raggrep 0.2.3 → 0.4.0

package/dist/cli/main.js

@@ -1,5 +1,21 @@
 #!/usr/bin/env node
+import { createRequire } from "node:module";
+var __create = Object.create;
+var __getProtoOf = Object.getPrototypeOf;
 var __defProp = Object.defineProperty;
+var __getOwnPropNames = Object.getOwnPropertyNames;
+var __hasOwnProp = Object.prototype.hasOwnProperty;
+var __toESM = (mod, isNodeMode, target) => {
+  target = mod != null ? __create(__getProtoOf(mod)) : {};
+  const to = isNodeMode || !mod || !mod.__esModule ? __defProp(target, "default", { value: mod, enumerable: true }) : target;
+  for (let key of __getOwnPropNames(mod))
+    if (!__hasOwnProp.call(to, key))
+      __defProp(to, key, {
+        get: () => mod[key],
+        enumerable: true
+      });
+  return to;
+};
 var __export = (target, all) => {
   for (var name in all)
     __defProp(target, name, {
@@ -10,9 +26,13 @@ var __export = (target, all) => {
     });
 };
 var __esm = (fn, res) => () => (fn && (res = fn(fn = 0)), res);
+var __require = /* @__PURE__ */ createRequire(import.meta.url);
 
 // src/infrastructure/embeddings/transformersEmbedding.ts
-import { pipeline, env } from "@xenova/transformers";
+import {
+  pipeline,
+  env
+} from "@xenova/transformers";
 import * as path from "path";
 import * as os from "os";
 
@@ -24,7 +44,8 @@ class TransformersEmbeddingProvider {
   constructor(config) {
     this.config = {
       model: config?.model ?? "all-MiniLM-L6-v2",
-      showProgress: config?.showProgress ?? false
+      showProgress: config?.showProgress ?? false,
+      logger: config?.logger
     };
   }
   async initialize(config) {
@@ -46,29 +67,55 @@ class TransformersEmbeddingProvider {
     this.isInitializing = true;
     this.initPromise = (async () => {
       const modelId = EMBEDDING_MODELS[this.config.model];
-      if (this.config.showProgress) {
-        console.log(`
-  Loading embedding model: ${this.config.model}`);
-        console.log(`  Cache: ${CACHE_DIR}`);
-      }
+      const logger = this.config.logger;
+      const showProgress = this.config.showProgress || !!logger;
+      const isCached = await isModelCached(this.config.model);
+      let hasDownloads = false;
       try {
         this.pipeline = await pipeline("feature-extraction", modelId, {
-          progress_callback: this.config.showProgress ? (progress) => {
+          progress_callback: showProgress && !isCached ? (progress) => {
             if (progress.status === "progress" && progress.file) {
+              if (!hasDownloads) {
+                hasDownloads = true;
+                if (logger) {
+                  logger.info(`Downloading embedding model: ${this.config.model}`);
+                } else {
+                  console.log(`
+  Loading embedding model: ${this.config.model}`);
+                  console.log(`  Cache: ${CACHE_DIR}`);
+                }
+              }
               const pct = progress.progress ? Math.round(progress.progress) : 0;
-              process.stdout.write(`\r  Downloading ${progress.file}: ${pct}%   `);
+              if (logger) {
+                logger.progress(`  Downloading ${progress.file}: ${pct}%`);
+              } else {
+                process.stdout.write(`\r  Downloading ${progress.file}: ${pct}%   `);
+              }
             } else if (progress.status === "done" && progress.file) {
-              process.stdout.write(`\r  Downloaded ${progress.file}              
+              if (logger) {
+                logger.clearProgress();
+                logger.info(`  Downloaded ${progress.file}`);
+              } else if (hasDownloads) {
+                process.stdout.write(`\r  Downloaded ${progress.file}              
 `);
+              }
             }
           } : undefined
         });
-        if (this.config.showProgress) {
-          console.log(`  Model ready.
+        if (hasDownloads) {
+          if (logger) {
+            logger.clearProgress();
+            logger.info(`Model ready: ${this.config.model}`);
+          } else {
+            console.log(`  Model ready.
