diff --git a/login_resources/generate-totp-standalone.mjs b/login_resources/generate-totp-standalone.mjs
deleted file mode 100644
index caeb5dc..0000000
--- a/login_resources/generate-totp-standalone.mjs
+++ /dev/null
@@ -1,131 +0,0 @@
-#!/usr/bin/env node
-
-import { createHmac } from 'crypto';
-
-/**
- * Standalone TOTP generator that doesn't require external dependencies
- * Based on RFC 6238 (TOTP: Time-Based One-Time Password Algorithm)
- */
-
-function parseArgs() {
-  const args = {};
-  for (let i = 2; i < process.argv.length; i++) {
-    if (process.argv[i] === '--secret' && i + 1 < process.argv.length) {
-      args.secret = process.argv[i + 1];
-      i++; // Skip the next argument since it's the value
-    } else if (process.argv[i] === '--help' || process.argv[i] === '-h') {
-      args.help = true;
-    }
-  }
-  return args;
-}
-
-function showHelp() {
-  console.log(`
-Usage: node generate-totp-standalone.mjs --secret <TOTP_SECRET>
-
-Generate a Time-based One-Time Password (TOTP) from a secret key.
-This standalone version doesn't require external dependencies.
-
-Options:
-  --secret <secret>  The base32-encoded TOTP secret key (required)
-  --help, -h        Show this help message
-
-Examples:
-  node generate-totp-standalone.mjs --secret "JBSWY3DPEHPK3PXP"
-  node generate-totp-standalone.mjs --secret "u4e2ewg3d6w7gya3p7plgkef6zgfzo23"
-
-Output:
-  A 6-digit TOTP code (e.g., 123456)
-`);
-}
-
-// Base32 decoding function
-function base32Decode(encoded) {
-  const alphabet = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ234567';
-  const cleanInput = encoded.toUpperCase().replace(/[^A-Z2-7]/g, '');
-  
-  if (cleanInput.length === 0) {
-    return Buffer.alloc(0);
-  }
-  
-  const output = [];
-  let bits = 0;
-  let value = 0;
-  
-  for (const char of cleanInput) {
-    const index = alphabet.indexOf(char);
-    if (index === -1) {
-      throw new Error(`Invalid base32 character: ${char}`);
-    }
-    
-    value = (value << 5) | index;
-    bits += 5;
-    
-    if (bits >= 8) {
-      output.push((value >>> (bits - 8)) & 255);
-      bits -= 8;
-    }
-  }
-  
-  return Buffer.from(output);
-}
-
-// HOTP implementation (RFC 4226)
-function generateHOTP(secret, counter, digits = 6) {
-  const key = base32Decode(secret);
-  
-  // Convert counter to 8-byte buffer (big-endian)
-  const counterBuffer = Buffer.alloc(8);
-  counterBuffer.writeBigUInt64BE(BigInt(counter));
-  
-  // Generate HMAC-SHA1
-  const hmac = createHmac('sha1', key);
-  hmac.update(counterBuffer);
-  const hash = hmac.digest();
-  
-  // Dynamic truncation
-  const offset = hash[hash.length - 1] & 0x0f;
-  const code = (
-    ((hash[offset] & 0x7f) << 24) |
-    ((hash[offset + 1] & 0xff) << 16) |
-    ((hash[offset + 2] & 0xff) << 8) |
-    (hash[offset + 3] & 0xff)
-  );
-  
-  // Generate digits
-  const otp = (code % Math.pow(10, digits)).toString().padStart(digits, '0');
-  return otp;
-}
-
-// TOTP implementation (RFC 6238)
-function generateTOTP(secret, timeStep = 30, digits = 6) {
-  const currentTime = Math.floor(Date.now() / 1000);
-  const counter = Math.floor(currentTime / timeStep);
-  return generateHOTP(secret, counter, digits);
-}
-
-function main() {
-  const args = parseArgs();
-  
-  if (args.help) {
-    showHelp();
-    return;
-  }
-  
-  if (!args.secret) {
-    console.error('Error: --secret parameter is required');
-    console.error('Use --help for usage information');
-    process.exit(1);
-  }
-  
-  try {
-    const totpCode = generateTOTP(args.secret);
-    console.log(totpCode);
-  } catch (error) {
-    console.error(`Error: ${error.message}`);
-    process.exit(1);
-  }
-}
-
-main();
\ No newline at end of file
diff --git a/mcp-server/src/index.js b/mcp-server/src/index.js
index 699f313..18e1fe0 100644
--- a/mcp-server/src/index.js
+++ b/mcp-server/src/index.js
@@ -28,16 +28,6 @@ export function createShannonHelperServer(targetDir) {
   });
 }
 
