agentsys 5.0.0

package/plugins/next-task/lib/enhance/cross-file-analyzer.js

@@ -0,0 +1,930 @@
+/**
+ * Cross-File Semantic Analyzer
+ * Analyzes relationships between agents, skills, and workflows
+ *
+ * Cross-platform compatible: Works with Claude Code, OpenCode, and Codex
+ *
+ * @author Avi Fenesh
+ * @license MIT
+ */
+
+const fs = require('fs');
+const path = require('path');
+const { parseMarkdownFrontmatter } = require('./agent-analyzer');
+const { crossFilePatterns, loadKnownTools } = require('./cross-file-patterns');
+
+// ============================================
+// CONSTANTS
+// ============================================
+
+/** Minimum instruction length to consider for duplicate/contradiction detection */
+const MIN_INSTRUCTION_LENGTH = 20;
+
+/** Minimum number of files for duplicate instruction flagging */
+const MIN_DUPLICATE_COUNT = 3;
+
+/** Similarity threshold for contradiction detection (0-1) */
+const CONTRADICTION_SIMILARITY_THRESHOLD = 0.6;
+
+/** Length of action text to compare for contradictions */
+const ACTION_COMPARISON_LENGTH = 30;
+
+/** Minimum word length for similarity calculation (filters noise) */
+const MIN_WORD_LENGTH = 3;
+
+/** Default analysis categories */
+const DEFAULT_ANALYSIS_CATEGORIES = ['tool-consistency', 'workflow', 'consistency', 'skill-alignment'];
+
+// ============================================
+// UTILITY FUNCTIONS
+// ============================================
+
+/**
+ * Escape regex special characters in a string
+ * @param {string} str - String to escape
+ * @returns {string} Escaped string safe for RegExp
+ */
+function escapeRegex(str) {
+  return str.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
+}
+
+/**
+ * Validate that a path is within the expected root directory
+ * Prevents path traversal attacks
+ * @param {string} targetPath - Path to validate
+ * @param {string} rootDir - Expected root directory
+ * @returns {boolean} True if path is safe
+ */
+function isPathWithinRoot(targetPath, rootDir) {
+  const resolvedTarget = path.resolve(targetPath);
+  const resolvedRoot = path.resolve(rootDir);
+  return resolvedTarget.startsWith(resolvedRoot + path.sep) || resolvedTarget === resolvedRoot;
+}
+
+/**
+ * Calculate simple string similarity (Jaccard index on words)
+ * @param {string} a - First string
+ * @param {string} b - Second string
+ * @returns {number} Similarity score 0-1
+ */
+function calculateSimilarity(a, b) {
+  if (!a || !b) return 0;
+
+  const wordsA = new Set(a.split(/\s+/).filter(w => w.length >= MIN_WORD_LENGTH));
+  const wordsB = new Set(b.split(/\s+/).filter(w => w.length >= MIN_WORD_LENGTH));
+
+  if (wordsA.size === 0 || wordsB.size === 0) return 0;
+
+  let intersection = 0;
+  for (const word of wordsA) {
+    if (wordsB.has(word)) intersection++;
+  }
+
+  const union = wordsA.size + wordsB.size - intersection;
+  return intersection / union;
+}
+
+// ============================================
+// PRE-COMPILED PATTERNS
+// ============================================
+
+/** Pre-compiled shell command patterns for Bash detection */
+const SHELL_PATTERNS = [
+  /\bgit\s+(?:add|commit|push|pull|branch|checkout|merge|rebase|status|diff|log)\b/i,
+  /\bnpm\s+(?:install|test|run|build|publish)\b/i,
+  /\bpnpm\s+/i,
+  /\byarn\s+/i,
+  /\bcargo\s+/i,
+  /\bgo\s+(?:build|test|run|mod)\b/i
+];
+
+/** Pre-compiled critical instruction patterns */
+const CRITICAL_PATTERNS = [
+  /\bMUST\b/,
+  /\bNEVER\b/,
+  /\bALWAYS\b/i,
+  /\bREQUIRED\b/i,
