chore: remove ~500 lines of dead code identified by knip

Remove unused files and exports to improve codebase maintainability:

Phase 1 - Deleted files (5):
- login_resources/generate-totp-standalone.mjs (replaced by MCP tool)
- mcp-server/src/tools/index.js (unused barrel export)
- mcp-server/src/utils/index.js (unused barrel export)
- mcp-server/src/validation/index.js (unused barrel export)
- src/agent-status.js (deprecated 309-line status manager)

Phase 2 - Removed unused exports (3):
- mcp-server/src/index.js: shannonHelperServer constant
- mcp-server/src/utils/error-formatter.js: createFileSystemError function
- src/utils/git-manager.js: cleanWorkspace (now internal-only)

Phase 3 - Unexported internal functions (4):
- src/checkpoint-manager.js: runSingleAgent, runAgentRange,
  runParallelVuln, runParallelExploit (internal use only)

All Shannon CLI commands tested and verified working.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

src/agent-status.js

@@ -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;
-  }
-}

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

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