  "trinity/templates/documentation/mermaid-diagrams/component-hierarchy.md",
+
+  // Guides (WO-002) - deployed without .template suffix
+  "trinity/templates/documentation/guides/getting-started.md",
+  "trinity/templates/documentation/guides/api-development.md",
+  "trinity/templates/documentation/guides/deployment.md",
+  "trinity/templates/documentation/guides/contributing.md",
+
+  // API docs (WO-002) - deployed without .template suffix
+  "trinity/templates/documentation/api-docs/README.md",
+
+  // Configuration (WO-003) - deployed without .template suffix
+  "trinity/templates/documentation/configuration/env-example-generator.md",
+
+  // JUNO internal report (WO-1.8) - deployed without .template suffix
+  "trinity/templates/documentation/reports/juno-internal-report.md"
+];
+
+const missing_templates = [];
+
+for (const template_path of required_templates) {
+  // Check if template file exists
+  if (!exists(template_path)) {
+    missing_templates.push(template_path);
+    ERROR: \`❌ Missing required template: \${template_path}\`;
+  } else {
+    LOG: \`  ✅ \${template_path}\`;
+  }
+}
+
+if (missing_templates.length > 0) {
+  ERROR: "";
+  ERROR: "❌ CRITICAL ERROR: Required templates missing";
+  ERROR: \`Missing \${missing_templates.length} template file(s)\`;
+  ERROR: "";
+  ERROR: "This indicates 'trinity update' CLI was not run or templates failed to deploy.";
+  ERROR: "";
+  ERROR: "REQUIRED ACTIONS:";
+  ERROR: "  1. Run: trinity update";
+  ERROR: "  2. Verify templates exist in trinity/templates/documentation/";
+  ERROR: "  3. Re-run this command";
+  ERROR: "";
+
+  // ABORT - Cannot proceed without templates
+  return {
+    status: "ABORTED",
+    reason: "Required templates missing",
+    missing_templates: missing_templates,
+    action_required: "Run 'trinity update' to deploy templates"
+  };
+}
+
+LOG: "";
+LOG: \`✅ Template validation PASSED: All \${required_templates.length} templates found\`;
+LOG: "";
+LOG: "=== PHASE 0 COMPLETE ===";
+LOG: "";
+
+LOG: "=== PHASE 1: JUNO DOCUMENTATION AUDIT ===";
+LOG: "";
+LOG: "Invoking JUNO (Quality Auditor) to analyze codebase...";
+LOG: "";
+
+// Track performance
+global.trinity_docs_session.performance_metrics.juno_start = Date.now();
+
+// Invoke JUNO agent
+Task({
+  subagent_type: "JUNO (Quality Auditor)",
+  description: "Audit codebase for documentation needs",
+  prompt: `
+# JUNO Documentation Audit Task
+
+**Objective:** Analyze the codebase and create a comprehensive documentation checklist report using the internal report template.
+
+## Your Mission
+
+You are JUNO, the Quality Auditor. Your task is to audit this codebase and generate a structured report for APO consumption.
+
+**CRITICAL:** This is a READ-ONLY operation. DO NOT create any documentation files. Only analyze and create the audit report.
+
+---
+
+## Report Template to Use
+
+**Template File:** \`trinity/templates/documentation/reports/juno-internal-report.md\`
+
+**Instructions:**
+1. **Read the template** to understand the complete structure required
+2. **Analyze the codebase** to gather all data for every {{VARIABLE}}
+3. **Replace ALL placeholders** with actual discovered values (no placeholders like "[Database detected]")
+4. **Output the completed report** to: \`trinity/reports/DOCS-AUDIT-{timestamp}.md\`
+
+**Timestamp Format:** YYYY-MM-DD-HHmm (e.g., 2026-01-15-1530)
+
+---
+
+## Critical Requirements
+
+**ZERO TOLERANCE RULES:**
+- ALL {{VARIABLE}} placeholders MUST be replaced with actual values
+- Component names MUST exist in codebase (verify with Glob)
+- Model names MUST come from actual schema files
+- Endpoint counts MUST match actual route files
+- Testing framework MUST be from package.json (not assumed)
+- Use ONLY discovered data - NO invented names, NO assumptions
+
+**Autonomous Execution:**
+- Do NOT ask user for input
+- Do NOT prompt for decisions
+- Proceed directly to analyze and generate report
+- If ambiguous: use sensible defaults based on codebase evidence
+
+---
+
+## Discovery Logic
+
+**Use discovery templates for codebase analysis:**
+
+- **Framework Detection:** See `trinity/templates/documentation/discovery/framework-detection.md` for package.json analysis patterns
+- **Component Discovery:** See `trinity/templates/documentation/discovery/component-discovery.md` for React/Vue/Angular/Svelte component patterns (CRITICAL: Zero tolerance for fake components)
+- **API Endpoints:** See `trinity/templates/documentation/discovery/api-endpoint-scanner.md` for Express/Fastify/NestJS/Koa route patterns
+- **Environment Variables:** See `trinity/templates/documentation/discovery/env-variable-extraction.md` for .env and process.env usage patterns
+
+**Database Schema Analysis:**
+- Prisma: Parse `prisma/schema.prisma` for models and relationships
+- TypeORM: Find `@Entity` decorator files
+- Mongoose: Find schema definitions
+
+---
+
+## Template Usage Instructions
+
+**Read the template first:**
+\`\`\`javascript
+const template_content = Read("trinity/templates/documentation/reports/juno-internal-report.md");
+// Study the structure to understand ALL {{VARIABLES}} you need to fill
+\`\`\`
+
+**Perform all discovery tasks above, then fill the template:**
+- Replace {{PROJECT_NAME}} with actual name from package.json
+- Replace {{BACKEND_FRAMEWORK}} with detected framework
+- Replace {{MODEL_COUNT}} with actual count from schema
+- Replace {{ENDPOINT_COUNT}} with actual discovered count
+- Replace {{COMPONENT_NAMES}} with comma-separated list of actual components
+- **ALL {{VARIABLES}} must be replaced - zero tolerance for placeholders**
+
+**Output the completed report:**
+\`\`\`javascript
+const completed_report = /* filled template with all variables replaced */;
+Write("trinity/reports/DOCS-AUDIT-{timestamp}.md", completed_report);
+\`\`\`
+
+---
+
+## Self-Validation (Rec 3)
+
+Before returning, verify report completeness:
+
+\`\`\`javascript
+const report_path = "trinity/reports/DOCS-AUDIT-{timestamp}.md";
+const report_content = Read(report_path);
+
+const validation_checks = {
+  file_exists: report_content.length > 0,
+  has_all_sections: report_content.includes("SECTION A") &&
+                    report_content.includes("SECTION B") &&
+                    report_content.includes("SECTION C"),
+  min_length: report_content.length >= 2000,
+  no_placeholders: !report_content.includes("[") && !report_content.includes("{{"),
+  component_verification: /* Glob each listed component path to verify exists */
+};
+
+// All checks must pass before proceeding
+if (!Object.values(validation_checks).every(v => v === true)) {
+  ERROR: "JUNO self-validation failed - fix report before returning";
+  return "VALIDATION_FAILED";
+}
+
+LOG: "✅ JUNO self-validation passed";
+\`\`\`
+
+---
+
+## Completion Summary
+
+Return concise summary after validation passes:
+
+\`\`\`
+JUNO Audit Complete
+Report: trinity/reports/DOCS-AUDIT-{timestamp}.md
+
+Architecture: [type]
+Backend: [framework] [version]
+Frontend: [framework] [version]
+Database: [type] ([N] models)
+API: [N] endpoints
+Components: [N] total
+Testing: [framework or None]
+
+Documentation: [N] files to generate
+Status: Ready for APO execution
+\`\`\`
+  `
+});
+
+LOG: "";
+LOG: "⏳ Waiting for JUNO audit to complete...";
+LOG: "";
+```
+
+### Step 1.2: Capture JUNO's Report Path and Validate (Rec 1)
+
+```javascript
+// After JUNO completes, extract report path from response
+const juno_response = [JUNO's returned message];
+
+// Track performance
+global.trinity_docs_session.performance_metrics.juno_end = Date.now();
+
+// Parse report path from JUNO's response
+const report_path_match = juno_response.match(/trinity\/reports\/DOCS-AUDIT-[\d-]+\.md/);
+
+if (!report_path_match) {
+  ERROR: "";
+  ERROR: "❌ CRITICAL ERROR: JUNO did not create audit report";
+  ERROR: "Expected report at: trinity/reports/DOCS-AUDIT-{timestamp}.md";
+  ERROR: "";
+  ERROR: "Cannot proceed without audit report.";
+  ERROR: "";
+  ABORT_COMMAND();
+}
+
+const audit_report_path = report_path_match[0];
+global.trinity_docs_session.audit_report = audit_report_path;
+
+LOG: `✅ JUNO audit complete: ${audit_report_path}`;
+
+// NEW: Validate JUNO report completeness (Recommendation 1)
+LOG: "";
+LOG: "Validating JUNO report completeness...";
+
+const juno_report = Read(audit_report_path);
+const juno_issues = [];
+
+// Check 1: Report size (should be substantial)
+if (juno_report.length < 1000) {
+  juno_issues.push({
+    severity: "HIGH",
+    issue: `Report suspiciously short (${juno_report.length} chars, expected 2000+)`
+  });
+}
+
+// Check 2: Required sections present
+const has_section_a = juno_report.includes("## SECTION A:");
+const has_section_b = juno_report.includes("## SECTION B:");
+const has_section_c = juno_report.includes("## SECTION C:");
+
+if (!has_section_a) {
+  juno_issues.push({
+    severity: "CRITICAL",
+    issue: "Section A (Architecture & Diagrams) missing"
+  });
+}
+
+if (!has_section_b) {
+  juno_issues.push({
+    severity: "CRITICAL",
+    issue: "Section B (API Documentation & Guides) missing"
+  });
+}
+
+if (!has_section_c) {
+  juno_issues.push({
+    severity: "CRITICAL",
+    issue: "Section C (Configuration & Setup) missing"
+  });
+}
+
+// Check 3: Executive Summary present
+const has_executive_summary = juno_report.includes("## Executive Summary") || juno_report.includes("Executive Summary:");
+if (!has_executive_summary) {
+  juno_issues.push({
+    severity: "HIGH",
+    issue: "Executive Summary missing"
+  });
+}
+
+// Check 4: Enhanced Placeholder Detection (Rec 4)
+LOG: "Checking for template placeholders...";
+
+// Rec 4: Multiple placeholder patterns
+const placeholder_patterns = [
+  /\[[A-Z][a-z]+( [a-z]+)+ detected\]/g,          // [Database type detected]
+  /\{\{[A-Z_]+\}\}/g,                             // {{VARIABLE}}
+  /\[YOUR_[A-Z_]+\]/g,                            // [YOUR_API_KEY]
+  /\bTBD\b/g,                                      // TBD
+  /\bTODO:/g,                                      // TODO:
+  /\[PLACEHOLDER\]/gi,                             // [PLACEHOLDER]
+  /\[Fill this in\]/gi,                            // [Fill this in]
+  /\[Add (.*?) here\]/gi                           // [Add X here]
+];
+
+const found_placeholders = [];
+let total_placeholder_count = 0;
+
+for (const pattern of placeholder_patterns) {
+  const matches = juno_report.match(pattern);
+  if (matches) {
+    total_placeholder_count += matches.length;
+    for (const match of matches) {
+      if (!found_placeholders.includes(match)) {
+        found_placeholders.push(match);
+      }
+    }
+  }
+}
+
+LOG: `Placeholder patterns checked: ${placeholder_patterns.length}`;
+LOG: `Unique placeholders found: ${found_placeholders.length}`;
+LOG: `Total occurrences: ${total_placeholder_count}`;
+
+if (total_placeholder_count > 3) {
+  juno_issues.push({
+    severity: "HIGH",
+    issue: `Too many placeholders detected (${total_placeholder_count} instances): ${found_placeholders.slice(0, 5).join(', ')}${found_placeholders.length > 5 ? '...' : ''}`
+  });
+
+  WARNING: `Found ${total_placeholder_count} placeholders in JUNO report:`;
+  for (const ph of found_placeholders.slice(0, 10)) {
+    WARNING: `  - ${ph}`;
+  }
+  if (found_placeholders.length > 10) {
+    WARNING: `  ... and ${found_placeholders.length - 10} more`;
+  }
+}
+
+// Check 5: Component Verification (Rec 3) - Verify no invented components
+LOG: "";
+LOG: "Performing component verification (Rec 3)...";
+
+// Extract component names documented in JUNO report
+const component_section = juno_report.match(/\*\*Discovered Components.*?(?=\n\*\*|$)/s);
+const documented_components = [];
+
+if (component_section) {
+  const component_lines = component_section[0].match(/^\d+\.\s+([A-Za-z0-9_]+)/gm);
+  if (component_lines) {
+    for (const line of component_lines) {
+      const component_name = line.match(/^\d+\.\s+([A-Za-z0-9_]+)/)[1];
+      documented_components.push(component_name);
+    }
+  }
+}
+
+LOG: `Documented components in report: ${documented_components.length}`;
+
+// Re-discover components from actual codebase
+// See trinity/templates/documentation/configuration/documentation-structure.md for full patterns
+const component_patterns = [
+  "client/**/*.{tsx,jsx,vue}",
+  "src/**/*.{tsx,jsx,vue}"
+];
+
+let actual_component_files = [];
+for (const pattern of component_patterns) {
+  const files = Glob({pattern: pattern});
+  actual_component_files = [...actual_component_files, ...files];
+}
+
+// Filter out non-component files
+const actual_components = actual_component_files.filter(f =>
+  !f.includes('.test.') &&
+  !f.includes('.spec.') &&
+  !f.endsWith('main.tsx') &&
+  !f.endsWith('main.jsx') &&
+  !f.endsWith('index.tsx') &&
+  !f.endsWith('index.jsx') &&
+  !f.includes('setupTests') &&
+  !f.includes('vite.config') &&
+  !f.includes('.config.')
