refactor: remove ~70 low-value comments across 13 files

- Remove empty section markers (// === ... ===, // --- ... ---) that duplicate JSDoc or function names
- Remove "what" comments that restate the next line of code (e.g. // Save to disk, // Check for retryable patterns)
- Remove file-level descriptions that restate the filename (e.g. // Pure functions for formatting console output)
- Fix "Added by client" comment referencing implementation history → "Used for audit correlation"
- Preserve all WHY comments: error classification groups, billing/session limit explanations, ESM interop, exactOptionalPropertyTypes, mutex reasoning

src/ai/message-handlers.ts

@@ -4,8 +4,6 @@
 // it under the terms of the GNU Affero General Public License version 3
 // as published by the Free Software Foundation.
 
-// Pure functions for processing SDK message types
-
 import { PentestError } from '../services/error-handling.js';
 import { ErrorCode } from '../types/errors.js';
 import { matchesBillingTextPattern } from '../utils/billing-detection.js';
@@ -263,14 +261,12 @@ function handleToolResultMessage(message: ToolResultMessage): ToolResultData {
   };
 }
 
-// Output helper for console logging
 function outputLines(lines: string[]): void {
   for (const line of lines) {
     console.log(line);
   }
 }
 
-// Message dispatch result types
 export type MessageDispatchAction =
   | { type: 'continue'; apiErrorDetected?: boolean | undefined; model?: string | undefined }
   | { type: 'complete'; result: string | null; cost: number }

src/ai/output-formatters.ts

@@ -4,14 +4,10 @@
 // it under the terms of the GNU Affero General Public License version 3
 // as published by the Free Software Foundation.
 
-// Pure functions for formatting console output
-
 import { extractAgentType, formatDuration } from '../utils/formatting.js';
 import { AGENTS } from '../session-manager.js';
 import type { ExecutionContext, ResultData } from './types.js';
 
-// --- Types for tool call filtering ---
-
 interface ToolCallInput {
   url?: string;
   element?: string;
@@ -32,8 +28,6 @@ interface ToolCall {
   input?: ToolCallInput;
 }
 
-// --- Agent prefix logic ---
-
 /**
  * Get agent prefix for parallel execution
  */
@@ -70,8 +64,6 @@ export function getAgentPrefix(description: string): string {
   return '[Agent]';
 }
 
-// --- Tool call filtering ---
-
 /**
  * Extract domain from URL for display
  */
@@ -273,8 +265,6 @@ export function filterJsonToolCalls(content: string | null | undefined): string
   return processedLines.join('\n');
 }
 
-// --- Console output formatting ---
-
 export function detectExecutionContext(description: string): ExecutionContext {
   const isParallelExecution =
     description.includes('vuln agent') || description.includes('exploit agent');

src/audit/audit-session.ts

@@ -112,24 +112,19 @@ export class AuditSession {
       await AgentLogger.savePrompt(this.sessionMetadata, agentName, promptContent);
     }
 
-    // Track current agent name for workflow logging
     this.currentAgentName = agentName;
 
-    // Create and initialize logger for this attempt
     this.currentLogger = new AgentLogger(this.sessionMetadata, agentName, attemptNumber);
     await this.currentLogger.initialize();
 
-    // Start metrics tracking
     this.metricsTracker.startAgent(agentName, attemptNumber);
 
-    // Log start event
     await this.currentLogger.logEvent('agent_start', {
       agentName,
       attemptNumber,
       timestamp: formatTimestamp(),
     });
 
-    // Log to unified workflow log
     await this.workflowLogger.logAgent(agentName, 'start', { attemptNumber });
   }
 
@@ -177,7 +172,6 @@ export class AuditSession {
    * End agent execution (mutex-protected)
    */
   async endAgent(agentName: string, result: AgentEndResult): Promise<void> {
-    // Log end event
     if (this.currentLogger) {
       await this.currentLogger.logEvent('agent_end', {
         agentName,
@@ -187,15 +181,12 @@ export class AuditSession {
         timestamp: formatTimestamp(),
       });
 
-      // Close logger
       await this.currentLogger.close();
       this.currentLogger = null;
     }
 
-    // Reset current agent name
     this.currentAgentName = null;
 
-    // Log to unified workflow log
     const agentLogDetails: AgentLogDetails = {
       attemptNumber: result.attemptNumber,
       duration_ms: result.duration_ms,
@@ -211,7 +202,6 @@ export class AuditSession {
       // Reload inside mutex to prevent lost updates during parallel exploitation phase
       await this.metricsTracker.reload();
 