-/**
- * Legacy export for backward compatibility
- * @deprecated Use createShannonHelperServer(targetDir) instead
- */
-export const shannonHelperServer = createSdkMcpServer({
-  name: 'shannon-helper',
-  version: '1.0.0',
-  tools: [saveDeliverableTool, generateTotpTool],
-});
-
 // Export tools for direct usage if needed
 export { saveDeliverableTool, generateTotpTool };
 
diff --git a/mcp-server/src/tools/index.js b/mcp-server/src/tools/index.js
deleted file mode 100644
index 7d50008..0000000
--- a/mcp-server/src/tools/index.js
+++ /dev/null
@@ -1,6 +0,0 @@
-/**
- * MCP Tools barrel export
- */
-
-export * from './save-deliverable.js';
-export * from './generate-totp.js';
diff --git a/mcp-server/src/utils/error-formatter.js b/mcp-server/src/utils/error-formatter.js
index d811e51..0f5883c 100644
--- a/mcp-server/src/utils/error-formatter.js
+++ b/mcp-server/src/utils/error-formatter.js
@@ -31,24 +31,6 @@ export function createValidationError(message, retryable = true, context) {
   };
 }
 
-/**
- * Create a file system error response
- *
- * @param {string} message
- * @param {boolean} [retryable=false]
- * @param {Record<string, unknown>} [context]
- * @returns {ErrorResponse}
- */
-export function createFileSystemError(message, retryable = false, context) {
-  return {
-    status: 'error',
-    message,
-    errorType: 'FileSystemError',
-    retryable,
-    context,
-  };
-}
-
 /**
  * Create a crypto error response
  *
diff --git a/mcp-server/src/utils/index.js b/mcp-server/src/utils/index.js
deleted file mode 100644
index cdf4357..0000000
--- a/mcp-server/src/utils/index.js
+++ /dev/null
@@ -1,6 +0,0 @@
-/**
- * Utilities barrel export
- */
-
-export * from './file-operations.js';
-export * from './error-formatter.js';
diff --git a/mcp-server/src/validation/index.js b/mcp-server/src/validation/index.js
deleted file mode 100644
index adf3caa..0000000
--- a/mcp-server/src/validation/index.js
+++ /dev/null
@@ -1,6 +0,0 @@
-/**
- * Validation layer barrel export
- */
-
-export * from './queue-validator.js';
-export * from './totp-validator.js';
diff --git a/src/agent-status.js b/src/agent-status.js
deleted file mode 100644
index aa3ba7f..0000000
--- a/src/agent-status.js
+++ /dev/null
@@ -1,309 +0,0 @@
-import chalk from 'chalk';
-import { path } from 'zx';
-
-export class AgentStatusManager {
-  constructor(options = {}) {
-    this.mode = options.mode || 'parallel'; // 'parallel' or 'single'
-    this.activeStatuses = new Map();
-    this.lastStatusLine = '';
-    this.hiddenOperationCount = 0;
-    this.lastSummaryCount = 0;
-    this.summaryInterval = options.summaryInterval || 10;
-    this.showTodos = options.showTodos !== false;
-
-    // Tools to completely hide in output
-    this.suppressedTools = new Set([
-      'Read', 'Write', 'Edit', 'MultiEdit',
-      'Grep', 'Glob', 'LS'
-    ]);
-
-    // Tools that might be noisy bash commands to hide
-    this.hiddenBashCommands = new Set([
-      'pwd', 'echo', 'ls', 'cd'
-    ]);
-  }
-
-  /**
-   * Update status for an agent based on its current turn data
-   */
-  updateAgentStatus(agentName, turnData) {
-    if (this.mode === 'single') {
-      this.handleSingleAgentOutput(agentName, turnData);
-    } else {
-      const status = this.extractMeaningfulStatus(turnData);
-      if (status) {
-        this.activeStatuses.set(agentName, status);
-        this.redrawStatusLine();
-      }
-    }
-  }
-
-  /**
-   * Handle output for single agent mode with clean formatting
-   */
-  handleSingleAgentOutput(agentName, turnData) {
-    const toolUse = turnData.tool_use;
-    const text = turnData.assistant_text;
-    const turnCount = turnData.turnCount;
-
-    // Check if this is a tool we should hide
