@liendev/lien 0.38.0 → 0.39.0

package/dist/index.js

@@ -58,6 +58,7 @@ function wrapInBox(text, footer, padding = 1) {
   return [top, ...paddedLines, separator, paddedFooter, bottom].join("\n");
 }
 function showBanner() {
+  if (!process.stderr.isTTY) return;
   const banner = figlet.textSync("LIEN", {
     font: "ANSI Shadow",
     horizontalLayout: "fitted",
@@ -69,6 +70,7 @@ function showBanner() {
   console.error();
 }
 function showCompactBanner() {
+  if (!process.stdout.isTTY) return;
   const banner = figlet.textSync("LIEN", {
     font: "ANSI Shadow",
     horizontalLayout: "fitted",
@@ -3656,50 +3658,154 @@ var require_dist = __commonJS({
 });
 
 // src/cli/index.ts
-import { Command } from "commander";
-import { createRequire as createRequire3 } from "module";
-import { fileURLToPath as fileURLToPath3 } from "url";
+import { Command, Option } from "commander";
+import { createRequire as createRequire4 } from "module";
+import { fileURLToPath as fileURLToPath4 } from "url";
 import { dirname as dirname3, join as join3 } from "path";
 
 // src/cli/init.ts
 init_banner();
 import fs from "fs/promises";
+import os from "os";
 import path from "path";
 import chalk2 from "chalk";
-var MCP_CONFIG = {
-  command: "lien",
-  args: ["serve"]
+var EDITORS = {
+  cursor: {
+    name: "Cursor",
+    configPath: (rootDir) => path.join(rootDir, ".cursor", "mcp.json"),
+    configKey: "mcpServers",
+    buildEntry: () => ({ command: "lien", args: ["serve"] }),
+    restartMessage: "Restart Cursor to activate."
+  },
+  "claude-code": {
+    name: "Claude Code",
+    configPath: (rootDir) => path.join(rootDir, ".mcp.json"),
+    configKey: "mcpServers",
+    buildEntry: () => ({ command: "lien", args: ["serve"] }),
+    restartMessage: "Restart Claude Code to activate."
+  },
+  windsurf: {
+    name: "Windsurf",
+    configPath: () => path.join(os.homedir(), ".codeium", "windsurf", "mcp_config.json"),
+    configKey: "mcpServers",
+    buildEntry: (rootDir) => ({
+      command: "lien",
+      args: ["serve", "--root", path.resolve(rootDir)]
+    }),
+    restartMessage: "Restart Windsurf to activate."
+  },
+  opencode: {
+    name: "OpenCode",
+    configPath: (rootDir) => path.join(rootDir, "opencode.json"),
+    configKey: "mcp",
+    buildEntry: () => ({ type: "local", command: ["lien", "serve"] }),
+    restartMessage: "Restart OpenCode to activate."
+  },
+  "kilo-code": {
+    name: "Kilo Code",
+    configPath: (rootDir) => path.join(rootDir, ".kilocode", "mcp.json"),
+    configKey: "mcpServers",
+    buildEntry: () => ({ command: "lien", args: ["serve"] }),
+    restartMessage: "Restart VS Code to activate."
+  },
+  antigravity: {
+    name: "Antigravity",
+    configPath: null,
+    configKey: "mcpServers",
+    buildEntry: () => ({ command: "lien", args: ["serve"] }),
+    restartMessage: "Add this to your Antigravity MCP settings."