+);
+
+// Extract actual component names
+const actual_component_names = actual_components.map(f => {
+  const path_parts = f.split('/');
+  const filename = path_parts[path_parts.length - 1];
+  return filename.replace(/\.(tsx|jsx|vue)$/, '');
+});
+
+LOG: `Actual components in codebase: ${actual_component_names.length}`;
+
+// Find invented components (in report but not in codebase)
+const invented_components = [];
+for (const doc_component of documented_components) {
+  if (!actual_component_names.includes(doc_component)) {
+    invented_components.push(doc_component);
+  }
+}
+
+if (invented_components.length > 0) {
+  juno_issues.push({
+    severity: "CRITICAL",
+    issue: `Invented components detected (${invented_components.length}): ${invented_components.join(', ')}`
+  });
+
+  ERROR: "";
+  ERROR: `❌ Component verification failed: ${invented_components.length} invented components`;
+  for (const invented of invented_components) {
+    ERROR: `   - ${invented} (NOT FOUND in codebase)`;
+  }
+  ERROR: "";
+} else {
+  LOG: `✅ Component verification passed: All ${documented_components.length} components exist in codebase`;
+}
+
+LOG: "";
+
+// Report validation results
+LOG: `Report size: ${juno_report.length} characters`;
+LOG: `Section A present: ${has_section_a ? "✅" : "❌"}`;
+LOG: `Section B present: ${has_section_b ? "✅" : "❌"}`;
+LOG: `Section C present: ${has_section_c ? "✅" : "❌"}`;
+LOG: `Executive Summary: ${has_executive_summary ? "✅" : "❌"}`;
+LOG: `Placeholders: ${placeholder_count} instances`;
+LOG: "";
+
+// Decision: Proceed with warnings or abort?
+const critical_issues = juno_issues.filter(i => i.severity === "CRITICAL");
+
+if (critical_issues.length >= 3) {
+  // All sections missing - report is too minimal
+  ERROR: "";
+  ERROR: "❌ JUNO REPORT VALIDATION: CRITICAL FAILURE";
+  ERROR: "";
+  ERROR: "JUNO report is too incomplete to proceed:";
+  for (const issue of juno_issues) {
+    ERROR: `   [${issue.severity}] ${issue.issue}`;
+  }
+  ERROR: "";
+  ERROR: "The report must contain Executive Summary and all 3 sections (A, B, C).";
+  ERROR: "Please investigate JUNO task execution.";
+  ERROR: "";
+  ABORT_COMMAND();
+} else if (juno_issues.length > 0) {
+  // Some issues but not critical failure
+  WARNING: "";
+  WARNING: "⚠️ JUNO REPORT VALIDATION: PARTIAL SUCCESS";
+  WARNING: "";
+  WARNING: "Issues detected in JUNO report:";
+  for (const issue of juno_issues) {
+    WARNING: `   [${issue.severity}] ${issue.issue}`;
+  }
+  WARNING: "";
+  WARNING: "APOs will activate fallback mechanisms (Phase 1.5).";
+  WARNING: "Enhanced verification will be applied to ensure quality.";
+  WARNING: "";
+
+  // Log for investigation
+  global.trinity_docs_session.juno_incomplete = true;
+  global.trinity_docs_session.juno_issues = juno_issues;
+} else {
+  LOG: "✅ JUNO report validation: PASSED";
+  global.trinity_docs_session.juno_incomplete = false;
+}
+
+// Rec 5: JUNO Execution Time Tracking
+LOG: "";
+LOG: "=== JUNO PERFORMANCE METRICS ===";
+LOG: "";
+
+const juno_duration = (global.trinity_docs_session.performance_metrics.juno_end - global.trinity_docs_session.performance_metrics.juno_start) / 1000;
+
+// Count files analyzed by JUNO (estimate from various patterns)
+const files_analyzed_match = juno_report.match(/Files analyzed:\s*(\d+)/i) ||
+                            juno_report.match(/(\d+)\s+files? analyzed/i) ||
+                            juno_report.match(/Total files:\s*(\d+)/i);
+const files_analyzed = files_analyzed_match ? parseInt(files_analyzed_match[1]) : "Unknown";
+
+// Extract discovered counts
+const component_count_match = juno_report.match(/Components?:\s*(\d+)/i) ||
+                              juno_report.match(/(\d+)\s+components?/i);
+const component_count = component_count_match ? parseInt(component_count_match[1]) : 0;
+
+const endpoint_count_match = juno_report.match(/API Endpoints?:\s*(\d+)/i) ||
+                             juno_report.match(/(\d+)\s+endpoints?/i);
+const endpoint_count = endpoint_count_match ? parseInt(endpoint_count_match[1]) : 0;
+
+const model_count_match = juno_report.match(/Models?:\s*(\d+)/i) ||
+                          juno_report.match(/(\d+)\s+models?/i);
+const model_count = model_count_match ? parseInt(model_count_match[1]) : 0;
+
+LOG: `Analysis Duration: ${juno_duration.toFixed(2)}s`;
+LOG: `Files Analyzed: ${files_analyzed}`;
+LOG: ``;
+LOG: `Discoveries:`;
+LOG: `  - Components: ${component_count}`;
+LOG: `  - API Endpoints: ${endpoint_count}`;
+LOG: `  - Data Models: ${model_count}`;
+LOG: ``;
+LOG: `Report Size: ${(juno_report.length / 1024).toFixed(2)} KB (${juno_report.length} chars)`;
+LOG: `Report Location: ${audit_report_path}`;
+LOG: "";
+
+// Calculate throughput
+if (files_analyzed !== "Unknown" && files_analyzed > 0) {
+  const files_per_second = (files_analyzed / juno_duration).toFixed(2);
+  LOG: `Throughput: ${files_per_second} files/second`;
+  LOG: "";
+}
+
+LOG: "";
+```
+
+---
+
+## Phase 1.5: APO Fallback Architecture (Rec 4)
+
+**Purpose:** Document resilience mechanisms when JUNO report is incomplete
+
+### When Fallback Activates
+
+Fallback mechanisms activate when:
+- JUNO report validation detects HIGH severity issues (not CRITICAL)
+- Sections are present but minimal or contain placeholders
+- Variable values are missing or incomplete
+- `global.trinity_docs_session.juno_incomplete === true`
+
+### APO Fallback Protocol
+
+When JUNO report is incomplete, each APO must:
+
+#### Step 1: Detect Incomplete Report
+
+```javascript
+// Each APO checks global state
+if (global.trinity_docs_session.juno_incomplete) {
+  LOG: "";
+  LOG: "⚠️ FALLBACK MODE ACTIVATED";
+  LOG: "JUNO report incomplete - using direct codebase analysis";
+  LOG: "";
+}
+```
+
+#### Step 2: Direct Codebase Analysis
+
+**Use discovery templates for fallback analysis:**
+
+**APO-1 (Diagrams):**
+- If diagram variables missing: Use `trinity/templates/documentation/discovery/api-endpoint-scanner.md` and `trinity/templates/documentation/discovery/component-discovery.md` patterns
+- If database schema empty: Parse database schema files directly (Prisma, TypeORM, Mongoose)
+- Generate Mermaid syntax from discovered data
+
+**APO-2 (Guides & Docs):**
+- If framework not specified: Use `trinity/templates/documentation/discovery/framework-detection.md` for package.json analysis
+- If environment variables missing: Use `trinity/templates/documentation/discovery/env-variable-extraction.md` for .env and process.env patterns
+- Fill template variables from direct detection
+
+**APO-3 (Config Files):**
+- If .env keys missing: Use `trinity/templates/documentation/discovery/env-variable-extraction.md` for process.env.KEY patterns
+- If README links undefined: Build links from expected file locations
+- Validate all file references before writing
+
+When JUNO report doesn't specify templates:
+- Use default template paths: `trinity/templates/documentation/`
+- Read template structure to determine required variables
+- Extract variables from codebase analysis
+
+**See trinity/templates/documentation/processes/fallback-mechanism.md for:**
+- Framework detection fallback
+- Component discovery fallback
+- Database schema fallback
+- API endpoints fallback
+- Environment variables fallback
+- Quality gates for fallback usage
+- Logging standards
+
+---
+
+## Phase 2: Parallel APO Execution
+
+**Purpose:** Generate documentation in parallel using JUNO's checklist
+
+### Step 2.1: Invoke Three APO Instances in Parallel
+
+```javascript
+LOG: "=== PHASE 2: PARALLEL DOCUMENTATION GENERATION ===";
+LOG: "";
+LOG: "Invoking 3 APO instances in parallel...";
+LOG: "  - APO-1: Architecture diagrams (Section A)";
+LOG: "  - APO-2: API docs and guides (Section B)";
+LOG: "  - APO-3: Configuration files (Section C)";
+LOG: "";
+
+// Track performance
+global.trinity_docs_session.performance_metrics.apo_start = Date.now();
+
+// Invoke 3 APO agents IN PARALLEL
+// This is done by making multiple Task calls in the same message
+
+// APO Instance 1: Architecture & Diagrams
+Task({
+  subagent_type: "APO",
+  description: "Generate architecture diagrams",
+  prompt: `
+# APO-1: Architecture Diagram Generation
+
+**Your Mission:** Generate Mermaid architecture diagrams using templates and JUNO's audit report.
+
+## Error Handling Protocol (Rec 5)
+
+**Tier 1: ABORT Conditions (Stop immediately, return error)**
+
+ABORT if:
+- ❌ Cannot read codebase (permission denied, files missing at system level)
+- ❌ Cannot write output files (permission denied, disk full, directory creation fails)
+- ❌ Critical templates completely missing AND cannot generate from scratch
+
+**Tier 2: WARN and CONTINUE (Report issue, activate fallback)**
+
+WARN if:
+- ⚠️ JUNO section A incomplete/missing (use direct codebase analysis - see Phase 1.5)
+- ⚠️ Some variable values missing (infer from codebase directly)
+- ⚠️ Template file missing but can generate Mermaid from scratch
+- ⚠️ Component list empty (use Glob to discover components)
+
+**Tier 3: LOG INFO (Normal process updates)**
+
+LOG if:
+- ℹ️ Reading templates
+- ℹ️ Creating diagram files
+- ℹ️ Replacing variables
+- ℹ️ Writing output files
+
+**Error Response Format:**
+
+\`\`\`javascript
+if (TIER_1_ERROR) {
+  ERROR: "";
+  ERROR: "❌ APO-1 CRITICAL ERROR: [Error description]";
+  ERROR: "Cannot proceed with diagram generation.";
+  ERROR: "";
+  return "APO-1 ABORTED: [Reason]";
+}
+
+if (TIER_2_ERROR) {
+  WARNING: "";
+  WARNING: "⚠️ APO-1 WARNING: [Issue description]";
+  WARNING: "Activating fallback mechanism...";
+  WARNING: "";
+  // Continue with fallback
+}
+\`\`\`
+
+## APO-1: Architecture Diagrams & Visual Documentation
+
+**Your Mission:** Generate Mermaid architecture diagrams using templates and JUNO's audit report.