-    if (toolUse && this.shouldHideTool(toolUse)) {
-      this.hiddenOperationCount++;
-
-      // Show summary every N hidden operations
-      if (this.hiddenOperationCount - this.lastSummaryCount >= this.summaryInterval) {
-        const operationCount = this.hiddenOperationCount - this.lastSummaryCount;
-        console.log(chalk.gray(`    [${operationCount} file operations...]`));
-        this.lastSummaryCount = this.hiddenOperationCount;
-      }
-      return;
-    }
-
-    // Format and show meaningful tools
-    if (toolUse) {
-      const formatted = this.formatMeaningfulTool(toolUse);
-      if (formatted) {
-        console.log(`🤖 ${formatted}`);
-        return;
-      }
-    }
-
-    // For turns without tool use, just ignore them silently
-    // These are planning/thinking turns that don't need any output
-  }
-
-  /**
-   * Check if a tool should be hidden from output
-   */
-  shouldHideTool(toolUse) {
-    const toolName = toolUse.name;
-
-    // Always hide these tools
-    if (this.suppressedTools.has(toolName)) {
-      return true;
-    }
-
-    // Hide TodoWrite unless we're configured to show todos
-    if (toolName === 'TodoWrite' && !this.showTodos) {
-      return true;
-    }
-
-    // Hide simple bash commands
-    if (toolName === 'Bash') {
-      const command = toolUse.input?.command || '';
-      const simpleCommand = command.split(' ')[0];
-      return this.hiddenBashCommands.has(simpleCommand);
-    }
-
-    return false;
-  }
-
-  /**
-   * Format meaningful tools for single agent display
-   */
-  formatMeaningfulTool(toolUse) {
-    const toolName = toolUse.name;
-    const input = toolUse.input || {};
-
-    switch (toolName) {
-      case 'Task':
-        const description = input.description || 'analysis agent';
-        return `🚀 Launching ${description}`;
-
-      case 'TodoWrite':
-        if (this.showTodos) {
-          return this.formatTodoUpdate(input);
-        }
-        return null;
-
-      case 'WebFetch':
-        const domain = this.extractDomain(input.url || '');
-        return `🌐 Fetching ${domain}`;
-
-      case 'Bash':
-        // Only show meaningful bash commands
-        const command = input.command || '';
-        if (command.includes('nmap') || command.includes('subfinder') || command.includes('whatweb')) {
-          const tool = command.split(' ')[0];
-          return `🔍 Running ${tool}`;
-        }
-        return null;
-
-      // Browser tools (keep existing formatting)
-      default:
-        if (toolName.startsWith('mcp__playwright__browser_')) {
-          return this.extractBrowserAction(toolUse);
-        }
-    }
-
-    return null;
-  }
-
-  /**
-   * Format TodoWrite updates for display
-   */
-  formatTodoUpdate(input) {
-    if (!input.todos || !Array.isArray(input.todos)) {
-      return null;
-    }
-
-    const todos = input.todos;
-    const inProgress = todos.filter(t => t.status === 'in_progress');
-    const completed = todos.filter(t => t.status === 'completed');
-
-    if (completed.length > 0) {
-      const recent = completed[completed.length - 1];
-      return `✅ ${recent.content.slice(0, 50)}${recent.content.length > 50 ? '...' : ''}`;
-    }
-
-    if (inProgress.length > 0) {
-      const current = inProgress[0];
-      return `🔄 ${current.content.slice(0, 50)}${current.content.length > 50 ? '...' : ''}`;
-    }
-
-    return null;
-  }
-
-  /**
-   * Extract meaningful status from turn data, suppressing internal operations
-   */
-  extractMeaningfulStatus(turnData) {
-    // Check for tool use first
-    if (turnData.tool_use?.name) {
-      // Suppress internal operations completely
-      if (this.suppressedTools.has(turnData.tool_use.name)) {
-        return null;
-      }
-
-      // Show browser testing actions