+  }
 };
-async function initCommand(options = {}) {
-  showCompactBanner();
-  const rootDir = options.path || process.cwd();
-  const cursorDir = path.join(rootDir, ".cursor");
-  const mcpConfigPath = path.join(cursorDir, "mcp.json");
-  let existingConfig = null;
+function isPlainObject(value) {
+  return value !== null && typeof value === "object" && !Array.isArray(value);
+}
+function displayPath(configPath, rootDir) {
+  const rel = path.relative(rootDir, configPath);
+  if (!rel.startsWith("..")) return rel;
+  const home = os.homedir();
+  if (configPath.startsWith(home)) return "~" + configPath.slice(home.length);
+  return configPath;
+}
+async function readJsonFile(filePath) {
   try {
-    const raw = await fs.readFile(mcpConfigPath, "utf-8");
+    const raw = await fs.readFile(filePath, "utf-8");
     const parsed = JSON.parse(raw);
-    if (parsed && typeof parsed === "object" && !Array.isArray(parsed)) {
-      existingConfig = parsed;
-    }
+    return isPlainObject(parsed) ? parsed : null;
   } catch {
+    return null;
+  }
+}
+async function writeEditorConfig(editor, rootDir) {
+  const configPath = editor.configPath(rootDir);
+  const entry = editor.buildEntry(rootDir);
+  const key = editor.configKey;
+  const label = displayPath(configPath, rootDir);
+  const existingConfig = await readJsonFile(configPath);
+  const existingSection = existingConfig?.[key];
+  if (existingSection?.lien) {
+    console.log(chalk2.green(`
+\u2713 Already configured \u2014 ${label} contains lien entry`));
+    return;
   }
-  if (existingConfig?.mcpServers?.lien) {
-    console.log(chalk2.green("\n\u2713 Already configured \u2014 .cursor/mcp.json contains lien entry"));
-  } else if (existingConfig) {
-    const servers = existingConfig.mcpServers;
-    const safeServers = servers && typeof servers === "object" && !Array.isArray(servers) ? servers : {};
-    safeServers.lien = MCP_CONFIG;
-    existingConfig.mcpServers = safeServers;
-    await fs.writeFile(mcpConfigPath, JSON.stringify(existingConfig, null, 2) + "\n");
-    console.log(chalk2.green("\n\u2713 Added lien to existing .cursor/mcp.json"));
+  if (existingConfig) {
+    const section = isPlainObject(existingSection) ? { ...existingSection } : {};
+    section.lien = entry;
+    existingConfig[key] = section;
+    await fs.writeFile(configPath, JSON.stringify(existingConfig, null, 2) + "\n");
+    console.log(chalk2.green(`
+\u2713 Added lien to existing ${label}`));
   } else {
-    await fs.mkdir(cursorDir, { recursive: true });
-    const config = { mcpServers: { lien: MCP_CONFIG } };
-    await fs.writeFile(mcpConfigPath, JSON.stringify(config, null, 2) + "\n");
-    console.log(chalk2.green("\n\u2713 Created .cursor/mcp.json"));
+    await fs.mkdir(path.dirname(configPath), { recursive: true });
+    const config = { [key]: { lien: entry } };
+    await fs.writeFile(configPath, JSON.stringify(config, null, 2) + "\n");
+    console.log(chalk2.green(`
+\u2713 Created ${label}`));
+  }
+}
+async function promptForEditor() {
+  const { default: inquirer } = await import("inquirer");
+  const { editor } = await inquirer.prompt([
+    {
+      type: "list",
+      name: "editor",
+      message: "Which editor are you using?",
+      choices: [
+        { name: "Cursor", value: "cursor" },
+        { name: "Claude Code", value: "claude-code" },
+        { name: "Windsurf", value: "windsurf" },
+        { name: "OpenCode", value: "opencode" },
+        { name: "Kilo Code", value: "kilo-code" },
+        { name: "Antigravity", value: "antigravity" }
+      ],
+      default: "cursor"
+    }
+  ]);
+  return editor;
+}
+async function initCommand(options = {}) {
+  showCompactBanner();
+  const rootDir = options.path || process.cwd();
+  let editorId;
+  if (options.editor) {
+    editorId = options.editor;
+  } else if (!process.stdout.isTTY) {
+    console.error(chalk2.red("Error: Use --editor to specify your editor in non-interactive mode."));
+    process.exit(1);
+  } else {
+    editorId = await promptForEditor();
+  }
+  const editor = EDITORS[editorId];
+  if (editor.configPath) {
+    await writeEditorConfig(editor, rootDir);
+    console.log(chalk2.dim(`  ${editor.restartMessage}
+`));
+  } else {
+    const entry = editor.buildEntry(rootDir);
+    const snippet = { [editor.configKey]: { lien: entry } };
+    console.log(chalk2.yellow(`
+${editor.restartMessage}`));
+    console.log(JSON.stringify(snippet, null, 2));
   }
-  console.log(chalk2.dim("  Restart Cursor to activate.\n"));
   const legacyConfigPath = path.join(rootDir, ".lien.config.json");
   try {
     await fs.access(legacyConfigPath);
@@ -3714,7 +3820,9 @@ init_banner();
 import chalk3 from "chalk";
 import fs2 from "fs/promises";
