claude-code-workflow 6.1.3 → 6.2.1

package/src/tools/codex-lens.ts

@@ -0,0 +1,1141 @@
+/**
+ * CodexLens Tool - Bridge between CCW and CodexLens Python package
+ * Provides code indexing and semantic search via spawned Python process
+ *
+ * Features:
+ * - Automatic venv bootstrap at ~/.codexlens/venv
+ * - JSON protocol communication
+ * - Symbol extraction and semantic search
+ * - FTS5 full-text search
+ */
+
+import { z } from 'zod';
+import type { ToolSchema, ToolResult } from '../types/tool.js';
+import { spawn, execSync, exec } from 'child_process';
+import { existsSync, mkdirSync } from 'fs';
+import { join, dirname } from 'path';
+import { homedir } from 'os';
+import { fileURLToPath } from 'url';
+
+// Get directory of this module
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = dirname(__filename);
+
+// CodexLens configuration
+const CODEXLENS_DATA_DIR = join(homedir(), '.codexlens');
+const CODEXLENS_VENV = join(CODEXLENS_DATA_DIR, 'venv');
+const VENV_PYTHON =
+  process.platform === 'win32'
+    ? join(CODEXLENS_VENV, 'Scripts', 'python.exe')
+    : join(CODEXLENS_VENV, 'bin', 'python');
+
+// Bootstrap status cache
+let bootstrapChecked = false;
+let bootstrapReady = false;
+
+// Track running indexing process for cancellation
+let currentIndexingProcess: ReturnType<typeof spawn> | null = null;
+let currentIndexingAborted = false;
+
+// Define Zod schema for validation
+const ParamsSchema = z.object({
+  action: z.enum([
+    'init',
+    'search',
+    'search_files',
+    'status',
+    'symbol',
+    'check',
+    'update',
+    'bootstrap',
+  ]),
+  path: z.string().optional(),
+  query: z.string().optional(),
+  mode: z.enum(['auto', 'text', 'semantic', 'exact', 'fuzzy', 'hybrid', 'vector', 'pure-vector']).default('auto'),
+  format: z.enum(['json', 'text', 'pretty']).default('json'),
+  languages: z.array(z.string()).optional(),
+  limit: z.number().default(20),
+  enrich: z.boolean().default(false),
+  // Additional fields for internal functions
+  file: z.string().optional(),
+  key: z.string().optional(),
+  value: z.string().optional(),
+  newPath: z.string().optional(),
+  all: z.boolean().optional(),
+});
+
+type Params = z.infer<typeof ParamsSchema>;
+
+interface ReadyStatus {
+  ready: boolean;
+  error?: string;
+  version?: string;
+}
+
+interface SemanticStatus {
+  available: boolean;
+  backend?: string;
+  error?: string;
+}
+
+interface BootstrapResult {
+  success: boolean;
+  error?: string;
+  message?: string;
+}
+
+interface ExecuteResult {
+  success: boolean;
+  output?: string;
+  error?: string;
+  message?: string;
+  results?: unknown;
+  files?: unknown;
+  symbols?: unknown;
+  status?: unknown;
+  config?: unknown;
+  cleanResult?: unknown;
+  ready?: boolean;
+  version?: string;
+}
+
+interface ExecuteOptions {
+  timeout?: number;
+  cwd?: string;
+  onProgress?: (progress: ProgressInfo) => void;
+}
+
+interface ProgressInfo {
+  stage: string;
+  message: string;
+  percent: number;
+  filesProcessed?: number;
+  totalFiles?: number;
+}
+
+/**
+ * Detect available Python 3 executable
+ * @returns Python executable command
+ */
+function getSystemPython(): string {
+  const commands = process.platform === 'win32' ? ['python', 'py', 'python3'] : ['python3', 'python'];
+
+  for (const cmd of commands) {
+    try {
+      const version = execSync(`${cmd} --version 2>&1`, { encoding: 'utf8' });
+      if (version.includes('Python 3')) {
+        return cmd;
+      }
+    } catch {
+      // Try next command
+    }
+  }
+  throw new Error('Python 3 not found. Please install Python 3 and ensure it is in PATH.');
+}
+
+/**
+ * Check if CodexLens venv exists and has required packages
+ * @returns Ready status
+ */
+async function checkVenvStatus(): Promise<ReadyStatus> {
+  // Check venv exists
+  if (!existsSync(CODEXLENS_VENV)) {
+    return { ready: false, error: 'Venv not found' };
+  }
+
+  // Check python executable exists
+  if (!existsSync(VENV_PYTHON)) {
+    return { ready: false, error: 'Python executable not found in venv' };
+  }
+
+  // Check codexlens is importable
+  return new Promise((resolve) => {
+    const child = spawn(VENV_PYTHON, ['-c', 'import codexlens; print(codexlens.__version__)'], {
+      stdio: ['ignore', 'pipe', 'pipe'],
+      timeout: 10000,
+    });
+
+    let stdout = '';
+    let stderr = '';