+
+**Agent Designation:** APO-1 (Section A)
+
+---
+
+## Workflow Overview
+
+Follow the **5-Phase APO Workflow** defined in:
+📄 **[trinity/templates/documentation/processes/apo-workflow-common.md](trinity/templates/documentation/processes/apo-workflow-common.md)**
+
+1. **Phase 1:** Read JUNO Report (`global.trinity_docs_session.audit_report`)
+2. **Phase 2:** Extract Template Variables (from Section A)
+3. **Phase 3:** Process Templates (generate Mermaid diagrams)
+4. **Phase 4:** Write Files (to `docs/architecture/`)
+5. **Phase 5:** Self-Validation (quality checks)
+
+---
+
+## Error Handling
+
+**Use 3-Tier Error System** defined in:
+📄 **[trinity/templates/documentation/processes/error-handling-protocol.md](trinity/templates/documentation/processes/error-handling-protocol.md)**
+
+- **Tier 1 (ABORT):** JUNO report missing, component verification failed, write permission denied
+- **Tier 2 (WARN):** JUNO incomplete, database schema missing, API endpoints not found
+- **Tier 3 (LOG):** Progress updates, file creation confirmations
+
+---
+
+## APO-1 Specific Tasks
+
+**See detailed instructions in:**
+📄 **[trinity/templates/documentation/processes/apo-diagram-specific.md](trinity/templates/documentation/processes/apo-diagram-specific.md)**
+
+### Diagrams to Generate:
+
+1. **MVC Flow Diagram** (`mvc-flow.md`) - Request → Controller → Model → View flow
+2. **Database ER Diagram** (`database-er.md`) - Entity-relationship diagram with models
+3. **API Endpoint Map** (`api-endpoint-map.md`) - API endpoint organization
+4. **Component Hierarchy** (`component-hierarchy.md`) - Frontend component structure
+
+### Mermaid Diagram Types:
+
+- **MVC Flow:** `graph TD` (flowchart top-down)
+- **Database ER:** `erDiagram` (entity-relationship)
+- **API Map:** `graph LR` (flowchart left-right)
+- **Components:** `graph TD` (flowchart top-down)
+
+---
+
+## Fallback Mechanisms
+
+**If JUNO report incomplete** (`global.trinity_docs_session.juno_incomplete === true`):
+
+**Use discovery templates for direct codebase analysis:**
+- 📄 **Framework Detection:** [trinity/templates/documentation/discovery/framework-detection.md](trinity/templates/documentation/discovery/framework-detection.md)
+- 📄 **Component Discovery:** [trinity/templates/documentation/discovery/component-discovery.md](trinity/templates/documentation/discovery/component-discovery.md)
+- 📄 **API Endpoint Scanner:** [trinity/templates/documentation/discovery/api-endpoint-scanner.md](trinity/templates/documentation/discovery/api-endpoint-scanner.md)
+
+**Example Fallback:**
+\`\`\`javascript
+if (global.trinity_docs_session.juno_incomplete) {
+  LOG: "⚠️ FALLBACK MODE ACTIVATED";
+  LOG: "JUNO report incomplete - using direct codebase analysis";
+
+  // Use discovery templates to extract missing data
+  // See trinity/templates/documentation/processes/apo-diagram-specific.md for patterns
+}
+\`\`\`
+
+---
+
+## Critical: Component Verification (ZERO TOLERANCE)
+
+**All component names MUST exist in codebase** - verified via Glob:
+
+\`\`\`javascript
+// Extract component names from JUNO report
+const component_section = juno_report.match(/\*\*CRITICAL FOR APO-1 - Use ONLY the components listed below:\*\*(.*?)(?=\n\n\*\*|$)/s);
+
+// Verify EACH component exists in codebase
+for (const component of juno_components) {
+  const possible_paths = [
+    \`**/$\{component}.tsx\`,
+    \`**/$\{component}.jsx\`,
+    \`**/$\{component}/index.tsx\`
+  ];
+
+  let found = false;
+  for (const pattern of possible_paths) {
+    if (Glob(pattern).length > 0) {
+      found = true;
+      break;
+    }
+  }
+
+  if (!found) {
+    ERROR: \`❌ CRITICAL - Component $\{component} not found in codebase\`;
+    ERROR: "ZERO TOLERANCE error - fake component names detected";
+    ABORT_COMMAND();
+  }
+}
+
+LOG: \`✅ All $\{juno_components.length} components verified in codebase\`;
+\`\`\`
+
+**See full verification logic in:**
+📄 **[trinity/templates/documentation/processes/apo-diagram-specific.md](trinity/templates/documentation/processes/apo-diagram-specific.md)** (lines 277-315)
+
+---
+
+## Self-Validation
+
+**Run comprehensive self-validation** after generating diagrams:
+
+📄 **[trinity/templates/documentation/validation/apo-self-validation.md](trinity/templates/documentation/validation/apo-self-validation.md)** - APO-1 Checklist
+
+**Key Checks:**
+- [ ] All expected diagrams created (2-4 files depending on project type)
+- [ ] File ≥10 lines minimum
+- [ ] Contains `\`\`\`mermaid` code block
+- [ ] Valid Mermaid diagram type (graph/erDiagram)
+- [ ] Zero placeholders (`{{VARIABLE}}`, `[TODO]`)
+- [ ] All components verified in codebase (ZERO TOLERANCE)
+- [ ] Mermaid syntax valid
+
+**See validation template for implementation:**
+📄 **[trinity/templates/documentation/validation/apo-self-validation.md](trinity/templates/documentation/validation/apo-self-validation.md)** (APO-1 validation code)
+
+---
+
+## Completion Summary
+
+**Return summary in this format:**
+
+\`\`\`
+APO-1: Architecture Diagrams Complete
+
+Files Created:
+- docs/architecture/mvc-flow.md (MVC flow diagram)
+- docs/architecture/database-er.md (ER diagram with X entities)
+- docs/architecture/api-endpoint-map.md (X endpoints)
+- docs/architecture/component-hierarchy.md (X components)
+
+Total: [N] diagram files created
+
+Self-Validation: ✅ PASSED
+
+Fallback Usage: [Yes/No] ([Description if used])
+
+Status: Section A complete
+\`\`\`
+  `
+});
+</invoke>
+// APO Instance 2: API Documentation & Guides
+Task({
+  subagent_type: "APO",
+  description: "Generate API docs and guides",
+  prompt: \`
+# APO-2: API Documentation & Development Guides
+
+**Your Mission:** Generate API documentation and developer guides using templates and JUNO's audit report.
+
+**Agent Designation:** APO-2 (Section B)
+
+---
+
+## Workflow Overview
+
+Follow the **5-Phase APO Workflow** defined in:
+📄 **[trinity/templates/documentation/processes/apo-workflow-common.md](trinity/templates/documentation/processes/apo-workflow-common.md)**
+
+1. **Phase 1:** Read JUNO Report (\`global.trinity_docs_session.audit_report\`)
+2. **Phase 2:** Extract Template Variables (from Section B)
+3. **Phase 3:** Process Templates (generate guides and API docs)
+4. **Phase 4:** Write Files (to \`docs/guides/\` and \`docs/api/\`)
+5. **Phase 5:** Self-Validation (quality checks)
+
+---
+
+## Error Handling
+
+**Use 3-Tier Error System** defined in:
+📄 **[trinity/templates/documentation/processes/error-handling-protocol.md](trinity/templates/documentation/processes/error-handling-protocol.md)**
+
+- **Tier 1 (ABORT):** JUNO report missing, cannot read templates, write permission denied
+- **Tier 2 (WARN):** JUNO incomplete, test framework unknown, deployment platform uncertain
+- **Tier 3 (LOG):** Progress updates, guide creation confirmations
+
+---
+
+## APO-2 Specific Tasks
+
+**See detailed instructions in:**
+📄 **[trinity/templates/documentation/processes/apo-guide-specific.md](trinity/templates/documentation/processes/apo-guide-specific.md)**
+
+### Guides to Generate:
+
+1. **getting-started.md** (REQUIRED, ≥50 lines) - Installation, configuration, running
+2. **api-development.md** (if API exists) - API development guide with examples
+3. **deployment.md** (REQUIRED, ≥50 lines) - Deployment instructions
+4. **contributing.md** (REQUIRED, ≥30 lines) - Contribution guidelines
+5. **docs/api/README.md** (if API exists) - Complete API reference documentation
+
+### Template Variables:
+
+- \`{{PROJECT_NAME}}\` - From package.json
+- \`{{FRAMEWORK}}\` - Express, NestJS, etc.
+- \`{{TEST_FRAMEWORK}}\` - Jest, Vitest, Mocha
+- \`{{TEST_COMMAND}}\` - \`npm test\` or equivalent
+- \`{{BUILD_COMMAND}}\` - \`npm run build\` or equivalent
+- \`{{START_COMMAND}}\` - \`npm start\` or equivalent
+- \`{{DEPLOYMENT_PLATFORM}}\` - Vercel, AWS, Docker, etc.
+
+---
+
+## Fallback Mechanisms
+
+**If JUNO report incomplete** (\`global.trinity_docs_session.juno_incomplete === true\`):
+
+**Use discovery templates for direct analysis:**
+- 📄 **Framework Detection:** [trinity/templates/documentation/discovery/framework-detection.md](trinity/templates/documentation/discovery/framework-detection.md)
+- 📄 **API Endpoint Scanner:** [trinity/templates/documentation/discovery/api-endpoint-scanner.md](trinity/templates/documentation/discovery/api-endpoint-scanner.md)
+
+**Example Fallback:**
+\\\`\\\`\\\`javascript
+if (global.trinity_docs_session.juno_incomplete) {
+  LOG: "⚠️ FALLBACK MODE ACTIVATED";
+
+  // Detect test framework from package.json
+  const pkg = JSON.parse(Read('package.json'));
+  const test_framework = pkg.devDependencies?.jest ? "Jest" :
+                         pkg.devDependencies?.vitest ? "Vitest" :
+                         pkg.devDependencies?.mocha ? "Mocha" : "Unknown";
+
+  LOG: \\\`⚠️ FALLBACK: Detected test framework: \\\${test_framework}\\\`;
+}
+\\\`\\\`\\\`
+
+**See full fallback patterns in:**
+📄 **[trinity/templates/documentation/processes/apo-guide-specific.md](trinity/templates/documentation/processes/apo-guide-specific.md)** (lines 150-237)
+
+---
+
+## Template Processing
+
+**Read templates from:** \`trinity/templates/documentation/guides/\`
+
+**Process each template:**
+1. Read template content
+2. Replace all \`{{VARIABLES}}\` with values from JUNO report
+3. Check for unreplaced placeholders (quality issue)
+4. Write to output path
+
+**Example:**
+\\\`\\\`\\\`javascript
+const template = Read('trinity/templates/documentation/guides/getting-started.md');
+
+let output = template
+  .replace(/{{PROJECT_NAME}}/g, variables.PROJECT_NAME)
+  .replace(/{{FRAMEWORK}}/g, variables.FRAMEWORK)
+  .replace(/{{TEST_COMMAND}}/g, variables.TEST_COMMAND);
+
+// Check for unreplaced variables
+const unreplaced = output.match(/{{[A-Z_]+}}/g);
+if (unreplaced) {
+  WARNING: \\\`⚠️ Unreplaced variables in output: \\\${unreplaced.join(', ')}\\\`;
+}
+
+Write('docs/guides/getting-started.md', output);
+\\\`\\\`\\\`
+
+---
+
+## Self-Validation
+
+**Run comprehensive self-validation** after generating guides:
+
+📄 **[trinity/templates/documentation/validation/apo-self-validation.md](trinity/templates/documentation/validation/apo-self-validation.md)** - APO-2 Checklist
+
+**Key Checks:**
+- [ ] All expected guides created (4-5 files depending on project type)
+- [ ] File ≥50 lines minimum (getting-started, deployment)
+- [ ] File ≥30 lines minimum (contributing)
+- [ ] Contains ≥2 code blocks per guide
+- [ ] Zero placeholders (\`{{VARIABLE}}\`, \`[TODO]\`)
+- [ ] Internal links valid
+- [ ] Framework-specific examples accurate
+
+**See validation template for implementation:**
+📄 **[trinity/templates/documentation/validation/apo-self-validation.md](trinity/templates/documentation/validation/apo-self-validation.md)** (APO-2 validation code)
+
+---
+
+## Completion Summary
+
+**Return summary in this format:**
+
+\\\`\\\`\\\`
+APO-2: API Documentation & Guides Complete
+
+Files Created:
+- docs/guides/getting-started.md (62 lines, 3 code blocks)
+- docs/guides/api-development.md (78 lines, 5 code blocks)
+- docs/guides/deployment.md (54 lines, 4 code blocks)
+- docs/guides/contributing.md (32 lines)
+- docs/api/README.md (91 lines, 8 endpoints documented)
+
+Total: [N] guide files created
+
+Self-Validation: ✅ PASSED
+
+Fallback Usage: [Yes/No] ([Description if used])
+
+Status: Section B complete
+\\\`\\\`\\\`
+  \`
+});
+
+// APO Instance 3: Configuration Files
+Task({
+  subagent_type: "APO",
+  description: "Generate config files",
+  prompt: \`
+# APO-3: Configuration Files & Setup Documentation
+
+**Your Mission:** Generate .env.example and update README.md using templates and JUNO's audit report.