 import path2 from "path";
-import os from "os";
+import os2 from "os";
+import { createRequire as createRequire2 } from "module";
+import { fileURLToPath as fileURLToPath2 } from "url";
 import {
   isGitRepo,
   getCurrentBranch,
@@ -3727,75 +3835,179 @@ import {
   DEFAULT_CHUNK_OVERLAP,
   DEFAULT_GIT_POLL_INTERVAL_MS
 } from "@liendev/core";
-async function statusCommand() {
-  const rootDir = process.cwd();
-  const repoId = extractRepoId(rootDir);
-  const indexPath = path2.join(os.homedir(), ".lien", "indices", repoId);
-  showCompactBanner();
-  console.log(chalk3.bold("Status\n"));
-  console.log(
-    chalk3.dim("Configuration:"),
-    chalk3.green("\u2713 Using defaults (no per-project config needed)")
-  );
+var VALID_FORMATS = ["text", "json"];
+async function getFileStats(filePath) {
   try {
-    const stats = await fs2.stat(indexPath);
-    console.log(chalk3.dim("Index location:"), indexPath);
-    console.log(chalk3.dim("Index status:"), chalk3.green("\u2713 Exists"));
-    try {
-      const files = await fs2.readdir(indexPath, { recursive: true });
-      console.log(chalk3.dim("Index files:"), files.length);
-    } catch {
-    }
-    console.log(chalk3.dim("Last modified:"), stats.mtime.toLocaleString());
-    try {
-      const version = await readVersionFile(indexPath);
-      if (version > 0) {
-        const versionDate = new Date(version);
-        console.log(chalk3.dim("Last reindex:"), versionDate.toLocaleString());
-      }
-    } catch {
-    }
+    return await fs2.stat(filePath);
+  } catch {
+    return null;
+  }
+}
+async function getFileCount(dirPath) {
+  try {
+    const files = await fs2.readdir(dirPath, { recursive: true });
+    return files.length;
+  } catch {
+    return null;
+  }
+}
+async function getLastReindex(indexPath) {
+  try {
+    const version = await readVersionFile(indexPath);
+    return version > 0 ? version : null;
+  } catch {
+    return null;
+  }
+}
+function getPackageVersion() {
+  const __filename4 = fileURLToPath2(import.meta.url);
+  const __dirname4 = path2.dirname(__filename4);
+  const require5 = createRequire2(import.meta.url);
+  try {
+    return require5(path2.join(__dirname4, "../package.json")).version;
+  } catch {
+    return require5(path2.join(__dirname4, "../../package.json")).version;
+  }
+}
+async function getGitState(rootDir) {
+  try {
+    const branch = await getCurrentBranch(rootDir);
+    const commit = await getCurrentCommit(rootDir);
+    return { branch, commit };
   } catch {
+    return null;
+  }
+}
+async function getStoredGitState(indexPath) {
+  try {
+    const content = await fs2.readFile(path2.join(indexPath, ".git-state.json"), "utf-8");
+    return JSON.parse(content);
+  } catch {
+    return null;
+  }
+}
+async function printIndexStatus(indexPath) {
+  const stats = await getFileStats(indexPath);
+  if (!stats) {
     console.log(chalk3.dim("Index status:"), chalk3.yellow("\u2717 Not indexed"));
     console.log(
       chalk3.yellow("\nRun"),
       chalk3.bold("lien index"),
       chalk3.yellow("to index your codebase")
     );
+    return;
   }
-  console.log(chalk3.bold("\nFeatures:"));
+  console.log(chalk3.dim("Index location:"), indexPath);
+  console.log(chalk3.dim("Index status:"), chalk3.green("\u2713 Exists"));
+  const fileCount = await getFileCount(indexPath);
+  if (fileCount !== null) {
+    console.log(chalk3.dim("Index files:"), fileCount);
+  }
+  console.log(chalk3.dim("Last modified:"), stats.mtime.toLocaleString());
+  const reindexTs = await getLastReindex(indexPath);
+  if (reindexTs !== null) {
+    console.log(chalk3.dim("Last reindex:"), new Date(reindexTs).toLocaleString());
+  }
+}
+async function printGitStatus(rootDir, indexPath) {
   const isRepo = await isGitRepo(rootDir);
-  if (isRepo) {
-    console.log(chalk3.dim("Git detection:"), chalk3.green("\u2713 Enabled"));
-    console.log(chalk3.dim("  Poll interval:"), `${DEFAULT_GIT_POLL_INTERVAL_MS / 1e3}s`);
-    try {
-      const branch = await getCurrentBranch(rootDir);
-      const commit = await getCurrentCommit(rootDir);
-      console.log(chalk3.dim("  Current branch:"), branch);
-      console.log(chalk3.dim("  Current commit:"), commit.substring(0, 8));
-      const gitStateFile = path2.join(indexPath, ".git-state.json");
-      try {
-        const gitStateContent = await fs2.readFile(gitStateFile, "utf-8");
-        const gitState = JSON.parse(gitStateContent);
-        if (gitState.branch !== branch || gitState.commit !== commit) {
-          console.log(chalk3.yellow("  \u26A0\uFE0F  Git state changed - will reindex on next serve"));
-        }
-      } catch {
-      }
-    } catch {
-    }
-  } else {
+  if (!isRepo) {