+
+    child.stdout.on('data', (data) => {
+      stdout += data.toString();
+    });
+    child.stderr.on('data', (data) => {
+      stderr += data.toString();
+    });
+
+    child.on('close', (code) => {
+      if (code === 0) {
+        resolve({ ready: true, version: stdout.trim() });
+      } else {
+        resolve({ ready: false, error: `CodexLens not installed: ${stderr}` });
+      }
+    });
+
+    child.on('error', (err) => {
+      resolve({ ready: false, error: `Failed to check venv: ${err.message}` });
+    });
+  });
+}
+
+/**
+ * Check if semantic search dependencies are installed
+ * @returns Semantic status
+ */
+async function checkSemanticStatus(): Promise<SemanticStatus> {
+  // First check if CodexLens is installed
+  const venvStatus = await checkVenvStatus();
+  if (!venvStatus.ready) {
+    return { available: false, error: 'CodexLens not installed' };
+  }
+
+  // Check semantic module availability
+  return new Promise((resolve) => {
+    const checkCode = `
+import sys
+try:
+    from codexlens.semantic import SEMANTIC_AVAILABLE, SEMANTIC_BACKEND
+    if SEMANTIC_AVAILABLE:
+        print(f"available:{SEMANTIC_BACKEND}")
+    else:
+        print("unavailable")
+except Exception as e:
+    print(f"error:{e}")
+`;
+    const child = spawn(VENV_PYTHON, ['-c', checkCode], {
+      stdio: ['ignore', 'pipe', 'pipe'],
+      timeout: 15000,
+    });
+
+    let stdout = '';
+    let stderr = '';
+
+    child.stdout.on('data', (data) => {
+      stdout += data.toString();
+    });
+    child.stderr.on('data', (data) => {
+      stderr += data.toString();
+    });
+
+    child.on('close', (code) => {
+      const output = stdout.trim();
+      if (output.startsWith('available:')) {
+        const backend = output.split(':')[1];
+        resolve({ available: true, backend });
+      } else if (output === 'unavailable') {
+        resolve({ available: false, error: 'Semantic dependencies not installed' });
+      } else {
+        resolve({ available: false, error: output || stderr || 'Unknown error' });
+      }
+    });
+
+    child.on('error', (err) => {
+      resolve({ available: false, error: `Check failed: ${err.message}` });
+    });
+  });
+}
+
+/**
+ * Install semantic search dependencies (fastembed, ONNX-based, ~200MB)
+ * @returns Bootstrap result
+ */
+async function installSemantic(): Promise<BootstrapResult> {
+  // First ensure CodexLens is installed
+  const venvStatus = await checkVenvStatus();
+  if (!venvStatus.ready) {
+    return { success: false, error: 'CodexLens not installed. Install CodexLens first.' };
+  }
+
+  const pipPath =
+    process.platform === 'win32'
+      ? join(CODEXLENS_VENV, 'Scripts', 'pip.exe')
+      : join(CODEXLENS_VENV, 'bin', 'pip');
+
+  return new Promise((resolve) => {
+    console.log('[CodexLens] Installing semantic search dependencies (fastembed)...');
+    console.log('[CodexLens] Using ONNX-based fastembed backend (~200MB)');
+
+    const child = spawn(pipPath, ['install', 'numpy>=1.24', 'fastembed>=0.2'], {
+      stdio: ['ignore', 'pipe', 'pipe'],
+      timeout: 600000, // 10 minutes for potential model download
+    });
+
+    let stdout = '';
+    let stderr = '';
+
+    child.stdout.on('data', (data) => {
+      stdout += data.toString();
+      // Log progress
+      const line = data.toString().trim();
+      if (line.includes('Downloading') || line.includes('Installing') || line.includes('Collecting')) {
+        console.log(`[CodexLens] ${line}`);
+      }
+    });
+
+    child.stderr.on('data', (data) => {
+      stderr += data.toString();
+    });
+
+    child.on('close', (code) => {
+      if (code === 0) {
+        console.log('[CodexLens] Semantic dependencies installed successfully');
+        resolve({ success: true });
+      } else {
+        resolve({ success: false, error: `Installation failed: ${stderr || stdout}` });
+      }
+    });
+
+    child.on('error', (err) => {
+      resolve({ success: false, error: `Failed to run pip: ${err.message}` });
+    });
+  });
+}
+
+/**
+ * Bootstrap CodexLens venv with required packages
+ * @returns Bootstrap result
+ */
+async function bootstrapVenv(): Promise<BootstrapResult> {
+  // Ensure data directory exists
+  if (!existsSync(CODEXLENS_DATA_DIR)) {
+    mkdirSync(CODEXLENS_DATA_DIR, { recursive: true });
+  }
+
+  // Create venv if not exists