-      // Update metrics
       await this.metricsTracker.endAgent(agentName, result);
     } finally {
       unlock();

src/audit/logger.ts

@@ -42,7 +42,6 @@ export class AgentLogger {
     this.attemptNumber = attemptNumber;
     this.timestamp = Date.now();
 
-    // Generate log file path and create stream
     const logPath = generateLogPath(sessionMetadata, agentName, this.timestamp, attemptNumber);
     this.logStream = new LogStream(logPath);
   }

src/audit/metrics-tracker.ts

@@ -227,7 +227,6 @@ export class MetricsTracker {
     // Recalculate aggregations
     this.recalculateAggregations();
 
-    // Save to disk
     await this.save();
   }
 

src/audit/workflow-logger.ts

@@ -59,7 +59,6 @@ export class WorkflowLogger {
       return;
     }
 
-    // Open the stream (LogStream.open() handles directory creation)
     await this.logStream.open();
 
     // Write header only if file is new (empty)

src/config-parser.ts

@@ -22,11 +22,9 @@ import type {
 const require = createRequire(import.meta.url);
 const addFormats: FormatsPlugin = require('ajv-formats');
 
-// Initialize AJV with formats
 const ajv = new Ajv({ allErrors: true, verbose: true });
 addFormats(ajv);
 
-// Load JSON Schema
 let configSchema: object;
 let validateSchema: ValidateFunction;
 
@@ -45,7 +43,6 @@ try {
   );
 }
 
-// Security patterns to block
 const DANGEROUS_PATTERNS: RegExp[] = [
   /\.\.\//, // Path traversal
   /[<>]/, // HTML/XML injection
@@ -179,10 +176,8 @@ function formatAjvErrors(errors: ErrorObject[]): string[] {
   return errors.map(formatAjvError);
 }
 
-// Parse and load YAML configuration file with enhanced safety
 export const parseConfig = async (configPath: string): Promise<Config> => {
   try {
-    // File existence check
     if (!(await fs.pathExists(configPath))) {
       throw new PentestError(
         `Configuration file not found: ${configPath}`,
@@ -193,7 +188,6 @@ export const parseConfig = async (configPath: string): Promise<Config> => {
       );
     }
 
-    // File size check (prevent extremely large files)
     const stats = await fs.stat(configPath);
     const maxFileSize = 1024 * 1024; // 1MB
     if (stats.size > maxFileSize) {
@@ -206,10 +200,8 @@ export const parseConfig = async (configPath: string): Promise<Config> => {
       );
     }
 
-    // Read file content
     const configContent = await fs.readFile(configPath, 'utf8');
 
-    // Basic content validation
     if (!configContent.trim()) {
       throw new PentestError(
         'Configuration file is empty',
@@ -220,7 +212,6 @@ export const parseConfig = async (configPath: string): Promise<Config> => {
       );
     }
 
-    // Parse YAML with safety options
     let config: unknown;
     try {
       config = yaml.load(configContent, {
@@ -239,7 +230,6 @@ export const parseConfig = async (configPath: string): Promise<Config> => {
       );
     }
 
-    // Additional safety check
     if (config === null || config === undefined) {
       throw new PentestError(
         'Configuration file resulted in null/undefined after parsing',
@@ -250,7 +240,6 @@ export const parseConfig = async (configPath: string): Promise<Config> => {
       );
     }
 
-    // Validate the configuration structure and content
     validateConfig(config as Config);
 
     return config as Config;
@@ -259,7 +248,6 @@ export const parseConfig = async (configPath: string): Promise<Config> => {
     if (error instanceof PentestError) {
       throw error;
     }
-    // Wrap other errors with context
     const errMsg = error instanceof Error ? error.message : String(error);
     throw new PentestError(
       `Failed to parse configuration file '${configPath}': ${errMsg}`,
@@ -271,9 +259,7 @@ export const parseConfig = async (configPath: string): Promise<Config> => {
   }
 };
 
-// Validate overall configuration structure using JSON Schema
 const validateConfig = (config: Config): void => {
-  // Basic structure validation
   if (!config || typeof config !== 'object') {
     throw new PentestError(
       'Configuration must be a valid object',
@@ -294,7 +280,6 @@ const validateConfig = (config: Config): void => {
     );
   }
 
-  // JSON Schema validation
   const isValid = validateSchema(config);
   if (!isValid) {
     const errors = validateSchema.errors || [];
@@ -308,10 +293,8 @@ const validateConfig = (config: Config): void => {
     );
   }
 