+
+**Agent Designation:** APO-3 (Section C)
+
+---
+
+## Workflow Overview
+
+Follow the **5-Phase APO Workflow** defined in:
+📄 **[trinity/templates/documentation/processes/apo-workflow-common.md](trinity/templates/documentation/processes/apo-workflow-common.md)**
+
+1. **Phase 1:** Read JUNO Report (\`global.trinity_docs_session.audit_report\`)
+2. **Phase 2:** Extract Template Variables (from Section C)
+3. **Phase 3:** Process Templates (generate .env.example and README updates)
+4. **Phase 4:** Write Files (to project root)
+5. **Phase 5:** Self-Validation (quality and security checks)
+
+---
+
+## Error Handling
+
+**Use 3-Tier Error System** defined in:
+📄 **[trinity/templates/documentation/processes/error-handling-protocol.md](trinity/templates/documentation/processes/error-handling-protocol.md)**
+
+- **Tier 1 (ABORT):** JUNO report missing, write permission denied, **SECURITY VIOLATION** (real secrets detected)
+- **Tier 2 (WARN):** No environment variables discovered, README.md doesn't exist
+- **Tier 3 (LOG):** Progress updates, file creation confirmations
+
+---
+
+## APO-3 Specific Tasks
+
+**See detailed instructions in:**
+📄 **[trinity/templates/documentation/processes/apo-config-specific.md](trinity/templates/documentation/processes/apo-config-specific.md)**
+
+### Files to Generate:
+
+1. **.env.example** (REQUIRED, ≥5 variables) - Environment variable template with **SAFE PLACEHOLDERS ONLY**
+2. **README.md** (REQUIRED, append/update) - Add Documentation, Configuration, Quick Start sections
+
+### Template Variables:
+
+- \`{{ENV_VARIABLES}}\` - List of environment variables from codebase
+- \`{{PORT}}\` - Default port number
+- \`{{DATABASE_URL}}\` - Database connection string pattern
+- \`{{PROJECT_NAME}}\` - From package.json
+- \`{{DESCRIPTION}}\` - Project description
+
+---
+
+## CRITICAL: Security Requirements
+
+**NEVER include real secrets in .env.example:**
+
+❌ **Forbidden:**
+- Real API keys, passwords, JWT secrets, database credentials
+- Production values, live keys, actual tokens
+
+✅ **Required:**
+- Safe placeholders: \`your_api_key_here\`, \`your_jwt_secret_here\`, \`change_in_production\`
+- Example values: \`example@email.com\`, \`http://localhost:3000\`, \`5432\`
+
+**Security Validation:**
+\\\`\\\`\\\`javascript
+const dangerous_patterns = [
+  /sk_live_[a-zA-Z0-9]+/,  // Stripe live keys
+  /AKIA[0-9A-Z]{16}/,      // AWS access keys
+  /AIza[0-9A-Za-z\\\\-_]{35}/,  // Google API keys
+  /[0-9a-f]{32}/,          // MD5 hashes (potential secrets)
+];
+
+const env_content = Read('.env.example');
+for (const pattern of dangerous_patterns) {
+  if (pattern.test(env_content)) {
+    ERROR: "❌ SECURITY VIOLATION - Real secrets detected in .env.example";
+    ERROR: "This is a CRITICAL error - must use safe placeholders only";
+    ABORT_COMMAND();
+  }
+}
+
+LOG: "✅ Security check passed: No real secrets in .env.example";
+\\\`\\\`\\\`
+
+**See full security validation in:**
+📄 **[trinity/templates/documentation/processes/apo-config-specific.md](trinity/templates/documentation/processes/apo-config-specific.md)** (lines 61-78)
+
+---
+
+## Fallback Mechanisms
+
+**If JUNO report incomplete** (\`global.trinity_docs_session.juno_incomplete === true\`):
+
+**Use discovery template for direct analysis:**
+- 📄 **Env Variable Extraction:** [trinity/templates/documentation/discovery/env-variable-extraction.md](trinity/templates/documentation/discovery/env-variable-extraction.md)
+
+**Example Fallback:**
+\\\`\\\`\\\`javascript
+if (global.trinity_docs_session.juno_incomplete) {
+  LOG: "⚠️ FALLBACK MODE ACTIVATED";
+
+  // Extract env variables from codebase
+  const env_files = ['.env', '.env.local', '.env.example'];
+  const discovered_vars = [];
+
+  for (const file of env_files) {
+    if (exists(file)) {
+      const content = Read(file);
+      const lines = content.split('\\\\n');
+      for (const line of lines) {
+        if (line.match(/^[A-Z_]+=/) {
+          const var_name = line.split('=')[0];
+          discovered_vars.push(var_name);
+        }
+      }
+    }
+  }
+
+  // Also search for process.env usage
+  const code_files = Glob('src/**/*.{ts,js}');
+  for (const file of code_files) {
+    const content = Read(file);
+    const matches = content.match(/process\\\\.env\\\\.([A-Z_]+)/g);
+    if (matches) {
+      for (const match of matches) {
+        const var_name = match.replace('process.env.', '');
+        if (!discovered_vars.includes(var_name)) {
+          discovered_vars.push(var_name);
+        }
+      }
+    }
+  }
+
+  LOG: \\\`⚠️ FALLBACK: Discovered \\\${discovered_vars.length} environment variables\\\`;
+}
+\\\`\\\`\\\`
+
+---
+
+## README.md Updates
+
+**IMPORTANT: Do NOT overwrite README.md - only append/update sections**
+
+**Sections to Add:**
+- \`## Documentation\` - Links to docs/guides/
+- \`## Configuration\` - Instructions for .env setup
+- \`## Quick Start\` - Fast getting started steps
+
+**Example:**
+\\\`\\\`\\\`javascript
+const readme_exists = exists('README.md');
+
+if (readme_exists) {
+  const existing_readme = Read('README.md');
+
+  // Check if sections already exist
+  if (!existing_readme.includes('## Documentation')) {
+    const documentation_section = \\\`
+## Documentation
+
+Complete documentation is available in the [\\\`docs/\\\`](docs/) directory:
+
+- [Getting Started Guide](docs/guides/getting-started.md)
+- [API Development](docs/guides/api-development.md)
+- [Deployment Guide](docs/guides/deployment.md)
+- [Contributing Guidelines](docs/guides/contributing.md)
+
+\\\`;
+
+    // Append sections to README
+    const updated_readme = existing_readme + '\\\\n' + documentation_section;
+    Write('README.md', updated_readme);
+
+    LOG: "✅ Updated README.md with documentation links";
+  } else {
+    LOG: "ℹ️ README.md already contains documentation section - skipping";
+  }
+} else {
+  WARNING: "⚠️ README.md doesn't exist - creating new README";
+  // Create minimal README with all sections
+}
+\\\`\\\`\\\`
+
+---
+
+## Self-Validation
+
+**Run comprehensive self-validation** after generating config files:
+
+📄 **[trinity/templates/documentation/validation/apo-self-validation.md](trinity/templates/documentation/validation/apo-self-validation.md)** - APO-3 Checklist
+
+**Key Checks:**
+- [ ] .env.example created with ≥5 variables (or all discovered)
+- [ ] Variables grouped by purpose (# comment headers)
+- [ ] All values are safe placeholders (no real secrets)
+- [ ] **SECURITY VALIDATED:** Zero real API keys, passwords, tokens
+- [ ] README.md updated (not overwritten)
+- [ ] Documentation section added with links
+- [ ] Configuration section added with .env instructions
+
+**See validation template for implementation:**
+📄 **[trinity/templates/documentation/validation/apo-self-validation.md](trinity/templates/documentation/validation/apo-self-validation.md)** (APO-3 validation code with security checks)
+
+---
+
+## Completion Summary
+
+**Return summary in this format:**
+
+\\\`\\\`\\\`
+APO-3: Configuration Files Complete
+
+Files Created/Updated:
+- .env.example (12 variables, grouped by purpose)
+- README.md (updated with Documentation, Configuration sections)
+
+Total: 2 files
+
+Self-Validation: ✅ PASSED
+Security Check: ✅ PASSED (zero real secrets)
+
+Fallback Usage: [Yes/No] ([Description if used])
+
+Status: Section C complete
+\\\`\\\`\\\`
+  \`
+});
+
+## Phase 3: Enhanced Verification (Rec 7)
+
+**Purpose:** Verify all documentation from checklist was created AND validate content quality
+
+### Step 3.1: Read JUNO's Audit Report
+
+```javascript
+LOG: "=== PHASE 3: ENHANCED VERIFICATION ===";
+LOG: "";
+LOG: "Reading JUNO's audit report to verify completeness...";
+LOG: "";
+
+// Track performance
+global.trinity_docs_session.performance_metrics.verification_start = Date.now();
+
+const audit_report = Read(audit_report_path);
+
+// Parse expected file counts from report
+let expected_diagrams = 0;
+let expected_guides = 0;
+let expected_api_docs = 0;
+let expected_config = 0;
+
+// Count "Required: YES" items in each section
+const section_a = audit_report.match(/SECTION A:.*?(?=SECTION B:)/s);
+const section_b = audit_report.match(/SECTION B:.*?(?=SECTION C:)/s);
+const section_c = audit_report.match(/SECTION C:.*$/s);
+
+if (section_a) {
+  expected_diagrams = (section_a[0].match(/Required: YES/g) || []).length;
+}
+
+if (section_b) {
+  const required_count = (section_b[0].match(/Required: YES/g) || []).length;
+  // Separate guides from API docs
+  expected_guides = required_count > 0 ? required_count - 1 : 0; // Assume 1 API doc + N guides
+  expected_api_docs = required_count > 0 ? 1 : 0;
+}
+
+if (section_c) {
+  expected_config = (section_c[0].match(/Required: YES/g) || []).length;
+}
+
+LOG: `Expected documentation:`;
+LOG: `  - Diagrams: ${expected_diagrams} files`;
+LOG: `  - Guides: ${expected_guides} files`;
+LOG: `  - API Docs: ${expected_api_docs} files`;
+LOG: `  - Config: ${expected_config} files`;
+LOG: `  - Total: ${expected_diagrams + expected_guides + expected_api_docs + expected_config} files`;
+LOG: "";
+```
+
+### Step 3.2: Verify File Creation (Tier 1: Completion)
+
+```javascript
+LOG: "=== TIER 1: FILE COMPLETION VERIFICATION ===";
+LOG: "";
+LOG: "Checking if all expected files were created...";
+LOG: "";
+
+// See trinity/templates/documentation/configuration/documentation-structure.md for verification patterns
+const diagram_files = Glob({pattern: "docs/images/*.md"});
+const guide_files = Glob({pattern: "docs/guides/*.md"});
+const api_doc_files = Glob({pattern: "docs/api/*.md"});
+
+const diagrams_ok = diagram_files.length === expected_diagrams;
+const guides_ok = guide_files.length === expected_guides;
+const api_docs_ok = api_doc_files.length === expected_api_docs;
+
+LOG: `Diagrams: ${diagram_files.length}/${expected_diagrams} ${diagrams_ok ? "✅" : "❌"}`;
+diagram_files.forEach(f => LOG: `  ✅ ${f}`);
+if (!diagrams_ok) ERROR: `❌ Diagram count mismatch: expected ${expected_diagrams}, got ${diagram_files.length}`;
+
+LOG: `Guides: ${guide_files.length}/${expected_guides} ${guides_ok ? "✅" : "❌"}`;
+guide_files.forEach(f => LOG: `  ✅ ${f}`);
+if (!guides_ok) ERROR: `❌ Guide count mismatch: expected ${expected_guides}, got ${guide_files.length}`;
+
+LOG: `API Docs: ${api_doc_files.length}/${expected_api_docs} ${api_docs_ok ? "✅" : "❌"}`;
+api_doc_files.forEach(f => LOG: `  ✅ ${f}`);
+
+if (!api_docs_ok) {
+  ERROR: "";
+  ERROR: `❌ API doc count mismatch: expected ${expected_api_docs}, got ${api_doc_files.length}`;
+}
+
+// Check config files
+const env_example_exists = Glob({pattern: "**/.env.example"}).length > 0;
+const config_ok = env_example_exists;
+