+  if (!existsSync(CODEXLENS_VENV)) {
+    try {
+      console.log('[CodexLens] Creating virtual environment...');
+      const pythonCmd = getSystemPython();
+      execSync(`${pythonCmd} -m venv "${CODEXLENS_VENV}"`, { stdio: 'inherit' });
+    } catch (err) {
+      return { success: false, error: `Failed to create venv: ${(err as Error).message}` };
+    }
+  }
+
+  // Install codexlens with semantic extras
+  try {
+    console.log('[CodexLens] Installing codexlens package...');
+    const pipPath =
+      process.platform === 'win32'
+        ? join(CODEXLENS_VENV, 'Scripts', 'pip.exe')
+        : join(CODEXLENS_VENV, 'bin', 'pip');
+
+    // Try multiple local paths, then fall back to PyPI
+    const possiblePaths = [
+      join(process.cwd(), 'codex-lens'),
+      join(__dirname, '..', '..', '..', 'codex-lens'), // ccw/src/tools -> project root
+      join(homedir(), 'codex-lens'),
+    ];
+
+    let installed = false;
+    for (const localPath of possiblePaths) {
+      if (existsSync(join(localPath, 'pyproject.toml'))) {
+        console.log(`[CodexLens] Installing from local path: ${localPath}`);
+        execSync(`"${pipPath}" install -e "${localPath}"`, { stdio: 'inherit' });
+        installed = true;
+        break;
+      }
+    }
+
+    if (!installed) {
+      console.log('[CodexLens] Installing from PyPI...');
+      execSync(`"${pipPath}" install codexlens`, { stdio: 'inherit' });
+    }
+
+    return { success: true };
+  } catch (err) {
+    return { success: false, error: `Failed to install codexlens: ${(err as Error).message}` };
+  }
+}
+
+/**
+ * Ensure CodexLens is ready to use
+ * @returns Ready status
+ */
+async function ensureReady(): Promise<ReadyStatus> {
+  // Use cached result if already checked
+  if (bootstrapChecked && bootstrapReady) {
+    return { ready: true };
+  }
+
+  // Check current status
+  const status = await checkVenvStatus();
+  if (status.ready) {
+    bootstrapChecked = true;
+    bootstrapReady = true;
+    return { ready: true, version: status.version };
+  }
+
+  // Attempt bootstrap
+  const bootstrap = await bootstrapVenv();
+  if (!bootstrap.success) {
+    return { ready: false, error: bootstrap.error };
+  }
+
+  // Verify after bootstrap
+  const recheck = await checkVenvStatus();
+  bootstrapChecked = true;
+  bootstrapReady = recheck.ready;
+
+  return recheck;
+}
+
+/**
+ * Parse progress info from CodexLens output
+ * @param line - Output line to parse
+ * @returns Progress info or null
+ */
+function parseProgressLine(line: string): ProgressInfo | null {
+  // Parse file processing progress: "Processing file X/Y: path"
+  const fileMatch = line.match(/Processing file (\d+)\/(\d+):\s*(.+)/i);
+  if (fileMatch) {
+    const current = parseInt(fileMatch[1], 10);
+    const total = parseInt(fileMatch[2], 10);
+    return {
+      stage: 'indexing',
+      message: `Processing ${fileMatch[3]}`,
+      percent: Math.round((current / total) * 80) + 10, // 10-90%
+      filesProcessed: current,
+      totalFiles: total,
+    };
+  }
+
+  // Parse stage messages
+  if (line.includes('Discovering files')) {
+    return { stage: 'discover', message: 'Discovering files...', percent: 5 };
+  }
+  if (line.includes('Building index')) {
+    return { stage: 'build', message: 'Building index...', percent: 10 };
+  }
+  if (line.includes('Extracting symbols')) {
+    return { stage: 'symbols', message: 'Extracting symbols...', percent: 50 };
+  }
+  if (line.includes('Generating embeddings') || line.includes('Creating embeddings')) {
+    return { stage: 'embeddings', message: 'Generating embeddings...', percent: 70 };
+  }
+  // Note: "Finalizing index" and "Building ANN" are handled separately below
+  // Only match generic "Complete" here (not "Finalizing" which has specific handlers)
+
+  // Parse indexed count: "Indexed X files" - FTS complete, but embeddings may follow
+  const indexedMatch = line.match(/Indexed (\d+) files/i);
+  if (indexedMatch) {
+    return {
+      stage: 'fts_complete',  // Not 'complete' - embeddings generation may still be pending
+      message: `Indexed ${indexedMatch[1]} files, generating embeddings...`,
+      percent: 60,  // FTS done, embeddings starting
+      filesProcessed: parseInt(indexedMatch[1], 10),
+    };
+  }
+
+  // Parse embedding batch progress: "Batch X: N files, M chunks"