+  /\bFORBIDDEN\b/i,
+  /\bCRITICAL\b/i,
+  /\bDO NOT\b/i,
+  /\bdon't\b/i
+];
+
+/** Pre-compiled pattern for extracting agent references */
+const SUBAGENT_PATTERN = /subagent_type\s*[=:]\s*["']([^"']+)["']/g;
+
+/** Pre-compiled patterns for cleaning content */
+const BAD_EXAMPLE_TAG_PATTERN = /<bad[_\- ]?example>[\s\S]*?<\/bad[_\- ]?example>/gi;
+const BAD_EXAMPLE_CODE_PATTERN = /```[^\n]*bad[^\n]*\n[\s\S]*?```/gi;
+
+// ============================================
+// TOOL PATTERN CACHE
+// ============================================
+
+/** Cache for compiled tool patterns */
+const toolPatternCache = new Map();
+
+/**
+ * Get or create compiled patterns for a tool name
+ * @param {string} tool - Tool name
+ * @returns {Object} Compiled patterns for the tool
+ */
+function getToolPatterns(tool) {
+  if (toolPatternCache.has(tool)) {
+    return toolPatternCache.get(tool);
+  }
+
+  const escapedTool = escapeRegex(tool);
+  const patterns = {
+    call: new RegExp(`\\b${escapedTool}\\s*\\(`),
+    mention: new RegExp(`\\b(?:use|invoke|call|with)\\s+(?:the\\s+)?${escapedTool}\\b`, 'i'),
+    noun: new RegExp(`\\b${escapedTool}\\s+tool\\b`, 'i')
+  };
+
+  toolPatternCache.set(tool, patterns);
+  return patterns;
+}
+
+// ============================================
+// EXTRACTION FUNCTIONS
+// ============================================
+
+/**
+ * Extract tool mentions from prompt content
+ * Detects tool usage patterns in prompt body
+ * @param {string} content - Prompt content
+ * @param {string[]} knownTools - List of known tool names
+ * @returns {string[]} Array of tool names found
+ */
+function extractToolMentions(content, knownTools) {
+  if (!content || typeof content !== 'string') return [];
+  if (!Array.isArray(knownTools)) return [];
+
+  const found = new Set();
+
+  // Skip content inside bad-example tags and code blocks with "bad" in info string
+  const cleanContent = content
+    .replace(BAD_EXAMPLE_TAG_PATTERN, '')
+    .replace(BAD_EXAMPLE_CODE_PATTERN, '');
+
+  for (const tool of knownTools) {
+    const patterns = getToolPatterns(tool);
+
+    // Pattern 1: Tool({ or Tool(
+    if (patterns.call.test(cleanContent)) {
+      found.add(tool);
+      continue;
+    }
+
+    // Pattern 2: "use the Tool tool" or "invoke Tool"
+    if (patterns.mention.test(cleanContent)) {
+      found.add(tool);
+      continue;
+    }
+
+    // Pattern 3: Tool tool (e.g., "Read tool", "Bash tool")
+    if (patterns.noun.test(cleanContent)) {
+      found.add(tool);
+    }
+  }
+
+  // Special case: Bash detection via shell commands
+  if (!found.has('Bash') && !found.has('Shell')) {
+    for (const pattern of SHELL_PATTERNS) {
+      if (pattern.test(cleanContent)) {
+        found.add('Bash');
+        break;
+      }
+    }
+  }
+
+  return Array.from(found);
+}
+
+/**
+ * Extract agent references from content
+ * Finds subagent_type references in Task() calls
+ * @param {string} content - Content to scan
+ * @returns {string[]} Array of referenced agent names (plugin:agent format)
+ */
+function extractAgentReferences(content) {
+  if (!content || typeof content !== 'string') return [];
+
+  const references = new Set();
+
+  // Use matchAll for safer iteration (no lastIndex issues)
+  const matches = content.matchAll(new RegExp(SUBAGENT_PATTERN.source, 'g'));
+  for (const match of matches) {
+    references.add(match[1]);
+  }
+
+  return Array.from(references);
+}
+
+/**
+ * Extract critical instructions (lines with MUST, NEVER, always, etc.)