     console.log(chalk3.dim("Git detection:"), chalk3.yellow("Not a git repo"));
+    return;
+  }
+  console.log(chalk3.dim("Git detection:"), chalk3.green("\u2713 Enabled"));
+  console.log(chalk3.dim("  Poll interval:"), `${DEFAULT_GIT_POLL_INTERVAL_MS / 1e3}s`);
+  const gitState = await getGitState(rootDir);
+  if (!gitState) return;
+  console.log(chalk3.dim("  Current branch:"), gitState.branch);
+  console.log(chalk3.dim("  Current commit:"), gitState.commit.substring(0, 8));
+  const storedGit = await getStoredGitState(indexPath);
+  if (storedGit && (storedGit.branch !== gitState.branch || storedGit.commit !== gitState.commit)) {
+    console.log(chalk3.yellow("  \u26A0\uFE0F  Git state changed - will reindex on next serve"));
   }
+}
+function printWatchStatus() {
   console.log(chalk3.dim("File watching:"), chalk3.green("\u2713 Enabled (default)"));
   console.log(chalk3.dim("  Batch window:"), "500ms (collects rapid changes, force-flush after 5s)");
   console.log(chalk3.dim("  Disable with:"), chalk3.bold("lien serve --no-watch"));
+}
+function printIndexingSettings() {
   console.log(chalk3.bold("\nIndexing Settings (defaults):"));
   console.log(chalk3.dim("Concurrency:"), DEFAULT_CONCURRENCY);
   console.log(chalk3.dim("Batch size:"), DEFAULT_EMBEDDING_BATCH_SIZE);
   console.log(chalk3.dim("Chunk size:"), DEFAULT_CHUNK_SIZE);
   console.log(chalk3.dim("Chunk overlap:"), DEFAULT_CHUNK_OVERLAP);
 }
+async function statusCommand(options = {}) {
+  const format = options.format || "text";
+  if (!VALID_FORMATS.includes(format)) {
+    console.error(
+      chalk3.red(`Error: Invalid --format value "${format}". Must be one of: text, json`)
+    );
+    process.exit(1);
+  }
+  const rootDir = process.cwd();
+  const repoId = extractRepoId(rootDir);
+  const indexPath = path2.join(os2.homedir(), ".lien", "indices", repoId);
+  if (format === "json") {
+    await outputJson(rootDir, indexPath);
+    return;
+  }
+  showCompactBanner();
+  console.log(chalk3.bold("Status\n"));
+  console.log(
+    chalk3.dim("Configuration:"),
+    chalk3.green("\u2713 Using defaults (no per-project config needed)")
+  );
+  await printIndexStatus(indexPath);
+  console.log(chalk3.bold("\nFeatures:"));
+  await printGitStatus(rootDir, indexPath);
+  printWatchStatus();
+  if (options.verbose) {
+    printIndexingSettings();
+  }
+}
+async function outputJson(rootDir, indexPath) {
+  const data = {
+    version: getPackageVersion(),
+    indexPath,
+    indexStatus: "not_indexed",
+    indexFiles: 0,
+    lastModified: null,
+    lastReindex: null,
+    git: { enabled: false, branch: null, commit: null },
+    features: { fileWatching: true, gitDetection: true },
+    settings: {
+      concurrency: DEFAULT_CONCURRENCY,
+      batchSize: DEFAULT_EMBEDDING_BATCH_SIZE,
+      chunkSize: DEFAULT_CHUNK_SIZE,
+      chunkOverlap: DEFAULT_CHUNK_OVERLAP
+    }
+  };
+  const stats = await getFileStats(indexPath);
+  if (stats) {
+    data.indexStatus = "exists";
+    data.lastModified = stats.mtime.toISOString();
+    const fileCount = await getFileCount(indexPath);
+    if (fileCount !== null) {
+      data.indexFiles = fileCount;
+    }
+    const reindexTs = await getLastReindex(indexPath);
+    if (reindexTs !== null) {
+      data.lastReindex = new Date(reindexTs).toISOString();
+    }
+  }
+  const isRepo = await isGitRepo(rootDir);
+  if (isRepo) {
+    const gitState = await getGitState(rootDir);
+    data.git = {
+      enabled: true,
+      branch: gitState?.branch ?? null,
+      commit: gitState ? gitState.commit.substring(0, 8) : null
+    };
+  }
+  console.log(JSON.stringify(data, null, 2));
+}
 
 // src/cli/index-cmd.ts
 init_banner();
@@ -4027,8 +4239,8 @@ import path7 from "path";
 // src/mcp/server.ts
 import { Server } from "@modelcontextprotocol/sdk/server/index.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
-import { createRequire as createRequire2 } from "module";
-import { fileURLToPath as fileURLToPath2 } from "url";
+import { createRequire as createRequire3 } from "module";
+import { fileURLToPath as fileURLToPath3 } from "url";
 import { dirname as dirname2, join as join2 } from "path";
 import { WorkerEmbeddings, VERSION_CHECK_INTERVAL_MS, createVectorDB } from "@liendev/core";
 
@@ -8595,6 +8807,7 @@ var GetComplexitySchema = external_exports.object({
   threshold: external_exports.number().int().min(1, "Threshold must be at least 1").optional().describe(
     "Only return functions above this complexity threshold.\n\nNote: Violations are first identified using the threshold from lien.config.json (default: 15). This parameter filters those violations to show only items above the specified value. Setting threshold below the config threshold will not show additional functions."