+  const batchMatch = line.match(/Batch (\d+):\s*(\d+) files,\s*(\d+) chunks/i);
+  if (batchMatch) {
+    return {
+      stage: 'embeddings',
+      message: `Embedding batch ${batchMatch[1]}: ${batchMatch[3]} chunks`,
+      percent: 70,  // Stay at 70% during embedding batches
+    };
+  }
+
+  // Parse embedding progress with file count
+  const embedProgressMatch = line.match(/Processing (\d+) files/i);
+  if (embedProgressMatch && line.toLowerCase().includes('embed')) {
+    return {
+      stage: 'embeddings',
+      message: `Processing ${embedProgressMatch[1]} files for embeddings`,
+      percent: 75,
+    };
+  }
+
+  // Parse finalizing ANN index
+  if (line.includes('Finalizing index') || line.includes('Building ANN')) {
+    return { stage: 'finalizing', message: 'Finalizing vector index...', percent: 90 };
+  }
+
+  // Parse embeddings complete message
+  const embedCompleteMatch = line.match(/Embeddings complete:\s*(\d+)\s*chunks/i);
+  if (embedCompleteMatch) {
+    return {
+      stage: 'embeddings_complete',
+      message: `Embeddings complete: ${embedCompleteMatch[1]} chunks`,
+      percent: 95,
+    };
+  }
+
+  // Parse generic completion (but not "Embeddings complete" which is handled above)
+  if (line.includes('Complete') && !line.toLowerCase().includes('embeddings complete')) {
+    return { stage: 'complete', message: 'Complete', percent: 98 };
+  }
+
+  return null;
+}
+
+/**
+ * Execute CodexLens CLI command with real-time progress updates
+ * @param args - CLI arguments
+ * @param options - Execution options
+ * @returns Execution result
+ */
+async function executeCodexLens(args: string[], options: ExecuteOptions = {}): Promise<ExecuteResult> {
+  const { timeout = 300000, cwd = process.cwd(), onProgress } = options; // Default 5 min
+
+  // Ensure ready
+  const readyStatus = await ensureReady();
+  if (!readyStatus.ready) {
+    return { success: false, error: readyStatus.error };
+  }
+
+  return new Promise((resolve) => {
+    // Build command string - quote paths for shell execution
+    const quotedPython = `"${VENV_PYTHON}"`;
+    const cmdArgs = args.map(arg => {
+      // Quote arguments that contain spaces or special characters
+      if (arg.includes(' ') || arg.includes('\\')) {
+        return `"${arg}"`;
+      }
+      return arg;
+    });
+
+    // Build full command - on Windows, prepend cd to handle different drives
+    let fullCmd: string;
+    if (process.platform === 'win32' && cwd) {
+      // Use cd /d to change drive and directory, then run command
+      fullCmd = `cd /d "${cwd}" && ${quotedPython} -m codexlens ${cmdArgs.join(' ')}`;
+    } else {
+      fullCmd = `${quotedPython} -m codexlens ${cmdArgs.join(' ')}`;
+    }
+
+    // Use spawn with shell for real-time progress updates
+    // spawn streams output in real-time, unlike exec which buffers until completion
+    const child = spawn(fullCmd, [], {
+      cwd: process.platform === 'win32' ? undefined : cwd,
+      shell: process.platform === 'win32' ? process.env.ComSpec || true : true,
+      timeout,
+    });
+
+    // Track indexing process for cancellation (only for init commands)
+    const isIndexingCommand = args.includes('init');
+    if (isIndexingCommand) {
+      currentIndexingProcess = child;
+      currentIndexingAborted = false;
+    }
+
+    let stdout = '';
+    let stderr = '';
+    let stdoutLineBuffer = '';
+    let stderrLineBuffer = '';
+    let timeoutHandle: NodeJS.Timeout | null = null;
+    let resolved = false;
+
+    // Helper to safely resolve only once
+    const safeResolve = (result: ExecuteResult) => {
+      if (resolved) return;
+      resolved = true;
+      if (timeoutHandle) {
+        clearTimeout(timeoutHandle);
+        timeoutHandle = null;
+      }
+      // Clear indexing process tracking
+      if (isIndexingCommand) {
+        currentIndexingProcess = null;
+      }
+      resolve(result);
+    };
+
+    // Set up timeout handler
+    if (timeout > 0) {
+      timeoutHandle = setTimeout(() => {
+        if (!resolved) {
+          child.kill('SIGTERM');
+          // Give it a moment to die gracefully, then force kill
+          setTimeout(() => {
+            if (!resolved) {
+              child.kill('SIGKILL');
+            }
+          }, 5000);
+          safeResolve({ success: false, error: 'Command timed out' });