+ * @param {string} content - Content to scan
+ * @returns {Array<{line: string, lineNumber: number}>} Critical instructions
+ */
+function extractCriticalInstructions(content) {
+  if (!content || typeof content !== 'string') return [];
+
+  const instructions = [];
+  const lines = content.split('\n');
+  let inCodeBlock = false;
+
+  for (let i = 0; i < lines.length; i++) {
+    const line = lines[i].trim();
+
+    // Track code block state
+    if (line.startsWith('```')) {
+      inCodeBlock = !inCodeBlock;
+      continue;
+    }
+
+    // Skip empty lines, headers, and content inside code blocks
+    if (!line || line.startsWith('#') || inCodeBlock) continue;
+
+    for (const pattern of CRITICAL_PATTERNS) {
+      if (pattern.test(line)) {
+        instructions.push({ line, lineNumber: i + 1 });
+        break;
+      }
+    }
+  }
+
+  return instructions;
+}
+
+// ============================================
+// FILE LOADING FUNCTIONS
+// ============================================
+
+/**
+ * Generic function to load prompt files from plugins directory
+ * @param {string} rootDir - Root directory
+ * @param {string} subDir - Subdirectory name ('agents' or 'skills')
+ * @param {Function} fileFilter - Function to filter files
+ * @param {Function} pathBuilder - Function to build file path
+ * @param {Object} options - Options including verbose flag
+ * @returns {Array<Object>} Array of parsed prompt objects
+ */
+function loadPromptFiles(rootDir, subDir, fileFilter, pathBuilder, options = {}) {
+  const results = [];
+  const errors = [];
+
+  const pluginsDir = path.join(rootDir, 'plugins');
+
+  // Validate path is within root
+  if (!isPathWithinRoot(pluginsDir, rootDir)) {
+    if (options.verbose) {
+      console.error('[cross-file] Invalid plugins directory path');
+    }
+    return results;
+  }
+
+  // Check if plugins directory exists
+  try {
+    fs.accessSync(pluginsDir);
+  } catch {
+    return results;
+  }
+
+  let plugins;
+  try {
+    plugins = fs.readdirSync(pluginsDir).filter(f => {
+      const fullPath = path.join(pluginsDir, f);
+      if (!isPathWithinRoot(fullPath, rootDir)) return false;
+      try {
+        return fs.statSync(fullPath).isDirectory();
+      } catch {
+        return false;
+      }
+    });
+  } catch (err) {
+    if (options.verbose) {
+      console.error('[cross-file] Failed to read plugins directory:', err.message);
+    }
+    return results;
+  }
+
+  for (const plugin of plugins) {
+    const targetDir = path.join(pluginsDir, plugin, subDir);
+
+    // Validate path
+    if (!isPathWithinRoot(targetDir, rootDir)) continue;
+
+    // Check if directory exists
+    try {
+      fs.accessSync(targetDir);
+    } catch {
+      continue;
+    }
+
+    let files;
+    try {
+      files = fs.readdirSync(targetDir).filter(fileFilter);
+    } catch (err) {
+      if (options.verbose) {
+        errors.push({ path: targetDir, error: err.message });
+      }
+      continue;
+    }
+
+    for (const file of files) {
+      const filePath = pathBuilder(targetDir, file);
+
+      // Validate path
+      if (!isPathWithinRoot(filePath, rootDir)) continue;
+
+      try {
+        const content = fs.readFileSync(filePath, 'utf8');
+        const { frontmatter, body } = parseMarkdownFrontmatter(content);
+
+        results.push({
+          plugin,
+          name: file.replace('.md', '').replace(/^SKILL$/, path.basename(path.dirname(filePath))),
+          path: filePath,
+          frontmatter: frontmatter || {},
+          body,
+          content
+        });
+      } catch (err) {
+        if (options.verbose) {
+          errors.push({ path: filePath, error: err.message });
+        }
+        // Skip files that can't be read - intentional for robustness
+      }
+    }
+  }
+
+  if (options.verbose && errors.length > 0) {
+    console.error('[cross-file] File read errors:', errors);
+  }
+
+  return results;
+}
+
+/**
+ * Load all agent files from a directory structure
+ * @param {string} rootDir - Root directory to scan
+ * @param {Object} options - Options including verbose flag