 `);
+          }
         }
       } catch (error) {
         this.pipeline = null;
+        if (logger) {
+          logger.clearProgress();
+        }
         throw new Error(`Failed to load embedding model: ${error}`);
       } finally {
         this.isInitializing = false;
@@ -122,9 +169,21 @@ class TransformersEmbeddingProvider {
 function getCacheDir() {
   return CACHE_DIR;
 }
+async function isModelCached(model) {
+  const modelId = EMBEDDING_MODELS[model];
+  const modelPath = path.join(CACHE_DIR, modelId);
+  try {
+    const fs = await import("fs/promises");
+    const onnxPath = path.join(modelPath, "onnx", "model_quantized.onnx");
+    await fs.access(onnxPath);
+    return true;
+  } catch {
+    return false;
+  }
+}
 function configureEmbeddings(config) {
   const newConfig = { ...globalConfig, ...config };
-  if (newConfig.model !== globalConfig.model) {
+  if (newConfig.model !== globalConfig.model || newConfig.logger !== globalConfig.logger) {
     globalProvider = null;
   }
   globalConfig = newConfig;
@@ -160,7 +219,8 @@ var init_transformersEmbedding = __esm(() => {
   };
   globalConfig = {
     model: "all-MiniLM-L6-v2",
-    showProgress: false
+    showProgress: false,
+    logger: undefined
   };
 });
 
@@ -168,8 +228,106 @@ var init_transformersEmbedding = __esm(() => {
 var init_embeddings = __esm(() => {
   init_transformersEmbedding();
 });
+
+// src/infrastructure/logger/loggers.ts
+class ConsoleLogger {
+  verbose;
+  constructor(options) {
+    this.verbose = options?.verbose ?? false;
+  }
+  info(message) {
+    console.log(message);
+  }
+  warn(message) {
+    console.warn(message);
+  }
+  error(message) {
+    console.error(message);
+  }
+  debug(message) {
+    if (this.verbose) {
+      console.log(message);
+    }
+  }
+  progress(message) {
+    console.log(message);
+  }
+  clearProgress() {}
+}
+
+class InlineProgressLogger {
+  verbose;
+  lastProgressLength = 0;
+  hasProgress = false;
+  constructor(options) {
+    this.verbose = options?.verbose ?? false;
+  }
+  info(message) {
+    this.clearProgress();
+    console.log(message);
+  }
+  warn(message) {
+    this.clearProgress();
+    console.warn(message);
+  }
+  error(message) {
+    this.clearProgress();
+    console.error(message);
+  }
+  debug(message) {
+    if (this.verbose) {
+      this.clearProgress();
+      console.log(message);
+    }
+  }
+  progress(message) {
+    process.stdout.write(`\r${message}`);
+    const padding = Math.max(0, this.lastProgressLength - message.length);
+    if (padding > 0) {
+      process.stdout.write(" ".repeat(padding));
+    }
+    this.lastProgressLength = message.length;
+    this.hasProgress = true;
+  }
+  clearProgress() {
+    if (this.hasProgress && this.lastProgressLength > 0) {
+      process.stdout.write("\r" + " ".repeat(this.lastProgressLength) + "\r");
+      this.lastProgressLength = 0;
+      this.hasProgress = false;
+    }
+  }
+}
+
+class SilentLogger {
+  info() {}
+  warn() {}
+  error() {}
+  debug() {}
+  progress() {}
+  clearProgress() {}
+}
+function createLogger(options) {
+  return new ConsoleLogger(options);
+}
+function createInlineLogger(options) {
+  return new InlineProgressLogger(options);
+}
+function createSilentLogger() {
+  return new SilentLogger;
+}
+
+// src/infrastructure/logger/index.ts
+var init_logger = () => {};
 // src/domain/entities/searchResult.ts
-var init_searchResult = () => {};
+var DEFAULT_SEARCH_OPTIONS;
+var init_searchResult = __esm(() => {
+  DEFAULT_SEARCH_OPTIONS = {
+    topK: 10,
+    minScore: 0.15,
+    filePatterns: [],
+    ensureFresh: true
+  };
+});
 
 // src/domain/entities/config.ts
 function createDefaultConfig() {
