@liendev/lien 0.37.0 → 0.38.1

package/README.md

@@ -109,7 +109,7 @@ Lien tracks code complexity with intuitive outputs:
 
 TypeScript • JavaScript • Vue • Python • PHP • Liquid • Go • Rust • Java • C/C++ • Ruby • Swift • Kotlin • C# • Scala • Markdown
 
-**Ecosystem Presets:** Node.js, Laravel, Python, Rust (auto-detected)
+**Ecosystem Presets:** 12 ecosystem presets including Node.js, Python, PHP, Laravel, Ruby, Rails, Rust, JVM, Swift, .NET, Django, and Astro (auto-detected)
 
 ## Contributing
 

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",
@@ -3656,9 +3658,9 @@ 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
@@ -3715,6 +3717,8 @@ import chalk3 from "chalk";
 import fs2 from "fs/promises";
 import path2 from "path";
 import os from "os";
+import { createRequire as createRequire2 } from "module";
+import { fileURLToPath as fileURLToPath2 } from "url";
 import {
   isGitRepo,
   getCurrentBranch,
@@ -3727,75 +3731,179 @@ 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(os.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();
@@ -4022,13 +4130,13 @@ async function indexCommand(options) {
 // src/cli/serve.ts
 import chalk6 from "chalk";
 import fs5 from "fs/promises";
-import path4 from "path";
+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";
 
@@ -4930,8 +5038,8 @@ function getErrorMap() {
 
 // ../../node_modules/zod/v3/helpers/parseUtil.js
 var makeIssue = (params) => {
-  const { data, path: path7, errorMaps, issueData } = params;
-  const fullPath = [...path7, ...issueData.path || []];
+  const { data, path: path10, errorMaps, issueData } = params;
+  const fullPath = [...path10, ...issueData.path || []];
   const fullIssue = {
     ...issueData,
     path: fullPath
@@ -5047,11 +5155,11 @@ var errorUtil;
 
 // ../../node_modules/zod/v3/types.js
 var ParseInputLazyPath = class {
-  constructor(parent, value, path7, key) {
+  constructor(parent, value, path10, key) {
     this._cachedPath = [];
     this.parent = parent;
     this.data = value;
-    this._path = path7;
+    this._path = path10;
     this._key = key;
   }
   get path() {
@@ -8524,10 +8632,15 @@ var FindSimilarSchema = external_exports.object({
 });
 
 // src/mcp/schemas/file.schema.ts
+import path4 from "path";
+var safeFilepath = external_exports.string().min(1, "Filepath cannot be empty").max(1e3).refine((p) => {
+  const normalized = p.replace(/\\/g, "/");
+  return !path4.isAbsolute(normalized) && !normalized.split("/").includes("..");
+}, 'Path must be relative and cannot contain ".." traversal');
 var GetFilesContextSchema = external_exports.object({
   filepaths: external_exports.union([
-    external_exports.string().min(1, "Filepath cannot be empty").max(1e3),
-    external_exports.array(external_exports.string().min(1, "Filepath cannot be empty").max(1e3)).min(1, "Array must contain at least one filepath").max(50, "Maximum 50 files per request")
+    safeFilepath,
+    external_exports.array(safeFilepath).min(1, "Array must contain at least one filepath").max(50, "Maximum 50 files per request")
   ]).describe(
     "Single filepath or array of filepaths (relative to workspace root).\n\nSingle file: 'src/components/Button.tsx'\nMultiple files: ['src/auth.ts', 'src/user.ts']\n\nMaximum 50 files per request for batch operations."
   ),
@@ -8554,8 +8667,12 @@ var ListFunctionsSchema = external_exports.object({
 });
 
 // src/mcp/schemas/dependents.schema.ts
+import path5 from "path";
 var GetDependentsSchema = external_exports.object({
-  filepath: external_exports.string().min(1, "Filepath cannot be empty").max(1e3).describe(
+  filepath: external_exports.string().min(1, "Filepath cannot be empty").max(1e3).refine((p) => {
+    const normalized = p.replace(/\\/g, "/");
+    return !path5.isAbsolute(normalized) && !normalized.split("/").includes("..");
+  }, 'Path must be relative and cannot contain ".." traversal').describe(
     "Path to file to find dependents for (relative to workspace root).\n\nExample: 'src/utils/validate.ts'\n\nReturns all files that import or depend on this file.\n\nNote: Scans up to 10,000 code chunks. For very large codebases,\nresults may be incomplete (a warning will be included if truncated)."
   ),
   symbol: external_exports.string().min(1, "Symbol cannot be an empty string").max(500).optional().describe(
@@ -8570,8 +8687,14 @@ var GetDependentsSchema = external_exports.object({
 });
 