+ * @returns {Array<Object>} Array of parsed agent objects
+ */
+function loadAllAgents(rootDir, options = {}) {
+  return loadPromptFiles(
+    rootDir,
+    'agents',
+    f => f.endsWith('.md') && f.toLowerCase() !== 'readme.md',
+    (dir, file) => path.join(dir, file),
+    options
+  );
+}
+
+/**
+ * Load all command files from a directory structure
+ * @param {string} rootDir - Root directory to scan
+ * @param {Object} options - Options including verbose flag
+ * @returns {Array<Object>} Array of parsed command objects
+ */
+function loadAllCommands(rootDir, options = {}) {
+  return loadPromptFiles(
+    rootDir,
+    'commands',
+    f => f.endsWith('.md') && f.toLowerCase() !== 'readme.md',
+    (dir, file) => path.join(dir, file),
+    options
+  );
+}
+
+/**
+ * Load all skill files from a directory structure
+ * @param {string} rootDir - Root directory to scan
+ * @param {Object} options - Options including verbose flag
+ * @returns {Array<Object>} Array of parsed skill objects
+ */
+function loadAllSkills(rootDir, options = {}) {
+  const skills = [];
+  const pluginsDir = path.join(rootDir, 'plugins');
+
+  // Validate path
+  if (!isPathWithinRoot(pluginsDir, rootDir)) {
+    return skills;
+  }
+
+  try {
+    fs.accessSync(pluginsDir);
+  } catch {
+    return skills;
+  }
+
+  let plugins;
+  try {
+    plugins = fs.readdirSync(pluginsDir).filter(f => {
+      const fullPath = path.join(pluginsDir, f);
+      if (!isPathWithinRoot(fullPath, rootDir)) return false;
+      try {
+        return fs.statSync(fullPath).isDirectory();
+      } catch {
+        return false;
+      }
+    });
+  } catch (err) {
+    if (options.verbose) {
+      console.error('[cross-file] Failed to read plugins directory:', err.message);
+    }
+    return skills;
+  }
+
+  for (const plugin of plugins) {
+    const skillsDir = path.join(pluginsDir, plugin, 'skills');
+
+    if (!isPathWithinRoot(skillsDir, rootDir)) continue;
+
+    try {
+      fs.accessSync(skillsDir);
+    } catch {
+      continue;
+    }
+
+    let skillDirs;
+    try {
+      skillDirs = fs.readdirSync(skillsDir).filter(f => {
+        const fullPath = path.join(skillsDir, f);
+        if (!isPathWithinRoot(fullPath, rootDir)) return false;
+        try {
+          return fs.statSync(fullPath).isDirectory();
+        } catch {
+          return false;
+        }
+      });
+    } catch (err) {
+      if (options.verbose) {
+        console.error('[cross-file] Failed to read skills directory:', skillsDir, err.message);
+      }
+      continue;
+    }
+
+    for (const skillDir of skillDirs) {
+      const skillPath = path.join(skillsDir, skillDir, 'SKILL.md');
+
+      if (!isPathWithinRoot(skillPath, rootDir)) continue;
+
+      try {
+        fs.accessSync(skillPath);
+        const content = fs.readFileSync(skillPath, 'utf8');
+        const { frontmatter, body } = parseMarkdownFrontmatter(content);
+
+        skills.push({
+          plugin,
+          name: skillDir,
+          path: skillPath,
+          frontmatter: frontmatter || {},
+          body,
+          content
+        });
+      } catch (err) {
+        if (options.verbose) {
+          console.error('[cross-file] Failed to read skill:', skillPath, err.message);
+        }
+        // Skip files that can't be read - intentional for robustness
+      }
+    }
+  }
+
+  return skills;
+}
+
+// ============================================
+// ANALYSIS FUNCTIONS
+// ============================================
+
+/**
+ * Analyze tool consistency between frontmatter and body
+ * @param {Array<Object>} agents - Parsed agents
+ * @param {string[]} knownTools - Known tool names
+ * @returns {Array<Object>} Findings
+ */
+function analyzeToolConsistency(agents, knownTools) {
+  const findings = [];
+  const pattern = crossFilePatterns.tool_not_in_allowed_list;
+
+  for (const agent of agents) {
+    const { frontmatter, body, name, path: agentPath } = agent;
+
+    // Get declared tools from frontmatter
+    let declaredTools = [];
+    if (frontmatter && frontmatter.tools) {
+      declaredTools = Array.isArray(frontmatter.tools)