-  // Additional security validation
   performSecurityValidation(config);
 
-  // Ensure at least some configuration is provided
   if (!config.rules && !config.authentication) {
     console.warn(
       '⚠️  Configuration file contains no rules or authentication. The pentest will run without any scoping restrictions or login capabilities.'
@@ -323,9 +306,7 @@ const validateConfig = (config: Config): void => {
   }
 };
 
-// Perform additional security validation beyond JSON Schema
 const performSecurityValidation = (config: Config): void => {
-  // Validate authentication section for security issues
   if (config.authentication) {
     const auth = config.authentication;
 
@@ -344,7 +325,6 @@ const performSecurityValidation = (config: Config): void => {
       }
     }
 
-    // Check for dangerous patterns in credentials
     if (auth.credentials) {
       for (const pattern of DANGEROUS_PATTERNS) {
         if (pattern.test(auth.credentials.username)) {
@@ -368,7 +348,6 @@ const performSecurityValidation = (config: Config): void => {
       }
     }
 
-    // Check login flow for dangerous patterns
     if (auth.login_flow) {
       auth.login_flow.forEach((step, index) => {
         for (const pattern of DANGEROUS_PATTERNS) {
@@ -386,24 +365,20 @@ const performSecurityValidation = (config: Config): void => {
     }
   }
 
-  // Validate rules section for security issues
   if (config.rules) {
     validateRulesSecurity(config.rules.avoid, 'avoid');
     validateRulesSecurity(config.rules.focus, 'focus');
 
-    // Check for duplicate and conflicting rules
     checkForDuplicates(config.rules.avoid || [], 'avoid');
     checkForDuplicates(config.rules.focus || [], 'focus');
     checkForConflicts(config.rules.avoid, config.rules.focus);
   }
 };
 
-// Validate rules for security issues
 const validateRulesSecurity = (rules: Rule[] | undefined, ruleType: string): void => {
   if (!rules) return;
 
   rules.forEach((rule, index) => {
-    // Security validation
     for (const pattern of DANGEROUS_PATTERNS) {
       if (pattern.test(rule.url_path)) {
         throw new PentestError(
@@ -425,12 +400,10 @@ const validateRulesSecurity = (rules: Rule[] | undefined, ruleType: string): voi
       }
     }
 
-    // Type-specific validation
     validateRuleTypeSpecific(rule, ruleType, index);
   });
 };
 
-// Validate rule based on its specific type
 const validateRuleTypeSpecific = (rule: Rule, ruleType: string, index: number): void => {
   const field = `rules.${ruleType}[${index}].url_path`;
 
@@ -486,7 +459,6 @@ const validateRuleTypeSpecific = (rule: Rule, ruleType: string, index: number):
     }
 
     case 'header':
-      // Header name validation (basic)
       if (!rule.url_path.match(/^[a-zA-Z0-9\-_]+$/)) {
         throw new PentestError(
           `${field} for type 'header' must be a valid header name (alphanumeric, hyphens, underscores only)`,
@@ -499,7 +471,6 @@ const validateRuleTypeSpecific = (rule: Rule, ruleType: string, index: number):
       break;
 
     case 'parameter':
-      // Parameter name validation (basic)
       if (!rule.url_path.match(/^[a-zA-Z0-9\-_]+$/)) {
         throw new PentestError(
           `${field} for type 'parameter' must be a valid parameter name (alphanumeric, hyphens, underscores only)`,
@@ -513,7 +484,6 @@ const validateRuleTypeSpecific = (rule: Rule, ruleType: string, index: number):
   }
 };
 
-// Check for duplicate rules
 const checkForDuplicates = (rules: Rule[], ruleType: string): void => {
   const seen = new Set<string>();
   rules.forEach((rule, index) => {
@@ -531,7 +501,6 @@ const checkForDuplicates = (rules: Rule[], ruleType: string): void => {
   });
 };
 
-// Check for conflicting rules between avoid and focus
 const checkForConflicts = (avoidRules: Rule[] = [], focusRules: Rule[] = []): void => {
   const avoidSet = new Set(avoidRules.map((rule) => `${rule.type}:${rule.url_path}`));
 
@@ -549,7 +518,6 @@ const checkForConflicts = (avoidRules: Rule[] = [], focusRules: Rule[] = []): vo
   });
 };
 
-// Sanitize and normalize rule values
 const sanitizeRule = (rule: Rule): Rule => {
   return {
     description: rule.description.trim(),
@@ -558,7 +526,6 @@ const sanitizeRule = (rule: Rule): Rule => {
   };
 };
 