+LOG: `Config: ${config_ok ? "1/1" : "0/1"} ${config_ok ? "✅" : "❌"}`;
+if (env_example_exists) {
+  LOG: "  ✅ .env.example";
+}
+
+if (!config_ok) {
+  ERROR: "";
+  ERROR: "❌ .env.example file missing";
+}
+
+// Tier 1 overall
+const tier1_passed = diagrams_ok && guides_ok && api_docs_ok && config_ok;
+
+LOG: "";
+if (tier1_passed) {
+  LOG: "✅ TIER 1 (COMPLETION): PASSED";
+} else {
+  ERROR: "❌ TIER 1 (COMPLETION): FAILED";
+  ERROR: "";
+  ERROR: "Not all expected files were created.";
+  ERROR: "Review APO execution logs to identify failures.";
+  ERROR: "";
+  ABORT_COMMAND();
+}
+
+LOG: "";
+```
+
+### Step 3.3: Content Quality Verification (Tier 2)
+
+```javascript
+LOG: "=== TIER 2: CONTENT QUALITY VERIFICATION ===";
+LOG: "";
+
+const all_docs = [...diagram_files, ...guide_files, ...api_doc_files];
+
+const verification_issues = {
+  template_placeholders: [],
+  broken_links: [],
+  mermaid_errors: [],
+  short_content: [],
+  stub_content: [] // Rec 22: Stub content detection
+};
+
+// Check 1: Template Placeholder Detection
+LOG: "Checking for template placeholders ({{VARIABLE}} syntax)...";
+
+for (const file of all_docs) {
+  const content = Read(file);
+  const placeholders = content.match(/\{\{[^}]+\}\}/g);
+
+  if (placeholders) {
+    for (const ph of placeholders) {
+      verification_issues.template_placeholders.push({
+        file: file,
+        placeholder: ph
+      });
+    }
+  }
+}
+
+if (verification_issues.template_placeholders.length === 0) {
+  LOG: "  ✅ No template placeholders found";
+} else {
+  LOG: `  ❌ Found ${verification_issues.template_placeholders.length} template placeholders`;
+  for (const issue of verification_issues.template_placeholders) {
+    ERROR: `     ${issue.file}: ${issue.placeholder}`;
+  }
+}
+
+// Check 2: Internal Link Validation
+LOG: "";
+LOG: "Validating internal markdown links...";
+
+for (const file of all_docs) {
+  const content = Read(file);
+  const markdown_links = content.matchAll(/\[([^\]]+)\]\(([^)]+)\)/g);
+
+  for (const link of markdown_links) {
+    const link_text = link[1];
+    const link_target = link[2];
+
+    // Skip external links and anchors
+    if (link_target.startsWith('http') || link_target.startsWith('#')) {
+      continue;
+    }
+
+    // Resolve relative path
+    const file_dir = file.split('/').slice(0, -1).join('/');
+    let resolved_path = link_target;
+
+    // Handle ../
+    if (link_target.startsWith('../')) {
+      const parts = link_target.split('/');
+      const up_levels = parts.filter(p => p === '..').length;
+      const dir_parts = file_dir.split('/');
+      const base = dir_parts.slice(0, dir_parts.length - up_levels).join('/');
+      const rest = parts.filter(p => p !== '..').join('/');
+      resolved_path = base + '/' + rest;
+    } else if (link_target.startsWith('./')) {
+      resolved_path = file_dir + '/' + link_target.slice(2);
+    } else if (!link_target.startsWith('/')) {
+      resolved_path = file_dir + '/' + link_target;
+    } else {
+      resolved_path = link_target.slice(1); // Remove leading /
+    }
+
+    // Check if target exists
+    if (!exists(resolved_path)) {
+      verification_issues.broken_links.push({
+        file: file,
+        link_text: link_text,
+        target: link_target,
+        resolved: resolved_path
+      });
+    }
+  }
+}
+
+if (verification_issues.broken_links.length === 0) {
+  LOG: "  ✅ All internal links valid";
+} else {
+  LOG: `  ❌ Found ${verification_issues.broken_links.length} broken links`;
+  for (const issue of verification_issues.broken_links) {
+    ERROR: `     ${issue.file}: [${issue.link_text}](${issue.target}) -> ${issue.resolved} (NOT FOUND)`;
+  }
+}
+
+// Check 3: Mermaid Syntax Validation
+LOG: "";
+LOG: "Validating Mermaid diagram syntax...";
+
+for (const file of diagram_files) {
+  const content = Read(file);
+  const mermaid_match = content.match(/```mermaid([\s\S]+?)```/);
+
+  if (!mermaid_match) {
+    verification_issues.mermaid_errors.push({
+      file: file,
+      error: "No Mermaid code block found (missing ```mermaid)"
+    });
+    continue;
+  }
+
+  const mermaid_block = mermaid_match[1].trim();
+
+  // Validate diagram type
+  const valid_types = ['graph', 'flowchart', 'sequenceDiagram', 'erDiagram', 'classDiagram', 'stateDiagram', 'journey', 'gantt'];
+  const has_valid_type = valid_types.some(type => mermaid_block.startsWith(type));
+
+  if (!has_valid_type) {
+    verification_issues.mermaid_errors.push({
+      file: file,
+      error: `Invalid diagram type. Must start with one of: ${valid_types.join(', ')}`
+    });
+    continue;
+  }
+
+  // Check for minimum content
+  if (mermaid_block.length < 50) {
+    verification_issues.mermaid_errors.push({
+      file: file,
+      error: `Mermaid block too short (${mermaid_block.length} chars, expected 50+)`
+    });
+    continue;
+  }
+
+  // Check for placeholders in Mermaid
+  if (mermaid_block.includes("{{") || mermaid_block.includes("[Add ") || mermaid_block.includes("[Define ")) {
+    verification_issues.mermaid_errors.push({
+      file: file,
+      error: "Mermaid block contains placeholders or incomplete syntax"
+    });
+    continue;
+  }
+}
+
+if (verification_issues.mermaid_errors.length === 0) {
+  LOG: "  ✅ All Mermaid diagrams valid";
+} else {
+  LOG: `  ❌ Found ${verification_issues.mermaid_errors.length} Mermaid errors`;
+  for (const issue of verification_issues.mermaid_errors) {
+    ERROR: `     ${issue.file}: ${issue.error}`;
+  }
+}
+
+// Check 4: Content Length (short files may indicate incomplete generation)
+LOG: "";
+LOG: "Checking content length...";
+
+for (const file of all_docs) {
+  const content = Read(file);
+  const min_length = file.includes('/images/') ? 100 : 200; // Diagrams can be shorter
+
+  if (content.length < min_length) {
+    verification_issues.short_content.push({
+      file: file,
+      length: content.length,
+      expected: min_length
+    });
+  }
+}
+
+if (verification_issues.short_content.length === 0) {
+  LOG: "  ✅ All files have substantial content";
+} else {
+  LOG: `  ⚠️ Found ${verification_issues.short_content.length} short files`;
+  for (const issue of verification_issues.short_content) {
+    WARNING: `     ${issue.file}: ${issue.length} chars (expected ${issue.expected}+)`;
+  }
+}
+
+// Check 5: Stub Content Detection (Rec 22)
+LOG: "";
+LOG: "Checking for stub content (coming soon, TODO, etc.)...";
+
+verification_issues.stub_content = [];
+
+const stub_patterns = [
+  /coming soon/gi,
+  /to be added/gi,
+  /will be added/gi,
+  /\[TODO\]/gi,
+  /\[TBD\]/gi,
+  /to be documented/gi,
+  /see .* \(coming soon\)/gi,
+  /placeholder/gi,
+  /under construction/gi,
+  /work in progress/gi
+];
+
+for (const file of all_docs) {
+  const content = Read(file);
+
+  for (const pattern of stub_patterns) {
+    const matches = content.match(pattern);
+    if (matches) {
+      // Check if stub content is in acceptable context (Future Enhancements section)
+      const has_future_section = content.match(/##+ Future Enhancements|##+ Roadmap|##+ Coming Soon/i);
+
+      // If stub content found, check context
+      let in_future_section = false;
+      if (has_future_section) {
+        // Simple heuristic: check if match is after Future Enhancements heading
+        const future_section_index = content.search(/##+ Future Enhancements|##+ Roadmap|##+ Coming Soon/i);
+        const match_index = content.search(pattern);
+        in_future_section = match_index > future_section_index;
+      }
+
+      if (!in_future_section) {
+        verification_issues.stub_content.push({
+          file: file,
+          pattern: matches[0],
+          context: content.substring(Math.max(0, content.search(pattern) - 50), Math.min(content.length, content.search(pattern) + 100))
+        });
+      }
+    }
+  }
+}
+
+if (verification_issues.stub_content.length === 0) {
+  LOG: "  ✅ No stub content detected";
+} else {
+  LOG: `  ❌ Found ${verification_issues.stub_content.length} instances of stub content`;
+  for (const issue of verification_issues.stub_content) {
+    ERROR: `     ${issue.file}: "${issue.pattern}"`;
+  }
+}
+
+// Rec 16: Fail-Fast Logic - ABORT immediately on first critical failure
+// Check each issue type and ABORT with specific error messages
+
+LOG: "";
+
+// Check 1: Template Placeholders (CRITICAL)
+if (verification_issues.template_placeholders.length > 0) {
+  ERROR: "";
+  ERROR: "╔════════════════════════════════════════════════════════════╗";
+  ERROR: "║  ❌ CRITICAL FAILURE: TEMPLATE PLACEHOLDERS DETECTED     ║";
+  ERROR: "╚════════════════════════════════════════════════════════════╝";
+  ERROR: "";
+  ERROR: `Found ${verification_issues.template_placeholders.length} unreplaced template variables in documentation:`;
+  ERROR: "";
+  for (const issue of verification_issues.template_placeholders) {
+    ERROR: `  File: ${issue.file}`;
+    ERROR: `  Placeholder: ${issue.placeholder}`;
+    ERROR: "";
+  }
+  ERROR: "ROOT CAUSE ANALYSIS:";
+  ERROR: "  1. APO did not replace all {{VARIABLE}} placeholders";
+  ERROR: "  2. JUNO report may have incomplete variable values";
+  ERROR: "  3. Template files may have undocumented variables";
+  ERROR: "";
+  ERROR: "RESOLUTION:";
+  ERROR: "  - Check JUNO report for missing variable values";
+  ERROR: "  - Verify APO read and processed JUNO report correctly";
+  ERROR: "  - Ensure templates use only documented variables";
+  ERROR: "";
+  ERROR: "Documentation generation ABORTED - placeholders must be resolved.";
+  ERROR: "";
+  ABORT_COMMAND();
+}
+
+// Check 2: Broken Links (CRITICAL)
+if (verification_issues.broken_links.length > 0) {
+  ERROR: "";
+  ERROR: "╔════════════════════════════════════════════════════════════╗";
+  ERROR: "║  ❌ CRITICAL FAILURE: BROKEN LINKS DETECTED              ║";
+  ERROR: "╚════════════════════════════════════════════════════════════╝";
+  ERROR: "";
+  ERROR: `Found ${verification_issues.broken_links.length} broken internal links in documentation:`;
+  ERROR: "";
+  for (const issue of verification_issues.broken_links) {
+    ERROR: `  File: ${issue.file}`;
+    ERROR: `  Link: [${issue.link_text}](${issue.target})`;
+    ERROR: `  Resolved Path: ${issue.resolved}`;
+    ERROR: `  Status: NOT FOUND`;
+    ERROR: "";
+  }
+  ERROR: "ROOT CAUSE ANALYSIS:";
+  ERROR: "  1. APO created links to files that don't exist";
+  ERROR: "  2. JUNO report listed files that APO didn't create";
+  ERROR: "  3. File paths in documentation don't match actual structure";
+  ERROR: "";
+  ERROR: "RESOLUTION:";
+  ERROR: "  - Verify all expected files were created by APOs";
+  ERROR: "  - Check JUNO report file paths match actual output paths";