@@ -231,10 +389,17 @@ var init_config = __esm(() => {
     ".tsx",
     ".js",
     ".jsx",
+    ".mjs",
+    ".cjs",
     ".py",
     ".go",
     ".rs",
     ".java",
+    ".json",
+    ".yaml",
+    ".yml",
+    ".toml",
+    ".sql",
     ".md",
     ".txt"
   ];
@@ -2690,6 +2855,57 @@ __export(exports_typescript, {
   DEFAULT_MIN_SCORE: () => DEFAULT_MIN_SCORE2
 });
 import * as path8 from "path";
+function detectQueryIntent(queryTerms) {
+  const hasImplementationTerm = queryTerms.some((term) => IMPLEMENTATION_TERMS.includes(term));
+  const hasDocumentationTerm = queryTerms.some((term) => DOCUMENTATION_TERMS.includes(term));
+  if (hasDocumentationTerm) {
+    return "documentation";
+  }
+  if (hasImplementationTerm) {
+    return "implementation";
+  }
+  return "neutral";
+}
+function calculateFileTypeBoost(filepath, queryTerms) {
+  const ext = path8.extname(filepath).toLowerCase();
+  const isSourceCode = SOURCE_CODE_EXTENSIONS.includes(ext);
+  const isDoc = DOC_EXTENSIONS.includes(ext);
+  const intent = detectQueryIntent(queryTerms);
+  if (intent === "implementation") {
+    if (isSourceCode) {
+      return 0.06;
+    }
+    return 0;
+  }
+  if (intent === "documentation") {
+    if (isDoc) {
+      return 0.08;
+    }
+    return 0;
+  }
+  return 0;
+}
+function calculateChunkTypeBoost(chunk) {
+  switch (chunk.type) {
+    case "function":
+      return 0.05;
+    case "class":
+    case "interface":
+      return 0.04;
+    case "type":
+    case "enum":
+      return 0.03;
+    case "variable":
+      return 0.02;
+    case "file":
+    case "block":
+    default:
+      return 0;
+  }
+}
+function calculateExportBoost(chunk) {
+  return chunk.isExported ? 0.03 : 0;
+}
 
 class TypeScriptModule {
   id = "language/typescript";
@@ -2700,8 +2916,16 @@ class TypeScriptModule {
   symbolicIndex = null;
   pendingSummaries = new Map;
   rootDir = "";
+  logger = undefined;
   async initialize(config) {
     this.embeddingConfig = getEmbeddingConfigFromModule(config);
+    this.logger = config.options?.logger;
+    if (this.logger) {
+      this.embeddingConfig = {
+        ...this.embeddingConfig,
+        logger: this.logger
+      };
+    }
     configureEmbeddings(this.embeddingConfig);
     this.pendingSummaries.clear();
   }
@@ -2859,7 +3083,11 @@ class TypeScriptModule {
       const semanticScore = cosineSimilarity(queryEmbedding, embedding);
       const bm25Score = bm25Scores.get(chunk.id) || 0;
       const pathBoost = pathBoosts.get(filepath) || 0;
-      const hybridScore = SEMANTIC_WEIGHT * semanticScore + BM25_WEIGHT * bm25Score + pathBoost;
+      const fileTypeBoost = calculateFileTypeBoost(filepath, queryTerms);
+      const chunkTypeBoost = calculateChunkTypeBoost(chunk);
+      const exportBoost = calculateExportBoost(chunk);
+      const totalBoost = pathBoost + fileTypeBoost + chunkTypeBoost + exportBoost;
+      const hybridScore = SEMANTIC_WEIGHT * semanticScore + BM25_WEIGHT * bm25Score + totalBoost;
       if (hybridScore >= minScore || bm25Score > 0.3) {
         results.push({
           filepath,
@@ -2869,7 +3097,10 @@ class TypeScriptModule {
           context: {
             semanticScore,
             bm25Score,
-            pathBoost
+            pathBoost,
+            fileTypeBoost,
+            chunkTypeBoost,
+            exportBoost
           }
         });
       }
@@ -2901,7 +3132,7 @@ class TypeScriptModule {
     return references;
   }
 }
-var DEFAULT_MIN_SCORE2 = 0.15, DEFAULT_TOP_K2 = 10, SEMANTIC_WEIGHT = 0.7, BM25_WEIGHT = 0.3;
+var DEFAULT_MIN_SCORE2 = 0.15, DEFAULT_TOP_K2 = 10, SEMANTIC_WEIGHT = 0.7, BM25_WEIGHT = 0.3, IMPLEMENTATION_TERMS, DOCUMENTATION_TERMS, SOURCE_CODE_EXTENSIONS, DOC_EXTENSIONS;