-// Distribute configuration sections to different agents with sanitization
 export const distributeConfig = (config: Config | null): DistributedConfig => {
   const avoid = config?.rules?.avoid || [];
   const focus = config?.rules?.focus || [];
@@ -571,7 +538,6 @@ export const distributeConfig = (config: Config | null): DistributedConfig => {
   };
 };
 
-// Sanitize and normalize authentication values
 const sanitizeAuthentication = (auth: Authentication): Authentication => {
   return {
     login_type: auth.login_type.toLowerCase().trim() as Authentication['login_type'],

src/services/error-handling.ts

@@ -15,7 +15,6 @@ import {
   matchesBillingTextPattern,
 } from '../utils/billing-detection.js';
 
-// Custom error class for pentest operations
 export class PentestError extends Error {
   override name = 'PentestError' as const;
   type: PentestErrorType;
@@ -43,8 +42,6 @@ export class PentestError extends Error {
   }
 }
 
-// Handle tool execution errors
-// Handle prompt loading errors
 export function handlePromptError(
   promptName: string,
   error: Error
@@ -60,7 +57,6 @@ export function handlePromptError(
   };
 }
 
-// Patterns that indicate retryable errors
 const RETRYABLE_PATTERNS = [
   // Network and connection errors
   'network',
@@ -104,12 +100,10 @@ const NON_RETRYABLE_PATTERNS = [
 export function isRetryableError(error: Error): boolean {
   const message = error.message.toLowerCase();
 
-  // Check for explicit non-retryable patterns first
   if (NON_RETRYABLE_PATTERNS.some((pattern) => message.includes(pattern))) {
     return false;
   }
 
-  // Check for retryable patterns
   return RETRYABLE_PATTERNS.some((pattern) => message.includes(pattern));
 }
 

src/temporal/activities.ts

@@ -194,8 +194,6 @@ async function runAgentActivity(
   }
 }
 
-// === Individual Agent Activity Exports ===
-
 export async function runPreReconAgent(input: ActivityInput): Promise<AgentMetrics> {
   return runAgentActivity('pre-recon', input);
 }
@@ -248,8 +246,6 @@ export async function runReportAgent(input: ActivityInput): Promise<AgentMetrics
   return runAgentActivity('report', input);
 }
 
-// === Report Assembly Activities ===
-
 /**
  * Assemble the final report by concatenating exploitation evidence files.
  */
@@ -282,8 +278,6 @@ export async function injectReportMetadataActivity(input: ActivityInput): Promis
   }
 }
 
-// === Exploitation Queue Check ===
-
 /**
  * Check if exploitation should run for a given vulnerability type.
  *
@@ -304,8 +298,6 @@ export async function checkExploitationQueue(
   return checker.checkQueue(vulnType, repoPath, logger);
 }
 
-// === Resume Activities ===
-
 interface SessionJson {
   session: {
     id: string;
@@ -511,8 +503,6 @@ export async function recordResumeAttempt(
   });
 }
 
-// === Phase Transition Activities ===
-
 /**
  * Log phase transition to the unified workflow log.
  */

src/temporal/client.ts

@@ -229,7 +229,6 @@ async function startPipeline(): Promise<void> {
       const workspaceExists = await fileExists(sessionPath);
 
       if (workspaceExists) {
-        // === Resume Mode: existing workspace ===
         isResume = true;
         console.log('=== RESUME MODE ===');
         console.log(`Workspace: ${resumeFromWorkspace}\n`);
@@ -255,7 +254,6 @@ async function startPipeline(): Promise<void> {
         workflowId = `${resumeFromWorkspace}_resume_${Date.now()}`;
         sessionId = resumeFromWorkspace;
       } else {
-        // === New Named Workspace ===
         if (!isValidWorkspaceName(resumeFromWorkspace)) {
           console.error(`ERROR: Invalid workspace name: "${resumeFromWorkspace}"`);
           console.error('  Must be 1-128 characters, alphanumeric/hyphens/underscores, starting with alphanumeric');
@@ -269,7 +267,6 @@ async function startPipeline(): Promise<void> {
         sessionId = resumeFromWorkspace;
       }
     } else {
-      // === New Auto-Named Workflow ===
       const hostname = sanitizeHostname(webUrl);
       workflowId = customWorkflowId || `${hostname}_shannon-${Date.now()}`;
       sessionId = workflowId;
@@ -278,8 +275,8 @@ async function startPipeline(): Promise<void> {
     const input: PipelineInput = {
       webUrl,
       repoPath,
-      workflowId, // Add for audit correlation
+      workflowId,
-      sessionId, // Workspace directory name
+      sessionId,
       ...(configPath && { configPath }),
       ...(outputPath && { outputPath }),
       ...(pipelineTestingMode && { pipelineTestingMode }),
@@ -287,7 +284,6 @@ async function startPipeline(): Promise<void> {
       ...(terminatedWorkflows.length > 0 && { terminatedWorkflows }),
     };
 