+  ERROR: "  - Ensure APO-3 README validation passed";
+  ERROR: "";
+  ERROR: "Documentation generation ABORTED - broken links unacceptable.";
+  ERROR: "";
+  ABORT_COMMAND();
+}
+
+// Check 3: Mermaid Syntax Errors (CRITICAL)
+if (verification_issues.mermaid_errors.length > 0) {
+  ERROR: "";
+  ERROR: "╔════════════════════════════════════════════════════════════╗";
+  ERROR: "║  ❌ CRITICAL FAILURE: INVALID MERMAID SYNTAX            ║";
+  ERROR: "╚════════════════════════════════════════════════════════════╝";
+  ERROR: "";
+  ERROR: `Found ${verification_issues.mermaid_errors.length} Mermaid syntax errors in diagrams:`;
+  ERROR: "";
+  for (const issue of verification_issues.mermaid_errors) {
+    ERROR: `  File: ${issue.file}`;
+    ERROR: `  Error: ${issue.error}`;
+    ERROR: "";
+  }
+  ERROR: "ROOT CAUSE ANALYSIS:";
+  ERROR: "  1. APO-1 generated invalid Mermaid syntax";
+  ERROR: "  2. Template files contain invalid Mermaid structure";
+  ERROR: "  3. JUNO report provided malformed data for diagrams";
+  ERROR: "";
+  ERROR: "RESOLUTION:";
+  ERROR: "  - Verify templates have valid Mermaid syntax";
+  ERROR: "  - Check JUNO report entity/relationship data is well-formed";
+  ERROR: "  - Ensure APO-1 self-validation caught this before completion";
+  ERROR: "";
+  ERROR: "Documentation generation ABORTED - invalid diagrams unacceptable.";
+  ERROR: "";
+  ABORT_COMMAND();
+}
+
+// Check 4: Stub Content (CRITICAL) - Rec 22
+if (verification_issues.stub_content.length > 0) {
+  ERROR: "";
+  ERROR: "╔════════════════════════════════════════════════════════════╗";
+  ERROR: "║  ❌ CRITICAL FAILURE: STUB CONTENT DETECTED              ║";
+  ERROR: "╚════════════════════════════════════════════════════════════╝";
+  ERROR: "";
+  ERROR: `Found ${verification_issues.stub_content.length} instances of stub content in documentation:`;
+  ERROR: "";
+  for (const issue of verification_issues.stub_content) {
+    ERROR: `  File: ${issue.file}`;
+    ERROR: `  Pattern: "${issue.pattern}"`;
+    ERROR: `  Context: ${issue.context.substring(0, 100)}...`;
+    ERROR: "";
+  }
+  ERROR: "ROOT CAUSE ANALYSIS:";
+  ERROR: "  1. APO-2 generated incomplete documentation with placeholder text";
+  ERROR: "  2. JUNO report provided insufficient data for complete documentation";
+  ERROR: "  3. Documentation was rushed and contains 'TODO' or 'coming soon' markers";
+  ERROR: "";
+  ERROR: "RESOLUTION:";
+  ERROR: "  - Ensure JUNO report provides complete, actionable data";
+  ERROR: "  - Verify APO-2 completes all documentation sections";
+  ERROR: "  - Remove all stub content - documentation must be production-ready";
+  ERROR: "  - Only 'Future Enhancements' sections may reference future features";
+  ERROR: "";
+  ERROR: "Documentation generation ABORTED - stub content unacceptable for production.";
+  ERROR: "";
+  ABORT_COMMAND();
+}
+
+// Check 5: Short Content (WARNING only - not critical)
+if (verification_issues.short_content.length > 0) {
+  WARNING: "";
+  WARNING: `⚠️ WARNING: ${verification_issues.short_content.length} files have minimal content`;
+  for (const issue of verification_issues.short_content) {
+    WARNING: `  ${issue.file}: ${issue.length} chars (expected ${issue.expected}+)`;
+  }
+  WARNING: "";
+  WARNING: "This may indicate incomplete documentation but does not block generation.";
+  WARNING: "";
+}
+
+// All Tier 2 checks passed
+LOG: "✅ TIER 2 (CONTENT QUALITY): PASSED - No critical issues detected";
+LOG: "";
+```
+
+### Step 3.4: Accuracy Verification (Tier 3 - Warnings Only)
+
+```javascript
+LOG: "=== TIER 3: ACCURACY VERIFICATION (NON-BLOCKING) ===";
+LOG: "";
+
+const accuracy_warnings = [];
+
+// Check 1: API Endpoint Count Accuracy (Rec 14: Enhanced Regex Patterns)
+LOG: "Checking API endpoint count accuracy...";
+
+// Count documented endpoints in API docs (using multiple patterns)
+let documented_endpoint_count = 0;
+if (api_doc_files.length > 0) {
+  const api_content = Read(api_doc_files[0]);
+
+  // Rec 14: Multiple endpoint detection patterns
+  const endpoint_patterns = [
+    // Markdown list format: - GET /api/users
+    /^[-*]\s+(GET|POST|PUT|PATCH|DELETE)\s+\/[^\s\n]+/gm,
+    // Direct format: GET /api/users
+    /^(GET|POST|PUT|PATCH|DELETE)\s+\/[^\s\n]+/gm,
+    // Heading format: ### GET /api/users
+    /^#{1,6}\s+(GET|POST|PUT|PATCH|DELETE)\s+\/[^\s\n]+/gm,
+    // Bold format: **GET /api/users**
+    /\*\*(GET|POST|PUT|PATCH|DELETE)\s+\/[^\s\n]+\*\*/gm,
+    // Code format: `GET /api/users`
+    /`(GET|POST|PUT|PATCH|DELETE)\s+\/[^\s\n]+`/gm
+  ];
+
+  const found_endpoints = new Set();
+
+  for (const pattern of endpoint_patterns) {
+    const matches = api_content.matchAll(pattern);
+    for (const match of matches) {
+      // Extract method and path
+      const full_match = match[0];
+      const method_match = full_match.match(/(GET|POST|PUT|PATCH|DELETE)/);
+      const path_match = full_match.match(/\/[^\s\n`*]+/);
+
+      if (method_match && path_match) {
+        const endpoint_key = `${method_match[0]} ${path_match[0]}`;
+        found_endpoints.add(endpoint_key);
+      }
+    }
+  }
+
+  documented_endpoint_count = found_endpoints.size;
+
+  LOG: `  Detection patterns used: ${endpoint_patterns.length}`;
+  LOG: `  Unique endpoints found: ${documented_endpoint_count}`;
+}
+
+// Count actual endpoints in codebase
+const route_patterns = [
+  "server/routes/**/*.{ts,js}",
+  "src/routes/**/*.{ts,js}",
+  "api/**/*.{ts,js}",
+  "server/api/**/*.{ts,js}"
+];
+
+let actual_endpoint_count = 0;
+for (const pattern of route_patterns) {
+  const route_files = Glob({pattern: pattern});
+
+  for (const route_file of route_files) {
+    const content = Read(route_file);
+    const http_methods = ['get', 'post', 'put', 'patch', 'delete'];
+
+    for (const method of http_methods) {
+      const regex = new RegExp(`\\.(${method})\\(['"\`]([^'"\`]+)['"\`]`, 'g');
+      const matches = content.match(regex);
+      actual_endpoint_count += matches ? matches.length : 0;
+    }
+  }
+}
+
+const endpoint_diff = Math.abs(documented_endpoint_count - actual_endpoint_count);
+
+// Rec 14: Increased tolerance from ±1 to ±5 (reduces false warnings)
+if (endpoint_diff > 5) {
+  accuracy_warnings.push({
+    severity: "MEDIUM",
+    category: "API Documentation",
+    issue: `Endpoint count mismatch: documented ${documented_endpoint_count}, actual ${actual_endpoint_count} (diff: ${endpoint_diff})`
+  });
+}
+
+LOG: `  Documented endpoints: ${documented_endpoint_count}`;
+LOG: `  Actual endpoints: ${actual_endpoint_count}`;
+LOG: `  Difference: ${endpoint_diff} ${endpoint_diff <= 5 ? "✅" : "⚠️"} (tolerance: ±5)`;
+
+// Check 2: Component Count Accuracy (if frontend detected)
+LOG: "";
+LOG: "Checking component count accuracy...";
+
+// Count components mentioned in component hierarchy diagram
+let documented_component_count = 0;
+const component_diagrams = diagram_files.filter(f => f.includes('component-hierarchy'));
+
+if (component_diagrams.length > 0) {
+  const diagram_content = Read(component_diagrams[0]);
+  // Count nodes in Mermaid flowchart (rough estimate)
+  const node_matches = diagram_content.match(/[A-Z][a-zA-Z0-9_]+(?=\[|-->)/g);
+  documented_component_count = node_matches ? new Set(node_matches).size : 0;
+}
+
+// Count actual component files
+const component_patterns = [
+  "client/**/*.{tsx,jsx}",
+  "src/**/*.{tsx,jsx}",
+  "client/**/*.vue",
+  "src/**/*.vue"
+];
+
+let actual_component_count = 0;
+for (const pattern of component_patterns) {
+  const files = Glob({pattern: pattern});
+  // Filter out test files, main files, index files
+  const actual = files.filter(f =>
+    !f.includes('.test.') &&
+    !f.includes('.spec.') &&
+    !f.endsWith('main.tsx') &&
+    !f.endsWith('index.tsx')
+  );
+  actual_component_count += actual.length;
+}
+
+const component_diff = Math.abs(documented_component_count - actual_component_count);
+
+if (component_diff > 2) {
+  accuracy_warnings.push({
+    severity: "LOW",
+    category: "Component Documentation",
+    issue: `Component count mismatch: documented ${documented_component_count}, actual ${actual_component_count} (diff: ${component_diff})`
+  });
+}
+
+LOG: `  Documented components: ${documented_component_count}`;
+LOG: `  Actual components: ${actual_component_count}`;
+LOG: `  Difference: ${component_diff} ${component_diff <= 2 ? "✅" : "⚠️"}`;
+
+// Check 3: Testing Framework Accuracy
+LOG: "";
+LOG: "Checking testing framework accuracy...";
+
+// Check what's mentioned in getting-started guide
+let documented_framework = "None";
+const getting_started = guide_files.find(f => f.includes('getting-started'));
+
+if (getting_started) {
+  const guide_content = Read(getting_started);
+
+  if (guide_content.includes("Jest")) {
+    documented_framework = "Jest";
+  } else if (guide_content.includes("Vitest")) {
+    documented_framework = "Vitest";
+  } else if (guide_content.includes("Mocha")) {
+    documented_framework = "Mocha";
+  }
+}
+
+// Detect actual testing framework
+let actual_framework = "None";
+const pkg = JSON.parse(Read("package.json"));
+
+if (pkg.devDependencies?.jest || pkg.dependencies?.jest) {
+  actual_framework = "Jest";
+} else if (pkg.devDependencies?.vitest || pkg.dependencies?.vitest) {
+  actual_framework = "Vitest";
+} else if (pkg.devDependencies?.mocha || pkg.dependencies?.mocha) {
+  actual_framework = "Mocha";
+}
+
+if (documented_framework !== actual_framework) {
+  accuracy_warnings.push({
+    severity: "HIGH",
+    category: "Testing Framework",
+    issue: `Framework mismatch: documented "${documented_framework}", actual "${actual_framework}"`
+  });
+}
+
+LOG: `  Documented framework: ${documented_framework}`;
+LOG: `  Actual framework: ${actual_framework}`;
+LOG: `  Match: ${documented_framework === actual_framework ? "✅" : "⚠️"}`;
+
+// Tier 3 Summary
+LOG: "";
+if (accuracy_warnings.length === 0) {
+  LOG: "✅ TIER 3 (ACCURACY): PASSED - No inaccuracies detected";
+} else {
+  WARNING: "";
+  WARNING: `⚠️ TIER 3 (ACCURACY): ${accuracy_warnings.length} WARNINGS`;
+  WARNING: "";
+  WARNING: "Documentation contains minor inaccuracies (non-blocking):";
+  for (const warning of accuracy_warnings) {
+    WARNING: `   [${warning.severity}] ${warning.category}: ${warning.issue}`;
+  }
+  WARNING: "";
+  WARNING: "These do not block deployment but should be reviewed.";
+  WARNING: "";
+}
+
+LOG: "";
+```
+
+### Step 3.5: Generate Verification Report
+
+```javascript
+LOG: "Generating verification report...";
+LOG: "";
+
+const timestamp = new Date().toISOString().replace(/[:.]/g, '-').slice(0, -5);
+const report_path = `trinity/reports/VERIFICATION-REPORT-${timestamp}.md`;
+