 var init_typescript = __esm(() => {
   init_embeddings();
   init_config2();
@@ -2909,6 +3140,52 @@ var init_typescript = __esm(() => {
   init_storage();
   init_keywords();
   init_keywords();
+  IMPLEMENTATION_TERMS = [
+    "function",
+    "method",
+    "class",
+    "interface",
+    "implement",
+    "implementation",
+    "endpoint",
+    "route",
+    "handler",
+    "controller",
+    "module",
+    "code"
+  ];
+  DOCUMENTATION_TERMS = [
+    "documentation",
+    "docs",
+    "guide",
+    "tutorial",
+    "readme",
+    "how",
+    "what",
+    "why",
+    "explain",
+    "overview",
+    "getting",
+    "started",
+    "requirements",
+    "setup",
+    "install",
+    "configure",
+    "configuration"
+  ];
+  SOURCE_CODE_EXTENSIONS = [
+    ".ts",
+    ".tsx",
+    ".js",
+    ".jsx",
+    ".mjs",
+    ".cjs",
+    ".py",
+    ".go",
+    ".rs",
+    ".java"
+  ];
+  DOC_EXTENSIONS = [".md", ".txt", ".rst"];
 });
 
 // src/modules/registry.ts
@@ -3380,6 +3657,7 @@ var init_watcher = __esm(() => {
 var exports_indexer = {};
 __export(exports_indexer, {
   watchDirectory: () => watchDirectory,
+  resetIndex: () => resetIndex,
   indexDirectory: () => indexDirectory,
   getIndexStatus: () => getIndexStatus,
   ensureIndexFresh: () => ensureIndexFresh,
@@ -3391,42 +3669,31 @@ import * as path12 from "path";
 async function indexDirectory(rootDir, options = {}) {
   const verbose = options.verbose ?? false;
   const quiet = options.quiet ?? false;
+  const logger = options.logger ? options.logger : quiet ? createSilentLogger() : createLogger({ verbose });
   rootDir = path12.resolve(rootDir);
   const location = getIndexLocation(rootDir);
-  if (!quiet) {
-    console.log(`Indexing directory: ${rootDir}`);
-    console.log(`Index location: ${location.indexDir}`);
-  }
+  logger.info(`Indexing directory: ${rootDir}`);
+  logger.info(`Index location: ${location.indexDir}`);
   const config = await loadConfig(rootDir);
   const introspection = new IntrospectionIndex(rootDir);
   await introspection.initialize();
-  if (verbose) {
-    const structure = introspection.getStructure();
-    if (structure?.isMonorepo) {
-      console.log(`Detected monorepo with ${structure.projects.length} projects`);
-    }
+  const structure = introspection.getStructure();
+  if (structure?.isMonorepo) {
+    logger.debug(`Detected monorepo with ${structure.projects.length} projects`);
   }
   await registerBuiltInModules();
   const enabledModules = registry.getEnabled(config);
   if (enabledModules.length === 0) {
-    if (!quiet) {
-      console.log("No modules enabled. Check your configuration.");
-    }
+    logger.info("No modules enabled. Check your configuration.");
     return [];
   }
-  if (!quiet) {
-    console.log(`Enabled modules: ${enabledModules.map((m) => m.id).join(", ")}`);
-  }
+  logger.info(`Enabled modules: ${enabledModules.map((m) => m.id).join(", ")}`);
   const files = await findFiles(rootDir, config);
-  if (!quiet) {
-    console.log(`Found ${files.length} files to index`);
-  }
+  logger.info(`Found ${files.length} files to index`);
   const results = [];
   for (const module of enabledModules) {
-    if (!quiet) {
-      console.log(`
+    logger.info(`
 [${module.name}] Starting indexing...`);
-    }
     const moduleConfig = getModuleConfig(config, module.id);
     if (module.initialize && moduleConfig) {
       const configWithOverrides = { ...moduleConfig };
@@ -3436,14 +3703,16 @@ async function indexDirectory(rootDir, options = {}) {
           embeddingModel: options.model
         };
       }
+      configWithOverrides.options = {
+        ...configWithOverrides.options,
+        logger
+      };