-      if (turnData.tool_use.name.startsWith('mcp__playwright__browser_')) {
-        return this.extractBrowserAction(turnData.tool_use);
-      }
-
-      // Show Task agent launches
-      if (turnData.tool_use.name === 'Task') {
-        const description = turnData.tool_use.input?.description || 'analysis';
-        return `🚀 ${description.slice(0, 40)}`;
-      }
-    }
-
-    // Parse assistant text for progress milestones
-    if (turnData.assistant_text) {
-      return this.extractProgressFromText(turnData.assistant_text);
-    }
-
-    return null; // Suppress everything else
-  }
-
-  /**
-   * Extract browser action details
-   */
-  extractBrowserAction(toolUse) {
-    const actionType = toolUse.name.split('_').pop();
-
-    switch (actionType) {
-      case 'navigate':
-        const url = toolUse.input?.url || '';
-        const domain = this.extractDomain(url);
-        return `🌐 Testing ${domain}`;
-
-      case 'click':
-        const element = toolUse.input?.element || 'element';
-        return `🖱️ Clicking ${element.slice(0, 20)}`;
-
-      case 'fill':
-      case 'form':
-        return `📝 Testing form inputs`;
-
-      case 'snapshot':
-        return `📸 Capturing page state`;
-
-      case 'type':
-        return `⌨️ Testing input fields`;
-
-      default:
-        return `🌐 Browser: ${actionType}`;
-    }
-  }
-
-  /**
-   * Extract meaningful progress from assistant text (single-agent mode only)
-   */
-  extractProgressFromText(text) {
-    // Only extract progress for single agents, not parallel ones
-    if (this.mode !== 'single') {
-      return null;
-    }
-
-    // For single agents, be very conservative about what we show
-    // Most progress should come from tool formatting, not text parsing
-    return null;
-  }
-
-  /**
-   * Extract domain from URL for display
-   */
-  extractDomain(url) {
-    try {
-      const urlObj = new URL(url);
-      return urlObj.hostname || url.slice(0, 30);
-    } catch {
-      return url.slice(0, 30);
-    }
-  }
-
-  /**
-   * Redraw the status line showing all active agents
-   */
-  redrawStatusLine() {
-    // Clear previous line
-    if (this.lastStatusLine) {
-      process.stdout.write('\r' + ' '.repeat(this.lastStatusLine.length) + '\r');
-    }
-
-    // Build new status line
-    const statusEntries = Array.from(this.activeStatuses.entries())
-      .map(([agent, status]) => `[${chalk.cyan(agent)}] ${status}`)
-      .join(' | ');
-
-    if (statusEntries) {
-      process.stdout.write(statusEntries);
-      this.lastStatusLine = statusEntries.replace(/\u001b\[[0-9;]*m/g, ''); // Remove ANSI codes for length calc
-    }
-  }
-
-  /**
-   * Clear status for a specific agent
-   */
-  clearAgentStatus(agentName) {
-    this.activeStatuses.delete(agentName);
-    this.redrawStatusLine();
-  }
-
-  /**
-   * Clear all statuses and finish the status line
-   */
-  finishStatusLine() {
-    if (this.lastStatusLine) {
-      process.stdout.write('\n'); // Move to next line
-      this.lastStatusLine = '';
-      this.activeStatuses.clear();
-    }
-  }
-
-  /**
-   * Parse JSON tool use from message content
-   */
-  parseToolUse(content) {
-    try {
-      // Look for JSON tool use patterns
-      const jsonMatch = content.match(/\{"type":"tool_use".*?\}/s);
-      if (jsonMatch) {
-        return JSON.parse(jsonMatch[0]);
-      }
-    } catch (error) {
-      // Ignore parsing errors
-    }
-    return null;
-  }
-}
\ No newline at end of file
diff --git a/src/checkpoint-manager.js b/src/checkpoint-manager.js
index f2783af..0685ad4 100644
--- a/src/checkpoint-manager.js
+++ b/src/checkpoint-manager.js
@@ -76,7 +76,7 @@ const rollbackGitToCommit = async (targetRepo, commitHash) => {
 };
 