+        ? frontmatter.tools
+        : frontmatter.tools.split(',').map(t => t.trim());
+    }
+
+    // Skip if no tools restriction (all tools allowed)
+    if (declaredTools.length === 0) continue;
+
+    // Extract used tools from body
+    const usedTools = extractToolMentions(body, knownTools);
+
+    const result = pattern.check({
+      declaredTools,
+      usedTools,
+      agentName: name
+    });
+
+    if (result) {
+      findings.push({
+        ...result,
+        file: agentPath,
+        certainty: pattern.certainty,
+        patternId: pattern.id,
+        source: 'cross-file'
+      });
+    }
+  }
+
+  return findings;
+}
+
+/**
+ * Analyze workflow completeness (referenced agents exist)
+ * @param {Array<Object>} agents - Parsed agents
+ * @returns {Array<Object>} Findings
+ */
+function analyzeWorkflowCompleteness(agents) {
+  const findings = [];
+  const pattern = crossFilePatterns.missing_workflow_agent;
+
+  // Build list of existing agents
+  const existingAgents = agents.map(a => ({
+    plugin: a.plugin,
+    name: a.name
+  }));
+
+  // Check each agent for references to other agents
+  for (const agent of agents) {
+    const { body, path: agentPath } = agent;
+    const references = extractAgentReferences(body);
+
+    for (const ref of references) {
+      const result = pattern.check({
+        referencedAgent: ref,
+        existingAgents,
+        sourceFile: path.basename(agentPath)
+      });
+
+      if (result) {
+        findings.push({
+          ...result,
+          file: agentPath,
+          certainty: pattern.certainty,
+          patternId: pattern.id,
+          source: 'cross-file'
+        });
+      }
+    }
+  }
+
+  return findings;
+}
+
+/**
+ * Analyze prompt consistency (duplicates, contradictions)
+ * Uses optimized O(n) contradiction detection via keyword indexing
+ * @param {Array<Object>} agents - Parsed agents
+ * @returns {Array<Object>} Findings
+ */
+function analyzePromptConsistency(agents) {
+  const findings = [];
+
+  // Collect all critical instructions with their sources
+  const instructionMap = new Map(); // normalized instruction -> [files]
+
+  for (const agent of agents) {
+    const instructions = extractCriticalInstructions(agent.body);
+
+    for (const { line } of instructions) {
+      const normalized = line.toLowerCase().trim();
+      if (normalized.length < MIN_INSTRUCTION_LENGTH) continue;
+
+      if (!instructionMap.has(normalized)) {
+        instructionMap.set(normalized, []);
+      }
+      instructionMap.get(normalized).push(agent.path);
+    }
+  }
+
+  // Find duplicates
+  const duplicatePattern = crossFilePatterns.duplicate_instructions;
+  for (const [instruction, files] of instructionMap.entries()) {
+    if (files.length >= MIN_DUPLICATE_COUNT) {
+      const result = duplicatePattern.check({ instruction, files });
+      if (result) {
+        findings.push({
+          ...result,
+          file: files[0],
+          certainty: duplicatePattern.certainty,
+          patternId: duplicatePattern.id,
+          source: 'cross-file'
+        });
+      }
+    }
+  }
+
+  // Find contradictions using keyword indexing (O(n) instead of O(n^2))
+  const contradictionPattern = crossFilePatterns.contradictory_rules;
+
+  // Index rules by keywords for efficient lookup
+  const alwaysRulesByKeyword = new Map(); // keyword -> [{rule, file}]
+  const neverRulesByKeyword = new Map();
+
+  for (const agent of agents) {
+    const instructions = extractCriticalInstructions(agent.body);
+
+    for (const { line } of instructions) {
+      const isAlways = /\bALWAYS\b/i.test(line);
+      const isNever = /\bNEVER\b/i.test(line) || /\bDO NOT\b/i.test(line);
+
+      if (!isAlways && !isNever) continue;
+
+      // Extract action keywords
+      let action;
+      if (isAlways) {
+        action = line.replace(/.*\bALWAYS\b\s*/i, '').substring(0, ACTION_COMPARISON_LENGTH);
+      } else {
+        action = line.replace(/.*\b(?:NEVER|DO NOT)\b\s*/i, '').substring(0, ACTION_COMPARISON_LENGTH);
+      }
+
+      // Extract significant keywords from action