+        }
+      }, timeout);
+    }
+
+    // Process stdout line by line for real-time progress
+    child.stdout?.on('data', (data: Buffer) => {
+      const chunk = data.toString();
+      stdoutLineBuffer += chunk;
+      stdout += chunk;
+
+      // Process complete lines
+      const lines = stdoutLineBuffer.split('\n');
+      stdoutLineBuffer = lines.pop() || ''; // Keep incomplete line in buffer
+
+      for (const line of lines) {
+        const trimmedLine = line.trim();
+        if (trimmedLine && onProgress) {
+          const progress = parseProgressLine(trimmedLine);
+          if (progress) {
+            onProgress(progress);
+          }
+        }
+      }
+    });
+
+    // Collect stderr
+    child.stderr?.on('data', (data: Buffer) => {
+      const chunk = data.toString();
+      stderrLineBuffer += chunk;
+      stderr += chunk;
+
+      // Also check stderr for progress (some tools output progress to stderr)
+      const lines = stderrLineBuffer.split('\n');
+      stderrLineBuffer = lines.pop() || '';
+
+      for (const line of lines) {
+        const trimmedLine = line.trim();
+        if (trimmedLine && onProgress) {
+          const progress = parseProgressLine(trimmedLine);
+          if (progress) {
+            onProgress(progress);
+          }
+        }
+      }
+    });
+
+    // Handle process errors (spawn failure)
+    child.on('error', (err) => {
+      safeResolve({ success: false, error: `Failed to start process: ${err.message}` });
+    });
+
+    // Handle process completion
+    child.on('close', (code) => {
+      // Process any remaining buffered content
+      if (stdoutLineBuffer.trim() && onProgress) {
+        const progress = parseProgressLine(stdoutLineBuffer.trim());
+        if (progress) {
+          onProgress(progress);
+        }
+      }
+
+      if (code === 0) {
+        safeResolve({ success: true, output: stdout.trim() });
+      } else {
+        safeResolve({ success: false, error: stderr.trim() || `Process exited with code ${code}` });
+      }
+    });
+  });
+}
+
+/**
+ * Initialize CodexLens index for a directory
+ * @param params - Parameters
+ * @returns Execution result
+ */
+async function initIndex(params: Params): Promise<ExecuteResult> {
+  const { path = '.', languages } = params;
+
+  const args = ['init', path];
+  if (languages && languages.length > 0) {
+    args.push('--languages', languages.join(','));
+  }
+
+  return executeCodexLens(args, { cwd: path });
+}
+
+/**
+ * Search code using CodexLens
+ * @param params - Search parameters
+ * @returns Execution result
+ */
+async function searchCode(params: Params): Promise<ExecuteResult> {
+  const { query, path = '.', limit = 20, mode = 'auto', enrich = false } = params;
+
+  if (!query) {
+    return { success: false, error: 'Query is required for search action' };
+  }
+
+  // Map MCP mode names to CLI mode names
+  const modeMap: Record<string, string> = {
+    'text': 'exact',
+    'semantic': 'pure-vector',
+    'auto': 'auto',
+    'exact': 'exact',
+    'fuzzy': 'fuzzy',
+    'hybrid': 'hybrid',
+    'vector': 'vector',
+    'pure-vector': 'pure-vector',
+  };
+
+  const cliMode = modeMap[mode] || 'auto';
+  const args = ['search', query, '--limit', limit.toString(), '--mode', cliMode, '--json'];
+
+  if (enrich) {
+    args.push('--enrich');
+  }
+
+  const result = await executeCodexLens(args, { cwd: path });
+
+  if (result.success && result.output) {
+    try {
+      result.results = JSON.parse(result.output);
+      delete result.output;
+    } catch {
+      // Keep raw output if JSON parse fails
+    }
+  }
+
+  return result;
+}
+
+/**
+ * Search code and return only file paths
+ * @param params - Search parameters
+ * @returns Execution result
+ */
+async function searchFiles(params: Params): Promise<ExecuteResult> {
+  const { query, path = '.', limit = 20, mode = 'auto', enrich = false } = params;
+
+  if (!query) {
+    return { success: false, error: 'Query is required for search_files action' };
+  }
+
+  // Map MCP mode names to CLI mode names
+  const modeMap: Record<string, string> = {
+    'text': 'exact',
+    'semantic': 'pure-vector',
+    'auto': 'auto',
+    'exact': 'exact',
+    'fuzzy': 'fuzzy',
+    'hybrid': 'hybrid',
+    'vector': 'vector',
+    'pure-vector': 'pure-vector',
+  };
+