+// Rec 15: Performance timing variables (estimated for individual phases)
+const apo1_time = "N/A"; // Individual APO times not tracked (parallel execution)
+const apo2_time = "N/A";
+const apo3_time = "N/A";
+const tier1_time = "~1s"; // Estimated based on typical execution
+const tier2_time = "~2s";
+const tier3_time = "~1s";
+const tier4_time = "~0.5s";
+const juno_files_analyzed = "Unknown"; // Would need to parse from JUNO report
+
+// Calculate quality score
+const tier1_score = tier1_passed ? 40 : 0;
+const tier2_score = tier2_critical_issues === 0 ? 40 : 0;
+
+// Tier 3: 15 points, deduct based on severity
+let tier3_score = 15;
+for (const warning of accuracy_warnings) {
+  if (warning.severity === "HIGH") tier3_score -= 5;
+  else if (warning.severity === "MEDIUM") tier3_score -= 3;
+  else tier3_score -= 1;
+}
+tier3_score = Math.max(0, tier3_score);
+
+// Tier 4: Excellence (Rec 23: Automated Readability Scoring)
+let tier4_score = 0;
+const tier4_checks = {
+  code_examples: 0,
+  clear_explanations: 0,
+  step_by_step: 0,
+  api_examples: 0,
+  professional_presentation: 0
+};
+
+// Check 1: Code Examples (count code blocks in guides)
+let total_code_blocks = 0;
+for (const file of guide_files) {
+  const content = Read(file);
+  const code_blocks = (content.match(/\`\`\`/g) || []).length / 2; // Each block has opening and closing
+  total_code_blocks += code_blocks;
+}
+if (total_code_blocks >= guide_files.length * 2) {
+  tier4_checks.code_examples = 1; // Average 2+ code blocks per guide
+  tier4_score += 1;
+}
+
+// Check 2: Clear Explanations (check average paragraph length - 50-200 chars is optimal)
+let paragraph_lengths = [];
+for (const file of guide_files) {
+  const content = Read(file);
+  const paragraphs = content.split('\n\n').filter(p => p.trim().length > 0 && !p.startsWith('#') && !p.startsWith('```'));
+  for (const para of paragraphs) {
+    paragraph_lengths.push(para.length);
+  }
+}
+if (paragraph_lengths.length > 0) {
+  const avg_length = paragraph_lengths.reduce((a, b) => a + b, 0) / paragraph_lengths.length;
+  if (avg_length >= 50 && avg_length <= 300) {
+    tier4_checks.clear_explanations = 1; // Optimal paragraph length
+    tier4_score += 1;
+  }
+}
+
+// Check 3: Step-by-Step Instructions (count numbered/bulleted lists)
+let total_steps = 0;
+for (const file of guide_files) {
+  const content = Read(file);
+  const numbered_steps = (content.match(/^\d+\./gm) || []).length;
+  const bulleted_steps = (content.match(/^- /gm) || []).length;
+  total_steps += numbered_steps + bulleted_steps;
+}
+if (total_steps >= guide_files.length * 5) {
+  tier4_checks.step_by_step = 1; // Average 5+ steps per guide
+  tier4_score += 1;
+}
+
+// Check 4: Complete API Documentation (examples per endpoint)
+if (api_doc_files.length > 0) {
+  let api_code_examples = 0;
+  for (const file of api_doc_files) {
+    const content = Read(file);
+    api_code_examples += (content.match(/\`\`\`/g) || []).length / 2;
+  }
+
+  // Estimate endpoints from JUNO report
+  const juno_report = Read(audit_report_path);
+  const endpoint_match = juno_report.match(/API Endpoints?:\s*(\d+)/i);
+  const endpoint_count = endpoint_match ? parseInt(endpoint_match[1]) : 10; // Default to 10 if not found
+
+  if (api_code_examples >= endpoint_count * 0.5) {
+    tier4_checks.api_examples = 1; // At least 50% of endpoints have examples
+    tier4_score += 1;
+  }
+}
+
+// Check 5: Professional Presentation (consistent heading structure)
+let consistent_headings = true;
+for (const file of all_docs) {
+  const content = Read(file);
+  const h1_count = (content.match(/^# /gm) || []).length;
+  const h2_count = (content.match(/^## /gm) || []).length;
+
+  // Each document should have exactly 1 H1 and at least 2 H2s
+  if (h1_count !== 1 || h2_count < 2) {
+    consistent_headings = false;
+    break;
+  }
+}
+if (consistent_headings) {
+  tier4_checks.professional_presentation = 1;
+  tier4_score += 1;
+}
+
+// Final tier4 score (max 5)
+tier4_score = Math.min(5, tier4_score);
+
+const total_score = tier1_score + tier2_score + tier3_score + tier4_score;
+
+let grade = "";
+if (total_score >= 95) grade = "Excellent (Production Ready)";
+else if (total_score >= 85) grade = "Good (Minor improvements recommended)";
+else if (total_score >= 70) grade = "Acceptable (Requires review and fixes)";
+else grade = "Poor (Significant issues, re-generation recommended)";
+
+// Build report
+let report = `# Trinity Documentation Verification Report
+
+**Generated:** ${new Date().toISOString()}
+**JUNO Report:** ${audit_report_path}
+
+---
+
+## Executive Summary
+
+**Overall Quality Score:** ${total_score}/100
+**Grade:** ${grade}
+
+**Completion:** ${tier1_passed ? "✅ PASSED" : "❌ FAILED"}
+**Content Quality:** ${tier2_critical_issues === 0 ? "✅ PASSED" : "❌ FAILED"}
+**Accuracy:** ${accuracy_warnings.length === 0 ? "✅ PASSED" : `⚠️ ${accuracy_warnings.length} WARNINGS`}
+
+---
+
+## Score Breakdown (Rec 17: Detailed Scoring)
+
+### Tier 1: Completion (${tier1_score}/40)
+
+**Scoring Formula:** All files created = 40 points | Any file missing = 0 points
+
+${tier1_passed ? "✅ All expected files created" : "❌ Some files missing"}
+
+**File Checklist:**
+- Diagrams: ${diagram_files.length}/${expected_diagrams} ${diagrams_ok ? "✅" : "❌"}
+  ${diagram_files.map(f => `  - ${f}`).join('\n')}
+- Guides: ${guide_files.length}/${expected_guides} ${guides_ok ? "✅" : "❌"}
+  ${guide_files.map(f => `  - ${f}`).join('\n')}
+- API Docs: ${api_doc_files.length}/${expected_api_docs} ${api_docs_ok ? "✅" : "❌"}
+  ${api_doc_files.map(f => `  - ${f}`).join('\n')}
+- Config: ${config_ok ? "1/1" : "0/1"} ${config_ok ? "✅" : "❌"}
+  ${config_ok ? "  - .env.example" : "  - (missing)"}
+
+**Total Files Created:** ${all_docs.length + (config_ok ? 1 : 0)}
+
+**Result:** ${tier1_score === 40 ? "PASSED - All files present" : "FAILED - Missing files detected"}
+
+### Tier 2: Content Quality (${tier2_score}/40)
+
+**Scoring Formula:** No critical issues = 40 points | Any critical issue = 0 points (fail-fast)
+
+${tier2_critical_issues === 0 ? "✅ All quality checks passed" : `❌ ${tier2_critical_issues} critical issues`}
+
+**Detailed Results:**
+1. **Template Placeholders** (CRITICAL): ${verification_issues.template_placeholders.length} ${verification_issues.template_placeholders.length === 0 ? "✅ PASS" : "❌ FAIL"}
+   - Requirement: Zero placeholders ({{VARIABLE}}) in output
+   - Found: ${verification_issues.template_placeholders.length} instances
+   ${verification_issues.template_placeholders.length > 0 ? verification_issues.template_placeholders.map(i => `   - ${i.file}: ${i.placeholder}`).join('\n') : ""}
+
+2. **Internal Link Validation** (CRITICAL): ${verification_issues.broken_links.length} ${verification_issues.broken_links.length === 0 ? "✅ PASS" : "❌ FAIL"}
+   - Requirement: All links must reference existing files
+   - Found: ${verification_issues.broken_links.length} broken links
+   ${verification_issues.broken_links.length > 0 ? verification_issues.broken_links.map(i => `   - ${i.file}: [${i.link_text}](${i.target})`).join('\n') : ""}
+
+3. **Mermaid Syntax Validation** (CRITICAL): ${verification_issues.mermaid_errors.length} ${verification_issues.mermaid_errors.length === 0 ? "✅ PASS" : "❌ FAIL"}
+   - Requirement: Valid Mermaid syntax with proper diagram types
+   - Found: ${verification_issues.mermaid_errors.length} syntax errors
+   ${verification_issues.mermaid_errors.length > 0 ? verification_issues.mermaid_errors.map(i => `   - ${i.file}: ${i.error}`).join('\n') : ""}
+
+4. **Stub Content Detection** (CRITICAL): ${verification_issues.stub_content ? verification_issues.stub_content.length : 0} ${(verification_issues.stub_content ? verification_issues.stub_content.length : 0) === 0 ? "✅ PASS" : "❌ FAIL"}
+   - Requirement: No "coming soon", "TODO", or stub content
+   - Found: ${verification_issues.stub_content ? verification_issues.stub_content.length : 0} instances
+   ${verification_issues.stub_content && verification_issues.stub_content.length > 0 ? verification_issues.stub_content.map(i => `   - ${i.file}: "${i.pattern}"`).join('\n') : ""}
+
+5. **Content Length** (WARNING): ${verification_issues.short_content.length} ${verification_issues.short_content.length === 0 ? "✅ PASS" : "⚠️ WARN"}
+   - Requirement: Substantial content (diagrams ≥100 chars, docs ≥200 chars)
+   - Found: ${verification_issues.short_content.length} short files (non-blocking)
+
+**Result:** ${tier2_score === 40 ? "PASSED - No critical issues" : "FAILED - Critical quality issues detected"}
+
+### Tier 3: Accuracy (${tier3_score}/15)
+
+**Scoring Formula:** 15 points base | -5 per HIGH severity | -3 per MEDIUM | -1 per LOW (min 0)
+
+${accuracy_warnings.length === 0 ? "✅ No inaccuracies detected" : `⚠️ ${accuracy_warnings.length} warnings (non-blocking)`}
+
+**Scoring Breakdown:**
+- Base Score: 15 points
+${accuracy_warnings.length > 0 ? accuracy_warnings.map(w => `- Deduction: -${w.severity === 'HIGH' ? 5 : w.severity === 'MEDIUM' ? 3 : 1} (${w.severity}) ${w.category}: ${w.issue}`).join('\n') : "- No deductions"}
+- **Final Score: ${tier3_score}/15**
+
+**Warnings:**
+${accuracy_warnings.length > 0 ? accuracy_warnings.map(w => `- [${w.severity}] ${w.category}: ${w.issue}`).join('\n') : "None"}
+
+**Result:** ${tier3_score >= 12 ? "GOOD" : tier3_score >= 8 ? "ACCEPTABLE" : "NEEDS REVIEW"}
+
+### Tier 4: Excellence (${tier4_score}/5) - Rec 23: Automated Readability Scoring
+
+**Scoring Criteria (Automated):**
+1. **Comprehensive Code Examples** (1 point): ${tier4_checks.code_examples ? "✅ PASS" : "❌ FAIL"}
+   - Requirement: Average 2+ code blocks per guide
+   - Found: ${(total_code_blocks / Math.max(1, guide_files.length)).toFixed(1)} blocks per guide
+   - Result: ${tier4_checks.code_examples ? "+1 point" : "+0 points"}
+
+2. **Clear Explanations** (1 point): ${tier4_checks.clear_explanations ? "✅ PASS" : "❌ FAIL"}
+   - Requirement: Optimal paragraph length (50-300 chars)
+   - Average: ${paragraph_lengths.length > 0 ? (paragraph_lengths.reduce((a, b) => a + b, 0) / paragraph_lengths.length).toFixed(0) + " chars" : "N/A"}
+   - Result: ${tier4_checks.clear_explanations ? "+1 point" : "+0 points"}
+
+3. **Step-by-Step Instructions** (1 point): ${tier4_checks.step_by_step ? "✅ PASS" : "❌ FAIL"}
+   - Requirement: Average 5+ steps/lists per guide
+   - Found: ${(total_steps / Math.max(1, guide_files.length)).toFixed(1)} steps per guide
+   - Result: ${tier4_checks.step_by_step ? "+1 point" : "+0 points"}
+
+4. **Complete API Documentation** (1 point): ${tier4_checks.api_examples ? "✅ PASS" : "❌ FAIL"}
+   - Requirement: ≥50% of endpoints have code examples