-    // Determine output directory for display (use sessionId for persistent directory)
     // Use displayOutputPath (host path) if provided, otherwise fall back to outputPath or default
     const effectiveDisplayPath = displayOutputPath || outputPath || './audit-logs';
     const outputDir = `${effectiveDisplayPath}/${sessionId}`;

src/temporal/shared.ts

@@ -3,15 +3,13 @@ import { defineQuery } from '@temporalio/workflow';
 export type { AgentMetrics } from '../types/metrics.js';
 import type { AgentMetrics } from '../types/metrics.js';
 
-// === Types ===
-
 export interface PipelineInput {
   webUrl: string;
   repoPath: string;
   configPath?: string;
   outputPath?: string;
   pipelineTestingMode?: boolean;
-  workflowId?: string; // Added by client, used for audit correlation
+  workflowId?: string; // Used for audit correlation
   sessionId?: string; // Workspace directory name (distinct from workflowId for named workspaces)
   resumeFromWorkspace?: string; // Workspace name to resume from
   terminatedWorkflows?: string[]; // Workflows terminated during resume
@@ -62,6 +60,4 @@ export interface VulnExploitPipelineResult {
   error: string | null;
 }
 
-// === Queries ===
-
 export const getProgress = defineQuery<PipelineProgress>('getProgress');

src/temporal/workflows.ts

@@ -105,11 +105,9 @@ export async function pentestPipelineWorkflow(
 ): Promise<PipelineState> {
   const { workflowId } = workflowInfo();
 
-  // Select activity proxy based on testing mode
   // Pipeline testing uses fast retry intervals (10s) for quick iteration
   const a = input.pipelineTestingMode ? testActs : acts;
 
-  // Workflow state (queryable)
   const state: PipelineState = {
     status: 'running',
     currentPhase: null,
@@ -122,7 +120,6 @@ export async function pentestPipelineWorkflow(
     summary: null,
   };
 
-  // Register query handler for real-time progress inspection
   setHandler(getProgress, (): PipelineProgress => ({
     ...state,
     workflowId,
@@ -147,18 +144,15 @@ export async function pentestPipelineWorkflow(
     }),
   };
 
-  // === RESUME LOGIC ===
   let resumeState: ResumeState | null = null;
 
   if (input.resumeFromWorkspace) {
-    // Load resume state from existing workspace
     resumeState = await a.loadResumeState(
       input.resumeFromWorkspace,
       input.webUrl,
       input.repoPath
     );
 
-    // Restore git checkpoint and clean up partial deliverables
     const incompleteAgents = ALL_AGENTS.filter(
       (agentName) => !resumeState!.completedAgents.includes(agentName)
     ) as AgentName[];
@@ -169,7 +163,6 @@ export async function pentestPipelineWorkflow(
       incompleteAgents
     );
 
-    // Check if all agents are already complete
     if (resumeState.completedAgents.length === ALL_AGENTS.length) {
       log.info(`All ${ALL_AGENTS.length} agents already completed. Nothing to resume.`);
       state.status = 'completed';
@@ -178,7 +171,6 @@ export async function pentestPipelineWorkflow(
       return state;
     }
 
-    // Record resume attempt in session.json and write resume header to workflow.log
     await a.recordResumeAttempt(
       activityInput,
       input.terminatedWorkflows || [],
@@ -190,7 +182,6 @@ export async function pentestPipelineWorkflow(
     log.info('Resume state loaded and workspace restored');
   }
 
-  // Helper to check if an agent should be skipped
   const shouldSkip = (agentName: string): boolean => {
     return resumeState?.completedAgents.includes(agentName) ?? false;
   };
@@ -413,7 +404,6 @@ export async function pentestPipelineWorkflow(
       state.completedAgents.push('report');
     }
 
-    // === Complete ===
     state.status = 'completed';
     state.currentPhase = null;
     state.currentAgent = null;

src/utils/metrics.ts

@@ -4,8 +4,6 @@
 // it under the terms of the GNU Affero General Public License version 3
 // as published by the Free Software Foundation.
 
-// Timing utilities
-
 export class Timer {
   name: string;
   startTime: number;