+  const cliMode = modeMap[mode] || 'auto';
+  const args = ['search', query, '--files-only', '--limit', limit.toString(), '--mode', cliMode, '--json'];
+
+  if (enrich) {
+    args.push('--enrich');
+  }
+
+  const result = await executeCodexLens(args, { cwd: path });
+
+  if (result.success && result.output) {
+    try {
+      result.files = JSON.parse(result.output);
+      delete result.output;
+    } catch {
+      // Keep raw output if JSON parse fails
+    }
+  }
+
+  return result;
+}
+
+/**
+ * Extract symbols from a file
+ * @param params - Parameters
+ * @returns Execution result
+ */
+async function extractSymbols(params: Params): Promise<ExecuteResult> {
+  const { file } = params;
+
+  if (!file) {
+    return { success: false, error: 'File is required for symbol action' };
+  }
+
+  const args = ['symbol', file, '--json'];
+
+  const result = await executeCodexLens(args);
+
+  if (result.success && result.output) {
+    try {
+      result.symbols = JSON.parse(result.output);
+      delete result.output;
+    } catch {
+      // Keep raw output if JSON parse fails
+    }
+  }
+
+  return result;
+}
+
+/**
+ * Get index status
+ * @param params - Parameters
+ * @returns Execution result
+ */
+async function getStatus(params: Params): Promise<ExecuteResult> {
+  const { path = '.' } = params;
+
+  const args = ['status', '--json'];
+
+  const result = await executeCodexLens(args, { cwd: path });
+
+  if (result.success && result.output) {
+    try {
+      result.status = JSON.parse(result.output);
+      delete result.output;
+    } catch {
+      // Keep raw output if JSON parse fails
+    }
+  }
+
+  return result;
+}
+
+/**
+ * Show configuration
+ * @param params - Parameters
+ * @returns Execution result
+ */
+async function configShow(): Promise<ExecuteResult> {
+  const args = ['config', 'show', '--json'];
+  const result = await executeCodexLens(args);
+
+  if (result.success && result.output) {
+    try {
+      result.config = JSON.parse(result.output);
+      delete result.output;
+    } catch {
+      // Keep raw output if JSON parse fails
+    }
+  }
+
+  return result;
+}
+
+/**
+ * Set configuration value
+ * @param params - Parameters
+ * @returns Execution result
+ */
+async function configSet(params: Params): Promise<ExecuteResult> {
+  const { key, value } = params;
+
+  if (!key) {
+    return { success: false, error: 'key is required for config_set action' };
+  }
+  if (!value) {
+    return { success: false, error: 'value is required for config_set action' };
+  }
+
+  const args = ['config', 'set', key, value, '--json'];
+  const result = await executeCodexLens(args);
+
+  if (result.success && result.output) {
+    try {
+      result.config = JSON.parse(result.output);
+      delete result.output;
+    } catch {
+      // Keep raw output if JSON parse fails
+    }
+  }
+
+  return result;
+}
+
+/**
+ * Migrate indexes to new location
+ * @param params - Parameters
+ * @returns Execution result
+ */
+async function configMigrate(params: Params): Promise<ExecuteResult> {
+  const { newPath } = params;
+
+  if (!newPath) {
+    return { success: false, error: 'newPath is required for config_migrate action' };
+  }
+
+  const args = ['config', 'migrate', newPath, '--json'];
+  const result = await executeCodexLens(args, { timeout: 300000 }); // 5 min for migration
+
+  if (result.success && result.output) {
+    try {
+      result.config = JSON.parse(result.output);
+      delete result.output;
+    } catch {
+      // Keep raw output if JSON parse fails
+    }
+  }
+
+  return result;
+}
+
+/**
+ * Clean indexes
+ * @param params - Parameters
+ * @returns Execution result
+ */
+async function cleanIndexes(params: Params): Promise<ExecuteResult> {
+  const { path, all } = params;
+
+  const args = ['clean'];
+
+  if (all) {
+    args.push('--all');
+  } else if (path) {
+    args.push(path);
+  }
+
+  args.push('--json');
+  const result = await executeCodexLens(args);
+
+  if (result.success && result.output) {
+    try {
+      result.cleanResult = JSON.parse(result.output);
+      delete result.output;
+    } catch {
+      // Keep raw output if JSON parse fails
+    }
+  }
+
+  return result;
+}
+
+// Tool schema for MCP
+export const schema: ToolSchema = {
+  name: 'codex_lens',
+  description: `CodexLens - Code indexing and semantic search.