 // Run a single agent with retry logic and checkpointing
-export const runSingleAgent = async (agentName, session, pipelineTestingMode, runClaudePromptWithRetry, loadPrompt, allowRerun = false, skipWorkspaceClean = false) => {
+const runSingleAgent = async (agentName, session, pipelineTestingMode, runClaudePromptWithRetry, loadPrompt, allowRerun = false, skipWorkspaceClean = false) => {
   // Validate agent first
   const agent = validateAgent(agentName);
 
@@ -299,7 +299,7 @@ export const runSingleAgent = async (agentName, session, pipelineTestingMode, ru
 };
 
 // Run multiple agents in sequence
-export const runAgentRange = async (startAgent, endAgent, session, pipelineTestingMode, runClaudePromptWithRetry, loadPrompt) => {
+const runAgentRange = async (startAgent, endAgent, session, pipelineTestingMode, runClaudePromptWithRetry, loadPrompt) => {
   const agents = validateAgentRange(startAgent, endAgent);
   
   console.log(chalk.cyan(`\n🔄 Running agent range: ${startAgent} to ${endAgent} (${agents.length} agents)`));
@@ -323,7 +323,7 @@ export const runAgentRange = async (startAgent, endAgent, session, pipelineTesti
 };
 
 // Run vulnerability agents in parallel
-export const runParallelVuln = async (session, pipelineTestingMode, runClaudePromptWithRetry, loadPrompt) => {
+const runParallelVuln = async (session, pipelineTestingMode, runClaudePromptWithRetry, loadPrompt) => {
   const vulnAgents = ['injection-vuln', 'xss-vuln', 'auth-vuln', 'ssrf-vuln', 'authz-vuln'];
   const activeAgents = vulnAgents.filter(agent => !session.completedAgents.includes(agent));
 
@@ -421,7 +421,7 @@ export const runParallelVuln = async (session, pipelineTestingMode, runClaudePro
 };
 
 // Run exploitation agents in parallel
-export const runParallelExploit = async (session, pipelineTestingMode, runClaudePromptWithRetry, loadPrompt) => {
+const runParallelExploit = async (session, pipelineTestingMode, runClaudePromptWithRetry, loadPrompt) => {
   const exploitAgents = ['injection-exploit', 'xss-exploit', 'auth-exploit', 'ssrf-exploit', 'authz-exploit'];
 
   // Get fresh session data to ensure we have the latest vulnerability analysis results
diff --git a/src/utils/git-manager.js b/src/utils/git-manager.js
index 83617a8..32ef3d8 100644
--- a/src/utils/git-manager.js
+++ b/src/utils/git-manager.js
@@ -72,7 +72,7 @@ export const executeGitCommandWithRetry = async (commandArgs, sourceDir, descrip
 };
 
 // Pure functions for Git workspace management
-export const cleanWorkspace = async (sourceDir, reason = 'clean start') => {
+const cleanWorkspace = async (sourceDir, reason = 'clean start') => {
   console.log(chalk.blue(`    🧹 Cleaning workspace for ${reason}`));
   try {
     // Check for uncommitted changes