+      const keywords = action.toLowerCase().split(/\s+/).filter(w => w.length >= MIN_WORD_LENGTH);
+
+      const ruleData = { line, file: agent.path, action: action.toLowerCase() };
+      const targetMap = isAlways ? alwaysRulesByKeyword : neverRulesByKeyword;
+
+      for (const keyword of keywords) {
+        if (!targetMap.has(keyword)) {
+          targetMap.set(keyword, []);
+        }
+        targetMap.get(keyword).push(ruleData);
+      }
+    }
+  }
+
+  // Find contradictions by checking overlapping keywords
+  const checkedPairs = new Set();
+
+  for (const [keyword, alwaysRules] of alwaysRulesByKeyword.entries()) {
+    const neverRules = neverRulesByKeyword.get(keyword);
+    if (!neverRules) continue;
+
+    for (const always of alwaysRules) {
+      for (const never of neverRules) {
+        // Skip same file
+        if (always.file === never.file) continue;
+
+        // Skip already checked pairs
+        const pairKey = `${always.line}|${never.line}`;
+        if (checkedPairs.has(pairKey)) continue;
+        checkedPairs.add(pairKey);
+
+        // Check similarity
+        const similarity = calculateSimilarity(always.action, never.action);
+        if (similarity > CONTRADICTION_SIMILARITY_THRESHOLD) {
+          const result = contradictionPattern.check({
+            rule1: always.line,
+            rule2: never.line,
+            file1: path.basename(always.file),
+            file2: path.basename(never.file)
+          });
+
+          if (result) {
+            findings.push({
+              ...result,
+              file: always.file,
+              certainty: contradictionPattern.certainty,
+              patternId: contradictionPattern.id,
+              source: 'cross-file'
+            });
+          }
+        }
+      }
+    }
+  }
+
+  return findings;
+}
+
+/**
+ * Analyze skill-agent alignment
+ * @param {Array<Object>} skills - Parsed skills
+ * @param {string[]} knownTools - Known tool names
+ * @returns {Array<Object>} Findings
+ */
+function analyzeSkillAlignment(skills, knownTools) {
+  const findings = [];
+  const pattern = crossFilePatterns.skill_tool_mismatch;
+
+  for (const skill of skills) {
+    const { frontmatter, body, name, path: skillPath } = skill;
+
+    // Get allowed-tools from frontmatter (supports multiple field names)
+    let allowedTools = [];
+    const toolsField = frontmatter['allowed-tools'] || frontmatter.allowedTools || frontmatter.tools;
+    if (toolsField) {
+      allowedTools = Array.isArray(toolsField)
+        ? toolsField
+        : toolsField.split(',').map(t => t.trim());
+    }
+
+    // Skip if no tools restriction
+    if (allowedTools.length === 0) continue;
+
+    // Extract used tools from body
+    const usedTools = extractToolMentions(body, knownTools);
+
+    const result = pattern.check({
+      skillName: name,
+      skillAllowedTools: allowedTools,
+      promptUsedTools: usedTools
+    });
+
+    if (result) {
+      findings.push({
+        ...result,
+        file: skillPath,
+        certainty: pattern.certainty,
+        patternId: pattern.id,
+        source: 'cross-file'
+      });
+    }
+  }
+
+  return findings;
+}
+
+/**
+ * Find orphaned agents (not referenced anywhere)
+ * @param {Array<Object>} agents - Parsed agents
+ * @param {Array<Object>} skills - Parsed skills
+ * @param {Array<Object>} commands - Parsed commands
+ * @returns {Array<Object>} Findings
+ */
+function analyzeOrphanedPrompts(agents, skills, commands = []) {
+  const findings = [];
+  const pattern = crossFilePatterns.orphaned_prompt;
+
+  // Collect all agent references
+  const allReferences = new Set();
+
+  // From agents
+  for (const agent of agents) {
+    const refs = extractAgentReferences(agent.body);
+    refs.forEach(r => allReferences.add(r));
+  }
+
+  // From skills
+  for (const skill of skills) {
+    const refs = extractAgentReferences(skill.body);
+    refs.forEach(r => allReferences.add(r));
+  }
+
+  // From commands (addresses false positives for command-invoked agents)
+  for (const command of commands) {