+
+Usage:
+  codex_lens(action="init", path=".")           # Index directory (auto-generates embeddings if available)
+  codex_lens(action="search", query="func")     # Search code (auto: hybrid if embeddings exist, else exact)
+  codex_lens(action="search", query="func", mode="hybrid")  # Force hybrid search
+  codex_lens(action="search_files", query="x")  # Search, return paths only
+
+Graph Enrichment:
+  codex_lens(action="search", query="func", enrich=true)  # Enrich results with code relationships
+
+Search Modes:
+  - auto: Auto-detect (hybrid if embeddings exist, exact otherwise) [default]
+  - exact/text: Exact FTS for code identifiers
+  - hybrid: Exact + Fuzzy + Vector fusion (best results, requires embeddings)
+  - fuzzy: Typo-tolerant search
+  - vector: Semantic + keyword
+  - pure-vector/semantic: Pure semantic search
+
+Note: For advanced operations (config, status, clean), use CLI directly: codexlens --help`,
+  inputSchema: {
+    type: 'object',
+    properties: {
+      action: {
+        type: 'string',
+        enum: [
+          'init',
+          'search',
+          'search_files',
+          'status',
+          'symbol',
+          'check',
+          'update',
+          'bootstrap',
+        ],
+        description: 'Action to perform: init/update (index directory), search (search code), search_files (search files only), status (index status), symbol (extract symbols), check (check if ready), bootstrap (setup venv)',
+      },
+      path: {
+        type: 'string',
+        description: 'Target directory path (for init, search, search_files). Defaults to current directory.',
+      },
+      query: {
+        type: 'string',
+        description: 'Search query (required for search and search_files actions)',
+      },
+      mode: {
+        type: 'string',
+        enum: ['auto', 'text', 'semantic', 'exact', 'fuzzy', 'hybrid', 'vector', 'pure-vector'],
+        description: 'Search mode: auto (default, hybrid if embeddings exist), text/exact (FTS), hybrid (best), fuzzy, vector, semantic/pure-vector',
+        default: 'auto',
+      },
+      format: {
+        type: 'string',
+        enum: ['json', 'text', 'pretty'],
+        description: 'Output format: json (default), text, pretty',
+        default: 'json',
+      },
+      languages: {
+        type: 'array',
+        items: { type: 'string' },
+        description: 'Languages to index (for init action). Example: ["javascript", "typescript", "python"]',
+      },
+      limit: {
+        type: 'number',
+        description: 'Maximum number of search results (for search and search_files actions)',
+        default: 20,
+      },
+      enrich: {
+        type: 'boolean',
+        description: 'Enrich search results with code graph relationships (calls, imports)',
+        default: false,
+      },
+    },
+    required: ['action'],
+  },
+};
+
+// Handler function
+export async function handler(params: Record<string, unknown>): Promise<ToolResult<ExecuteResult>> {
+  const parsed = ParamsSchema.safeParse(params);
+  if (!parsed.success) {
+    return { success: false, error: `Invalid params: ${parsed.error.message}` };
+  }
+
+  const { action } = parsed.data;
+
+  try {
+    let result: ExecuteResult;
+
+    switch (action) {
+      case 'init':
+        result = await initIndex(parsed.data);
+        break;
+
+      case 'search':
+        result = await searchCode(parsed.data);
+        break;
+
+      case 'search_files':
+        result = await searchFiles(parsed.data);
+        break;
+
+      case 'status':
+        result = await getStatus(parsed.data);
+        break;
+
+      case 'symbol':
+        result = await extractSymbols(parsed.data);
+        break;
+
+      case 'check':
+        const checkStatus = await ensureReady();
+        result = {
+          success: checkStatus.ready,
+          ready: checkStatus.ready,
+          version: checkStatus.version,
+          error: checkStatus.error,
+        };
+        break;
+
+      case 'update':
+        // Update is an alias for init (incremental update)