   ),
+  metricType: external_exports.enum(["cyclomatic", "cognitive", "halstead_effort", "halstead_bugs"]).optional().describe("Filter violations to a specific metric type. If omitted, returns all types."),
   crossRepo: external_exports.boolean().default(false).describe(
     "If true, analyze complexity across all repos in the organization (requires a cross-repo-capable backend, currently Qdrant).\n\nDefault: false (single-repo analysis)\nWhen enabled, results are aggregated by repository."
   ),
@@ -8750,7 +8963,7 @@ Use for tech debt analysis and refactoring prioritization:
 
 Examples:
   get_complexity({ top: 10 })
-  get_complexity({ files: ["src/auth.ts", "src/api/user.ts"] })
+  get_complexity({ files: ["src/auth.ts"], metricType: "cognitive" })
   get_complexity({ threshold: 15 })
 
 Returns:
@@ -10075,15 +10288,15 @@ async function fetchCrossRepoChunks(vectorDB, crossRepo, repoIds, log) {
   }
   return { chunks: [], fallback: true };
 }
-function processViolations(report, threshold, top) {
+function processViolations(report, threshold, top, metricType) {
   const allViolations = (0, import_collect.default)(Object.entries(report.files)).flatMap(
     ([
       ,
       /* filepath unused */
       fileData
-    ]) => fileData.violations.map((v) => transformViolation(v, fileData))
+    ]) => fileData.violations.filter((v) => !metricType || v.metricType === metricType).filter((v) => threshold === void 0 || v.complexity >= threshold).map((v) => transformViolation(v, fileData))
   ).sortByDesc("complexity").all();
-  const violations = threshold !== void 0 ? allViolations.filter((v) => v.complexity >= threshold) : allViolations;
+  const violations = allViolations;
   const severityCounts = (0, import_collect.default)(violations).countBy("severity").all();
   return {
     violations,
@@ -10100,7 +10313,7 @@ function buildCrossRepoFallbackNote(fallback) {
 async function handleGetComplexity(args, ctx) {
   const { vectorDB, log, checkAndReconnect, getIndexMetadata } = ctx;
   return await wrapToolHandler(GetComplexitySchema, async (validatedArgs) => {
-    const { crossRepo, repoIds, files, top, threshold } = validatedArgs;
+    const { crossRepo, repoIds, files, top, threshold, metricType } = validatedArgs;
     log(`Analyzing complexity${crossRepo ? " (cross-repo)" : ""}...`);
     await checkAndReconnect();
     const { chunks: allChunks, fallback } = await fetchCrossRepoChunks(
@@ -10115,7 +10328,8 @@ async function handleGetComplexity(args, ctx) {
     const { violations, topViolations, bySeverity } = processViolations(
       report,
       threshold,
-      top ?? 10
+      top ?? 10,
+      metricType
     );
     const note = buildCrossRepoFallbackNote(fallback);
     if (note) {
@@ -10366,9 +10580,8 @@ import {
   normalizeToRelativePath as normalizeToRelativePath2,
   createGitignoreFilter
 } from "@liendev/core";
-async function handleFileDeletion(filepath, vectorDB, log) {
+async function handleFileDeletion(filepath, vectorDB, manifest, log) {
   log(`\u{1F5D1}\uFE0F  File deleted: ${filepath}`);
-  const manifest = new ManifestManager(vectorDB.dbPath);
   try {
     await vectorDB.deleteByFile(filepath);
     await manifest.removeFile(filepath);
@@ -10378,8 +10591,7 @@ async function handleFileDeletion(filepath, vectorDB, log) {
     throw error;
   }
 }
-async function handleBatchDeletions(deletedFiles, vectorDB, log) {
-  const manifest = new ManifestManager(vectorDB.dbPath);
+async function handleBatchDeletions(deletedFiles, vectorDB, manifest, log) {
   const failures = [];
   for (const filepath of deletedFiles) {
     log(`\u{1F5D1}\uFE0F  File deleted: ${filepath}`);
@@ -10396,8 +10608,7 @@ async function handleBatchDeletions(deletedFiles, vectorDB, log) {
     throw new Error(`Failed to delete ${failures.length} file(s): ${failures.join(", ")}`);
   }
 }
-async function canSkipReindex(filepath, rootDir, vectorDB, log) {