+    const refs = extractAgentReferences(command.body);
+    refs.forEach(r => allReferences.add(r));
+  }
+
+  // Check each agent
+  for (const agent of agents) {
+    const fullName = `${agent.plugin}:${agent.name}`;
+    const shortName = agent.name;
+
+    // Check if referenced
+    const isReferenced = allReferences.has(fullName) || allReferences.has(shortName);
+
+    // Entry point agents are typically called by commands, not other agents
+    const isEntryPoint = /orchestrator|discoverer|validator|monitor|fixer|checker|reporter|manager/i.test(agent.name);
+
+    if (!isReferenced && !isEntryPoint) {
+      const result = pattern.check({
+        promptFile: path.basename(agent.path),
+        referencedBy: []
+      });
+
+      if (result) {
+        findings.push({
+          ...result,
+          file: agent.path,
+          certainty: pattern.certainty,
+          patternId: pattern.id,
+          source: 'cross-file'
+        });
+      }
+    }
+  }
+
+  return findings;
+}
+
+// ============================================
+// MAIN ANALYSIS FUNCTION
+// ============================================
+
+/**
+ * Main cross-file analysis function
+ * @param {string} rootDir - Root directory to analyze
+ * @param {Object} options - Analysis options
+ * @param {boolean} options.verbose - Include all findings and log errors
+ * @param {string[]} options.categories - Specific categories to check
+ * @returns {Object} Analysis results
+ */
+function analyze(rootDir, options = {}) {
+  const {
+    verbose = false,
+    categories = DEFAULT_ANALYSIS_CATEGORIES
+  } = options;
+
+  const results = {
+    rootDir,
+    findings: [],
+    summary: {
+      agentsAnalyzed: 0,
+      skillsAnalyzed: 0,
+      totalFindings: 0,
+      byCategory: {}
+    }
+  };
+
+  // Load known tools (config file or platform defaults)
+  const knownTools = loadKnownTools(rootDir);
+
+  // Load all agents, skills, and commands
+  const agents = loadAllAgents(rootDir, { verbose });
+  const skills = loadAllSkills(rootDir, { verbose });
+  const commands = loadAllCommands(rootDir, { verbose });
+
+  results.summary.agentsAnalyzed = agents.length;
+  results.summary.skillsAnalyzed = skills.length;
+  results.summary.commandsAnalyzed = commands.length;
+
+  // Run analysis for each category
+  if (categories.includes('tool-consistency')) {
+    const toolFindings = analyzeToolConsistency(agents, knownTools);
+    results.findings.push(...toolFindings);
+    results.summary.byCategory['tool-consistency'] = toolFindings.length;
+  }
+
+  if (categories.includes('workflow')) {
+    const workflowFindings = analyzeWorkflowCompleteness(agents);
+    results.findings.push(...workflowFindings);
+    results.summary.byCategory['workflow'] = workflowFindings.length;
+  }
+
+  if (categories.includes('consistency')) {
+    const consistencyFindings = analyzePromptConsistency(agents);
+    const orphanFindings = analyzeOrphanedPrompts(agents, skills, commands);
+    results.findings.push(...consistencyFindings, ...orphanFindings);
+    results.summary.byCategory['consistency'] = consistencyFindings.length + orphanFindings.length;
+  }
+
+  if (categories.includes('skill-alignment')) {
+    const skillFindings = analyzeSkillAlignment(skills, knownTools);
+    results.findings.push(...skillFindings);
+    results.summary.byCategory['skill-alignment'] = skillFindings.length;
+  }
+
+  results.summary.totalFindings = results.findings.length;
+
+  return results;
+}
+
+// ============================================
+// EXPORTS
+// ============================================
+
+module.exports = {
+  // Extraction functions
+  extractToolMentions,
+  extractAgentReferences,
+  extractCriticalInstructions,
+
+  // Loading functions
+  loadAllAgents,
+  loadAllSkills,
+  loadAllCommands,
+
+  // Analysis functions
+  analyzeToolConsistency,
+  analyzeWorkflowCompleteness,
+  analyzePromptConsistency,
+  analyzeSkillAlignment,
+  analyzeOrphanedPrompts,
+
+  // Main entry point
+  analyze,
+
+  // Utilities (exported for testing)
+  calculateSimilarity,
+  escapeRegex,
+  isPathWithinRoot
+};