 // src/mcp/schemas/complexity.schema.ts
+import path6 from "path";
 var GetComplexitySchema = external_exports.object({
-  files: external_exports.array(external_exports.string().min(1, "Filepath cannot be empty").max(1e3)).optional().describe(
+  files: external_exports.array(
+    external_exports.string().min(1, "Filepath cannot be empty").max(1e3).refine((p) => {
+      const normalized = p.replace(/\\/g, "/");
+      return !path6.isAbsolute(normalized) && !normalized.split("/").includes("..");
+    }, 'Path must be relative and cannot contain ".." traversal')
+  ).optional().describe(
     "Specific files to analyze. If omitted, analyzes entire codebase.\n\nExample: ['src/auth.ts', 'src/api/user.ts']"
   ),
   top: external_exports.number().int().min(1, "Top must be at least 1").max(50, "Top cannot exceed 50").default(10).describe(
@@ -9091,7 +9214,7 @@ async function handleSemanticSearch(args, ctx) {
     const shaped = shapeResults(results, "semantic_search");
     if (shaped.length === 0) {
       notes.push(
-        '0 results. Try rephrasing as a full question (e.g. "How does X work?"), or use grep for exact string matches. If the codebase was recently updated, run "lien reindex".'
+        '0 results. Try rephrasing as a full question (e.g. "How does X work?"), or use grep for exact string matches. If the codebase was recently updated, run "lien index".'
       );
     }
     return {
@@ -9209,10 +9332,10 @@ async function findRelatedChunks(filepaths, fileChunksMap, ctx) {
 }
 function createPathCache(workspaceRoot) {
   const cache = /* @__PURE__ */ new Map();
-  const normalize = (path7) => {
-    if (cache.has(path7)) return cache.get(path7);
-    const normalized = normalizePath(path7, workspaceRoot);
-    cache.set(path7, normalized);
+  const normalize = (path10) => {
+    if (cache.has(path10)) return cache.get(path10);
+    const normalized = normalizePath(path10, workspaceRoot);
+    cache.set(path10, normalized);
     return normalized;
   };
   return { normalize, cache };
@@ -9400,7 +9523,7 @@ async function handleListFunctions(args, ctx) {
       );
     }
     if (queryResult.method === "content") {
-      notes.push('Using content search. Run "lien reindex" to enable faster symbol-based queries.');
+      notes.push('Using content search. Run "lien index" to enable faster symbol-based queries.');
     }
     return {
       indexInfo: getIndexMetadata(),
@@ -9587,11 +9710,11 @@ async function scanChunksPaginated(vectorDB, crossRepo, log, normalizePathCached
 function createPathNormalizer() {
   const workspaceRoot = process.cwd().replace(/\\/g, "/");
   const cache = /* @__PURE__ */ new Map();
-  return (path7) => {
-    if (!cache.has(path7)) {
-      cache.set(path7, normalizePath2(path7, workspaceRoot));
+  return (path10) => {
+    if (!cache.has(path10)) {
+      cache.set(path10, normalizePath2(path10, workspaceRoot));
     }
-    return cache.get(path7);
+    return cache.get(path10);
   };
 }
 function groupChunksByFile(chunks) {
@@ -10351,9 +10474,8 @@ 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);
@@ -10363,8 +10485,7 @@ 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}`);
@@ -10381,8 +10502,7 @@ 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];
@@ -10400,11 +10520,11 @@ 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");
     }
@@ -10462,9 +10582,8 @@ 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(
@@ -10476,13 +10595,13 @@ 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;
@@ -10490,24 +10609,20 @@ 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];
@@ -10517,7 +10632,15 @@ 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(
@@ -10528,11 +10651,11 @@ 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) {
@@ -10564,6 +10687,7 @@ 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;
@@ -10577,10 +10701,18 @@ 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();
@@ -10590,6 +10722,7 @@ function createFileChangeHandler(rootDir, vectorDB, embeddings, log, reindexStat
         rootDir,
         vectorDB,
         embeddings,
+        manifest,
         log,
         reindexStateManager
       );
@@ -10852,9 +10985,9 @@ 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"));
@@ -11067,7 +11200,7 @@ async function startMCPServer(options) {
 // src/cli/serve.ts
 init_banner();
 async function serveCommand(options) {
-  const rootDir = options.root ? path4.resolve(options.root) : process.cwd();
+  const rootDir = options.root ? path7.resolve(options.root) : process.cwd();
   try {
     if (options.root) {
       try {
@@ -11113,12 +11246,12 @@ async function serveCommand(options) {
 // src/cli/complexity.ts
 import chalk7 from "chalk";
 import fs6 from "fs";
-import path5 from "path";
+import path8 from "path";
 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(
@@ -11128,7 +11261,7 @@ 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`)
     );
@@ -11138,7 +11271,7 @@ function validateFormat(format) {
 function validateFilesExist(files, rootDir) {
   if (!files || files.length === 0) return;
   const missingFiles = files.filter((file) => {
-    const fullPath = path5.isAbsolute(file) ? file : path5.join(rootDir, file);
+    const fullPath = path8.isAbsolute(file) ? file : path8.join(rootDir, file);
     return !fs6.existsSync(fullPath);
   });
   if (missingFiles.length > 0) {
@@ -11184,10 +11317,10 @@ async function complexityCommand(options) {
 
 // src/cli/config.ts
 import chalk8 from "chalk";
-import path6 from "path";
+import path9 from "path";
 import os2 from "os";
 import { loadGlobalConfig, mergeGlobalConfig } from "@liendev/core";
-var CONFIG_PATH = path6.join(os2.homedir(), ".lien", "config.json");
+var CONFIG_PATH = path9.join(os2.homedir(), ".lien", "config.json");
 var ALLOWED_KEYS = {
   backend: {
     values: ["lancedb", "qdrant"],
@@ -11274,9 +11407,9 @@ 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"));
@@ -11289,13 +11422,18 @@ program.command("init").description("Initialize Lien in the current directory").
 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
 `);