-  const manifest = new ManifestManager(vectorDB.dbPath);
+async function canSkipReindex(filepath, rootDir, manifest, log) {
   const normalizedPath = normalizeToRelativePath2(filepath, rootDir);
   const manifestData = await manifest.load();
   const existingEntry = manifestData?.files[normalizedPath];
@@ -10415,11 +10626,11 @@ async function canSkipReindex(filepath, rootDir, vectorDB, log) {
   }
   return false;
 }
-async function handleSingleFileChange(filepath, type, rootDir, vectorDB, embeddings, log, reindexStateManager) {
+async function handleSingleFileChange(filepath, type, rootDir, vectorDB, embeddings, manifest, log, reindexStateManager) {
   const action = type === "add" ? "added" : "changed";
   if (type === "change") {
     try {
-      if (await canSkipReindex(filepath, rootDir, vectorDB, log)) return;
+      if (await canSkipReindex(filepath, rootDir, manifest, log)) return;
     } catch (error) {
       log(`Content hash check failed, will reindex: ${error}`, "warning");
     }
@@ -10477,9 +10688,8 @@ async function updateUnchangedMtimes(manifest, results) {
     return null;
   });
 }
-async function filterModifiedFilesByHash(modifiedFiles, rootDir, vectorDB, log) {
+async function filterModifiedFilesByHash(modifiedFiles, rootDir, manifest, log) {
   if (modifiedFiles.length === 0) return [];
-  const manifest = new ManifestManager(vectorDB.dbPath);
   const manifestData = await manifest.load();
   if (!manifestData) return modifiedFiles;
   const checkResults = await checkFilesAgainstManifest(
@@ -10491,13 +10701,13 @@ async function filterModifiedFilesByHash(modifiedFiles, rootDir, vectorDB, log)
   await updateUnchangedMtimes(manifest, checkResults);
   return checkResults.filter((r) => r.shouldReindex).map((r) => r.filepath);
 }
-async function prepareFilesForReindexing(event, rootDir, vectorDB, log) {
+async function prepareFilesForReindexing(event, rootDir, manifest, log) {
   const addedFiles = event.added || [];
   const modifiedFiles = event.modified || [];
   const deletedFiles = event.deleted || [];
   let modifiedFilesToReindex = [];
   try {
-    modifiedFilesToReindex = await filterModifiedFilesByHash(modifiedFiles, rootDir, vectorDB, log);
+    modifiedFilesToReindex = await filterModifiedFilesByHash(modifiedFiles, rootDir, manifest, log);
   } catch (error) {
     log(`Hash-based filtering failed, will reindex all modified files: ${error}`, "warning");
     modifiedFilesToReindex = modifiedFiles;
@@ -10505,24 +10715,20 @@ async function prepareFilesForReindexing(event, rootDir, vectorDB, log) {
   const filesToIndex = [...addedFiles, ...modifiedFilesToReindex];
   return { filesToIndex, deletedFiles };
 }
-async function executeReindexOperations(filesToIndex, deletedFiles, rootDir, vectorDB, embeddings, log) {
-  const operations = [];
+async function executeReindexOperations(filesToIndex, deletedFiles, rootDir, vectorDB, embeddings, manifest, log) {
   if (filesToIndex.length > 0) {
     log(`\u{1F4C1} ${filesToIndex.length} file(s) changed, reindexing...`);
-    operations.push(
-      indexMultipleFiles(filesToIndex, vectorDB, embeddings, { verbose: false, rootDir })
-    );
+    await indexMultipleFiles(filesToIndex, vectorDB, embeddings, { verbose: false, rootDir });
   }
   if (deletedFiles.length > 0) {
-    operations.push(handleBatchDeletions(deletedFiles, vectorDB, log));
+    await handleBatchDeletions(deletedFiles, vectorDB, manifest, log);
   }
-  await Promise.all(operations);
 }
-async function handleBatchEvent(event, rootDir, vectorDB, embeddings, log, reindexStateManager) {
+async function handleBatchEvent(event, rootDir, vectorDB, embeddings, manifest, log, reindexStateManager) {
   const { filesToIndex, deletedFiles } = await prepareFilesForReindexing(
     event,
     rootDir,
-    vectorDB,
+    manifest,
     log
   );
   const allFiles = [...filesToIndex, ...deletedFiles];
@@ -10532,7 +10738,15 @@ async function handleBatchEvent(event, rootDir, vectorDB, embeddings, log, reind