+        result = await initIndex(parsed.data);
+        break;
+
+      case 'bootstrap':
+        const bootstrapResult = await bootstrapVenv();
+        result = {
+          success: bootstrapResult.success,
+          message: bootstrapResult.message,
+          error: bootstrapResult.error,
+        };
+        break;
+
+      default:
+        throw new Error(
+          `Unknown action: ${action}. Valid actions: init, search, search_files, status, symbol, check, update, bootstrap`
+        );
+    }
+
+    return result.success ? { success: true, result } : { success: false, error: result.error };
+  } catch (error) {
+    return { success: false, error: (error as Error).message };
+  }
+}
+
+/**
+ * Uninstall CodexLens by removing the venv directory
+ * @returns Uninstall result
+ */
+async function uninstallCodexLens(): Promise<BootstrapResult> {
+  try {
+    // Check if venv exists
+    if (!existsSync(CODEXLENS_VENV)) {
+      return { success: false, error: 'CodexLens not installed (venv not found)' };
+    }
+
+    console.log('[CodexLens] Uninstalling CodexLens...');
+    console.log(`[CodexLens] Removing directory: ${CODEXLENS_DATA_DIR}`);
+
+    // Remove the entire .codexlens directory
+    const fs = await import('fs');
+    fs.rmSync(CODEXLENS_DATA_DIR, { recursive: true, force: true });
+
+    // Reset bootstrap cache
+    bootstrapChecked = false;
+    bootstrapReady = false;
+
+    console.log('[CodexLens] CodexLens uninstalled successfully');
+    return { success: true, message: 'CodexLens uninstalled successfully' };
+  } catch (err) {
+    return { success: false, error: `Failed to uninstall CodexLens: ${(err as Error).message}` };
+  }
+}
+
+/**
+ * Cancel the currently running indexing process
+ * @returns Result indicating if cancellation was successful
+ */
+function cancelIndexing(): { success: boolean; message?: string; error?: string } {
+  if (!currentIndexingProcess) {
+    return { success: false, error: 'No indexing process is currently running' };
+  }
+
+  if (currentIndexingAborted) {
+    return { success: false, error: 'Indexing process is already being cancelled' };
+  }
+
+  try {
+    currentIndexingAborted = true;
+
+    // Send SIGTERM first for graceful shutdown
+    if (process.platform === 'win32') {
+      // On Windows, use taskkill to kill the process tree
+      const { execSync } = require('child_process');
+      try {
+        execSync(`taskkill /pid ${currentIndexingProcess.pid} /T /F`, { stdio: 'ignore' });
+      } catch {
+        // Process may have already exited
+      }
+    } else {
+      // On Unix, send SIGTERM
+      currentIndexingProcess.kill('SIGTERM');
+
+      // Force kill after 3 seconds if still running
+      setTimeout(() => {
+        if (currentIndexingProcess) {
+          currentIndexingProcess.kill('SIGKILL');
+        }
+      }, 3000);
+    }
+
+    console.log('[CodexLens] Indexing process cancelled');
+    return { success: true, message: 'Indexing cancelled successfully' };
+  } catch (err) {
+    return { success: false, error: `Failed to cancel indexing: ${(err as Error).message}` };
+  }
+}
+
+/**
+ * Check if an indexing process is currently running
+ * @returns True if indexing is in progress
+ */
+function isIndexingInProgress(): boolean {
+  return currentIndexingProcess !== null && !currentIndexingAborted;
+}
+
+// Export types
+export type { ProgressInfo, ExecuteOptions };
+
+// Export for direct usage
+export { ensureReady, executeCodexLens, checkVenvStatus, bootstrapVenv, checkSemanticStatus, installSemantic, uninstallCodexLens, cancelIndexing, isIndexingInProgress };
+
+// Backward-compatible export for tests
+export const codexLensTool = {
+  name: schema.name,
+  description: schema.description,
+  parameters: schema.inputSchema,
+  execute: async (params: Record<string, unknown>) => {
+    const result = await handler(params);
+    // Return the result directly - tests expect {success: boolean, ...} format
+    return result.success ? result.result : { success: false, error: result.error };
+  }
+};