+   - Found: ${api_doc_files.length > 0 ? (api_code_examples + " examples for ~" + endpoint_count + " endpoints") : "No API docs"}
+   - Result: ${tier4_checks.api_examples ? "+1 point" : "+0 points"}
+
+5. **Professional Presentation** (1 point): ${tier4_checks.professional_presentation ? "✅ PASS" : "❌ FAIL"}
+   - Requirement: Consistent heading structure (1 H1, 2+ H2s per doc)
+   - Result: ${tier4_checks.professional_presentation ? "✅ Consistent" : "❌ Inconsistent"}
+   - Result: ${tier4_checks.professional_presentation ? "+1 point" : "+0 points"}
+
+**Final Score:** ${tier4_score}/5 points
+
+**Result:** ${tier4_score === 5 ? "EXCELLENT" : tier4_score >= 3 ? "GOOD" : "NEEDS IMPROVEMENT"}
+
+---
+
+## Files Created
+
+### Architecture Diagrams (${diagram_files.length})
+
+${diagram_files.map(f => `- ${f}`).join('\n')}
+
+### Developer Guides (${guide_files.length})
+
+${guide_files.map(f => `- ${f}`).join('\n')}
+
+### API Documentation (${api_doc_files.length})
+
+${api_doc_files.map(f => `- ${f}`).join('\n')}
+
+### Configuration Files (${config_ok ? 1 : 0})
+
+${config_ok ? "- .env.example" : "- (none created)"}
+- README.md (updated)
+
+---
+
+## Performance Metrics (Rec 15)
+
+### Execution Times
+
+- **JUNO Audit**: ${((global.trinity_docs_session.performance_metrics.juno_end - global.trinity_docs_session.performance_metrics.juno_start) / 1000).toFixed(2)}s
+- **APO Parallel Execution**: ${((global.trinity_docs_session.performance_metrics.apo_end - global.trinity_docs_session.performance_metrics.apo_start) / 1000).toFixed(2)}s
+  - APO-1 (Diagrams): ${apo1_time}s (estimated)
+  - APO-2 (Guides): ${apo2_time}s (estimated)
+  - APO-3 (Config): ${apo3_time}s (estimated)
+- **Verification**: ${((Date.now() - global.trinity_docs_session.performance_metrics.verification_start) / 1000).toFixed(2)}s
+  - Tier 1 (Completion): ${tier1_time}s
+  - Tier 2 (Content Quality): ${tier2_time}s
+  - Tier 3 (Accuracy): ${tier3_time}s
+  - Tier 4 (Excellence): ${tier4_time}s
+- **Total Execution**: ${((Date.now() - global.trinity_docs_session.performance_metrics.total_start) / 1000).toFixed(2)}s
+
+### Efficiency Metrics
+
+- **Parallel Efficiency**: ${(((global.trinity_docs_session.performance_metrics.apo_end - global.trinity_docs_session.performance_metrics.apo_start) / (apo1_time + apo2_time + apo3_time)) * 100).toFixed(1)}% (3x theoretical speedup: ${((apo1_time + apo2_time + apo3_time) / (global.trinity_docs_session.performance_metrics.apo_end - global.trinity_docs_session.performance_metrics.apo_start)).toFixed(2)}x)
+- **Throughput**: ${(all_docs.length / ((Date.now() - global.trinity_docs_session.performance_metrics.total_start) / 1000)).toFixed(2)} files/second
+- **JUNO Analysis Rate**: ${juno_files_analyzed && juno_files_analyzed !== "Unknown" ? (juno_files_analyzed / ((global.trinity_docs_session.performance_metrics.juno_end - global.trinity_docs_session.performance_metrics.juno_start) / 1000)).toFixed(2) + " files/second" : "N/A"}
+
+### Resource Usage
+
+- **Total Files Generated**: ${all_docs.length}
+- **Total Documentation Size**: ${(all_docs.reduce((acc, f) => acc + Read(f).length, 0) / 1024).toFixed(2)} KB
+- **Average File Size**: ${(all_docs.reduce((acc, f) => acc + Read(f).length, 0) / all_docs.length / 1024).toFixed(2)} KB
+- **JUNO Report Size**: ${(Read(audit_report_path).length / 1024).toFixed(2)} KB
+
+---
+
+## Recommendations
+
+${total_score >= 95 ? "✅ Documentation is production-ready. No action required." : ""}
+${total_score >= 85 && total_score < 95 ? "⚠️ Documentation is good but has minor issues. Review warnings above." : ""}
+${total_score >= 70 && total_score < 85 ? "⚠️ Documentation requires review and fixes before deployment." : ""}
+${total_score < 70 ? "❌ Documentation quality is insufficient. Re-generation recommended." : ""}
+
+${accuracy_warnings.length > 0 ? "\n### Action Items:\n\n" + accuracy_warnings.map((w, i) => `${i + 1}. ${w.category}: ${w.issue}`).join('\n') : ""}
+
+---
+
+**Report Generated by:** Trinity Documentation Generator v2.0.9
+**Architecture:** Multi-agent orchestration (JUNO + 3 parallel APOs)
+`;
+
+Write(report_path, report);
+
+LOG: `✅ Verification report saved: ${report_path}`;
+LOG: "";
+
+global.trinity_docs_session.verification = {
+  score: total_score,
+  grade: grade,
+  report_path: report_path
+};
+```
+
+---
+
+## Phase 4: Completion Report
+
+```javascript
+// Track final performance
+global.trinity_docs_session.performance_metrics.verification_end = Date.now();
+global.trinity_docs_session.performance_metrics.total_end = Date.now();
+
+const perf = global.trinity_docs_session.performance_metrics;
+
+LOG: "=== TRINITY DOCUMENTATION GENERATION COMPLETE ===";
+LOG: "";
+LOG: "╔════════════════════════════════════════════════════════════╗";
+LOG: "║                   🎉 SUCCESS                               ║";
+LOG: "╚════════════════════════════════════════════════════════════╝";
+LOG: "";
+LOG: "Quality Score: " + global.trinity_docs_session.verification.score + "/100";
+LOG: "Grade: " + global.trinity_docs_session.verification.grade;
+LOG: "";
+LOG: "Documentation Summary:";
+LOG: `  Architecture Diagrams: ${diagram_files.length} files`;
+LOG: `  Developer Guides: ${guide_files.length} files`;
+LOG: `  API Documentation: ${api_doc_files.length} files`;
+LOG: `  Configuration Files: ${config_ok ? 1 : 0} files`;
+LOG: `  Total: ${diagram_files.length + guide_files.length + api_doc_files.length + (config_ok ? 1 : 0)} files`;
+LOG: "";
+LOG: "📁 Documentation Structure:";
+LOG: "  docs/";
+LOG: "  ├── images/        (Architecture diagrams)";
+LOG: "  ├── guides/        (Developer guides)";
+LOG: "  ├── api/           (API reference)";
+LOG: "  └── README.md      (Documentation home)";
+LOG: "";
+LOG: "⏱️ Performance Metrics:";
+LOG: `  JUNO Audit: ${((perf.juno_end - perf.juno_start) / 1000).toFixed(2)}s`;
+LOG: `  APO Parallel Execution: ${((perf.apo_end - perf.apo_start) / 1000).toFixed(2)}s`;
+LOG: `  Verification: ${((perf.verification_end - perf.verification_start) / 1000).toFixed(2)}s`;
+LOG: `  Total Time: ${((perf.total_end - perf.total_start) / 1000).toFixed(2)}s`;
+LOG: "";
+LOG: "🚀 Next Steps:";
+LOG: "  1. Review generated documentation in docs/ directory";
+LOG: "  2. Verify Mermaid diagrams render correctly";
+LOG: "  3. Check API documentation accuracy";
+LOG: "  4. Update .env.example with project-specific values if needed";
+LOG: "";
+LOG: "📊 Reports:";
+LOG: `  Audit Report: ${audit_report_path}`;
+LOG: `  Verification Report: ${global.trinity_docs_session.verification.report_path}`;
+LOG: "";
+LOG: "✨ Documentation generated using Trinity Method v2.0.9 (Orchestration Architecture)";
+LOG: "";
+```
+
+---
+
+## Architecture Notes
+
+### Why This Approach Works
+
+**Context Isolation:**
+- JUNO reads codebase (focused analysis task)
+- Each APO reads <100 lines (their specific section from report)
+- No single agent reads massive context
+
+**Parallel Execution:**
+- APO-1, APO-2, APO-3 run simultaneously
+- 3x faster than sequential execution
+- Independent sections prevent blocking
+
+**Quality Gates:**
+- JUNO self-validation ensures report completeness (Rec 3)
+- JUNO report validation catches incomplete audits (Rec 1)
+- APO self-validation ensures file creation and quality (Rec 6)
+- Enhanced verification enforces content quality (Rec 7)
+- 4-tier success criteria with objective scoring (Rec 9)
+
+**Resilience:**
+- APO fallback mechanisms handle incomplete JUNO reports (Rec 4)
+- Error handling protocol prevents silent failures (Rec 5)
+- README link validation prevents broken references (Rec 8)
+
+**Intelligence:**
+- Testing framework detection prevents inaccuracies (Rec 11)
+- Component discovery ensures accurate diagrams (Rec 12)
+- Enhanced JUNO prompt clarity improves report quality (Rec 2)
+
+**Observability:**
+- Performance tracking across all phases (Rec 10)
+- Verification report with quality score
+- Clear ABORT vs WARN vs LOG distinction
+
+### Comparison to Previous Architecture
+
+| Metric | v2.0.x (Sequential) | v3.0.0 (Orchestrated) | v3.1 (Enhanced) |
+|--------|---------------------|------------------------|-----------------|
+| Command Size | 4,656 lines | 888 lines | ~1,800 lines |
+| Largest Context | 4,656 lines (APO) | ~300 lines (JUNO) | ~400 lines (APO-1) |
+| Execution | Sequential | Parallel (3x) | Parallel (3x) |
+| Quality Gates | After generation | JUNO validation | JUNO + APO + Verification |
+| Failure Mode | Silent skips | File count check | Content quality ABORT |
+| Success Rate | 0% (v2.0.8 test) | 94% (v3.0.0 test) | 98-100% (expected) |
+| Fallback | None | Undocumented | Documented (Phase 1.5) |
+| Self-Validation | None | None | JUNO + 3 APOs |
+| Link Validation | None | None | APO-3 + Verification |
+| Accuracy Checks | None | None | Verification Tier 3 |
+
+### Quality Improvements (v3.1)
+
+**Issues Resolved:**
+1. ✅ JUNO incomplete reports (Rec 1: validation with ABORT/WARN)
+2. ✅ Broken README links (Rec 8: comprehensive link validation)
+3. ✅ Template placeholders (Rec 7: verification with ABORT)
+4. ✅ Invalid Mermaid syntax (Rec 7: validation with ABORT)
+5. ✅ Testing framework inaccuracies (Rec 11: detection in JUNO)
+6. ✅ Non-existent components (Rec 12: discovery in JUNO)
+
+**New Capabilities:**
+1. ✅ Objective quality scoring (0-100) (Rec 9)
+2. ✅ Performance tracking across phases (Rec 10)
+3. ✅ APO fallback architecture (Rec 4)
+4. ✅ Error handling protocol (Rec 5)
+5. ✅ Self-validation at all levels (Rec 3, 6)
+6. ✅ Enhanced verification with 4 tiers (Rec 7)
+
+---
+
+## Error Handling
+
+### If Verification Fails
+
+**Tier 1 Failure (Completion):**
+- ABORT command immediately
+- Review JUNO's audit report (lists what should exist)
+- Review APO execution logs (shows what was attempted)
+- Check for APO errors or exceptions
+- Re-run command if transient failure
+
+**Tier 2 Failure (Content Quality):**
+- ABORT command immediately
+- Review specific issues:
+  - Template placeholders: APO didn't replace variables
+  - Broken links: APO-3 created links to non-existent files
+  - Mermaid errors: APO-1 generated invalid syntax
+- Fix underlying APO issue or JUNO report incompleteness
+- Re-run command
+
+**Tier 3 Warnings (Accuracy):**
+- Command completes successfully
+- Review warnings in verification report
+- Manually fix inaccuracies if needed
+- No re-run required
+
+### If JUNO Fails
+
+**Incomplete Report:**
+- JUNO validation catches this (Rec 1)
+- Warnings logged, APO fallback activates
+- Documentation still generated (may be lower quality)
+
+**No Report Created:**
+- Command ABORTs in Phase 1
+- Check codebase structure (package.json exists?)
+- Verify framework detection logic
+- Check JUNO agent availability
+
+---