   const startTime = Date.now();
   reindexStateManager.startReindex(allFiles);
   try {
-    await executeReindexOperations(filesToIndex, deletedFiles, rootDir, vectorDB, embeddings, log);
+    await executeReindexOperations(
+      filesToIndex,
+      deletedFiles,
+      rootDir,
+      vectorDB,
+      embeddings,
+      manifest,
+      log
+    );
     const duration = Date.now() - startTime;
     reindexStateManager.completeReindex(duration);
     log(
@@ -10543,11 +10757,11 @@ async function handleBatchEvent(event, rootDir, vectorDB, embeddings, log, reind
     log(`Batch reindex failed: ${error}`, "warning");
   }
 }
-async function handleUnlinkEvent(filepath, vectorDB, log, reindexStateManager) {
+async function handleUnlinkEvent(filepath, vectorDB, manifest, log, reindexStateManager) {
   const startTime = Date.now();
   reindexStateManager.startReindex([filepath]);
   try {
-    await handleFileDeletion(filepath, vectorDB, log);
+    await handleFileDeletion(filepath, vectorDB, manifest, log);
     const duration = Date.now() - startTime;
     reindexStateManager.completeReindex(duration);
   } catch (error) {
@@ -10579,6 +10793,7 @@ function hasGitignoreChange(event) {
 }
 function createFileChangeHandler(rootDir, vectorDB, embeddings, log, reindexStateManager, checkAndReconnect) {
   let ignoreFilter = null;
+  const manifest = new ManifestManager(vectorDB.dbPath);
   return async (event) => {
     if (hasGitignoreChange(event)) {
       ignoreFilter = null;
@@ -10592,10 +10807,18 @@ function createFileChangeHandler(rootDir, vectorDB, embeddings, log, reindexStat
       const totalToProcess = filtered.added.length + filtered.modified.length + filtered.deleted.length;
       if (totalToProcess === 0) return;
       await checkAndReconnect();
-      await handleBatchEvent(filtered, rootDir, vectorDB, embeddings, log, reindexStateManager);
+      await handleBatchEvent(
+        filtered,
+        rootDir,
+        vectorDB,
+        embeddings,
+        manifest,
+        log,
+        reindexStateManager
+      );
     } else if (type === "unlink") {
       await checkAndReconnect();
-      await handleUnlinkEvent(event.filepath, vectorDB, log, reindexStateManager);
+      await handleUnlinkEvent(event.filepath, vectorDB, manifest, log, reindexStateManager);
     } else {
       if (isFileIgnored(event.filepath, rootDir, ignoreFilter)) return;
       await checkAndReconnect();
@@ -10605,6 +10828,7 @@ function createFileChangeHandler(rootDir, vectorDB, embeddings, log, reindexStat
         rootDir,
         vectorDB,
         embeddings,
+        manifest,
         log,
         reindexStateManager
       );
@@ -10867,9 +11091,9 @@ function setupCleanupHandlers(server, versionCheckInterval, gitPollInterval, fil
 }
 
 // src/mcp/server.ts
-var __filename2 = fileURLToPath2(import.meta.url);
+var __filename2 = fileURLToPath3(import.meta.url);
 var __dirname2 = dirname2(__filename2);
-var require3 = createRequire2(import.meta.url);
+var require3 = createRequire3(import.meta.url);
 var packageJson2;
 try {
   packageJson2 = require3(join2(__dirname2, "../package.json"));
@@ -11133,7 +11357,7 @@ import { VectorDB } from "@liendev/core";
 import { ComplexityAnalyzer as ComplexityAnalyzer2 } from "@liendev/core";
 import { formatReport } from "@liendev/core";
 var VALID_FAIL_ON = ["error", "warning"];
-var VALID_FORMATS = ["text", "json", "sarif"];
+var VALID_FORMATS2 = ["text", "json", "sarif"];
 function validateFailOn(failOn) {
   if (failOn && !VALID_FAIL_ON.includes(failOn)) {
     console.error(
@@ -11143,7 +11367,7 @@ function validateFailOn(failOn) {
   }
 }
 function validateFormat(format) {
-  if (!VALID_FORMATS.includes(format)) {
+  if (!VALID_FORMATS2.includes(format)) {
     console.error(
       chalk7.red(`Error: Invalid --format value "${format}". Must be one of: text, json, sarif`)
     );
@@ -11200,9 +11424,9 @@ async function complexityCommand(options) {
 // src/cli/config.ts
 import chalk8 from "chalk";
 import path9 from "path";
-import os2 from "os";
+import os3 from "os";
 import { loadGlobalConfig, mergeGlobalConfig } from "@liendev/core";
-var CONFIG_PATH = path9.join(os2.homedir(), ".lien", "config.json");
+var CONFIG_PATH = path9.join(os3.homedir(), ".lien", "config.json");
 var ALLOWED_KEYS = {
   backend: {
     values: ["lancedb", "qdrant"],
@@ -11289,9 +11513,9 @@ async function configListCommand() {
 }
 
 // src/cli/index.ts
-var __filename3 = fileURLToPath3(import.meta.url);
+var __filename3 = fileURLToPath4(import.meta.url);
 var __dirname3 = dirname3(__filename3);
-var require4 = createRequire3(import.meta.url);
+var require4 = createRequire4(import.meta.url);
 var packageJson3;
 try {
   packageJson3 = require4(join3(__dirname3, "../package.json"));
@@ -11300,17 +11524,31 @@ try {
 }
 var program = new Command();
 program.name("lien").description("Local semantic code search for AI assistants via MCP").version(packageJson3.version);
-program.command("init").description("Initialize Lien in the current directory").option("-u, --upgrade", "Upgrade existing config with new options").option("-y, --yes", "Skip interactive prompts and use defaults").option("-p, --path <path>", "Path to initialize (defaults to current directory)").action(initCommand);
+program.command("init").description("Initialize Lien in the current directory").addOption(
+  new Option("-e, --editor <editor>", "Editor to configure MCP for").choices([
+    "cursor",
+    "claude-code",
+    "windsurf",
+    "opencode",
+    "kilo-code",
+    "antigravity"
+  ])
+).option("-p, --path <path>", "Path to initialize (defaults to current directory)").action(initCommand);
 program.command("index").description("Index the codebase for semantic search").option("-f, --force", "Force full reindex (skip incremental)").option("-v, --verbose", "Show detailed logging during indexing").action(indexCommand);
 program.command("serve").description(
   "Start the MCP server (works with Cursor, Claude Code, Windsurf, and any MCP client)"
-).option("-p, --port <port>", "Port number (for future use)", "7133").option("--no-watch", "Disable file watching for this session").option("-w, --watch", "[DEPRECATED] File watching is now enabled by default").option("-r, --root <path>", "Root directory to serve (defaults to current directory)").action(serveCommand);
-program.command("status").description("Show indexing status and statistics").action(statusCommand);
+).option("-p, --port <port>", "Port number (for future use)", "7133").option("--no-watch", "Disable file watching for this session").addOption(
+  new Option("-w, --watch", "[DEPRECATED] File watching is now enabled by default").hideHelp()
+).option("-r, --root <path>", "Root directory to serve (defaults to current directory)").action(serveCommand);
+program.command("status").description("Show indexing status and statistics").option("-v, --verbose", "Show detailed settings").option("--format <type>", "Output format: text, json", "text").action(statusCommand);
 program.command("complexity").description("Analyze code complexity").option("--files <paths...>", "Specific files to analyze").option("--format <type>", "Output format: text, json, sarif", "text").option("--fail-on <severity>", "Exit 1 if violations: error, warning").action(complexityCommand);
 var configCmd = program.command("config").description("Manage global configuration (~/.lien/config.json)");
 configCmd.command("set <key> <value>").description("Set a global config value").action(configSetCommand);
 configCmd.command("get <key>").description("Get a config value").action(configGetCommand);
 configCmd.command("list").description("Show all current config").action(configListCommand);
+program.action(() => {
+  program.help();
+});
 program.addHelpText("beforeAll", `Quick start: run 'lien serve' in your project directory
 `);