       await module.initialize(configWithOverrides);
     }
-    const result = await indexWithModule(rootDir, files, module, config, verbose, introspection);
+    const result = await indexWithModule(rootDir, files, module, config, verbose, introspection, logger);
     results.push(result);
     if (module.finalize) {
-      if (!quiet) {
-        console.log(`[${module.name}] Building secondary indexes...`);
-      }
+      logger.info(`[${module.name}] Building secondary indexes...`);
       const ctx = {
         rootDir,
         config,
@@ -3459,9 +3728,7 @@ async function indexDirectory(rootDir, options = {}) {
       };
       await module.finalize(ctx);
     }
-    if (!quiet) {
-      console.log(`[${module.name}] Complete: ${result.indexed} indexed, ${result.skipped} skipped, ${result.errors} errors`);
-    }
+    logger.info(`[${module.name}] Complete: ${result.indexed} indexed, ${result.skipped} skipped, ${result.errors} errors`);
   }
   await introspection.save(config);
   await updateGlobalManifest(rootDir, enabledModules, config);
@@ -3484,28 +3751,37 @@ async function deleteIndex(rootDir) {
     await fs6.rm(indexDir, { recursive: true, force: true });
   } catch {}
 }
+async function resetIndex(rootDir) {
+  rootDir = path12.resolve(rootDir);
+  const status = await getIndexStatus(rootDir);
+  if (!status.exists) {
+    throw new Error(`No index found for ${rootDir}`);
+  }
+  await deleteIndex(rootDir);
+  return {
+    success: true,
+    indexDir: status.indexDir
+  };
+}
 async function ensureIndexFresh(rootDir, options = {}) {
   const verbose = options.verbose ?? false;
   const quiet = options.quiet ?? false;
+  const logger = options.logger ? options.logger : quiet ? createSilentLogger() : createLogger({ verbose });
   rootDir = path12.resolve(rootDir);
   const status = await getIndexStatus(rootDir);
   if (!status.exists) {
-    if (!quiet) {
-      console.log(`No index found. Creating index...
+    logger.info(`No index found. Creating index...
 `);
-    }
-    const results = await indexDirectory(rootDir, { ...options, quiet });
+    const results = await indexDirectory(rootDir, { ...options, logger });
     const totalIndexed2 = results.reduce((sum, r) => sum + r.indexed, 0);
     return { indexed: totalIndexed2, removed: 0, unchanged: 0 };
   }
   const versionCompatible = await isIndexVersionCompatible(rootDir);
   if (!versionCompatible) {
-    if (!quiet) {
-      console.log(`Index version incompatible. Rebuilding...
+    logger.info(`Index version incompatible. Rebuilding...
 `);
-    }
     await deleteIndex(rootDir);
-    const results = await indexDirectory(rootDir, { ...options, quiet });
+    const results = await indexDirectory(rootDir, { ...options, logger });
     const totalIndexed2 = results.reduce((sum, r) => sum + r.indexed, 0);
     return { indexed: totalIndexed2, removed: 0, unchanged: 0 };
   }
@@ -3532,6 +3808,10 @@ async function ensureIndexFresh(rootDir, options = {}) {
           embeddingModel: options.model
         };
       }
+      configWithOverrides.options = {
+        ...configWithOverrides.options,
+        logger
+      };
       await module.initialize(configWithOverrides);
     }
     const manifest = await loadModuleManifest(rootDir, module.id, config);
@@ -3543,9 +3823,7 @@ async function ensureIndexFresh(rootDir, options = {}) {
       }
     }
     for (const filepath of filesToRemove) {
-      if (verbose) {
-        console.log(`  Removing stale: ${filepath}`);
-      }
+      logger.debug(`  Removing stale: ${filepath}`);
       const indexFilePath = path12.join(indexPath, filepath.replace(/\.[^.]+$/, ".json"));
       try {
         await fs6.unlink(indexFilePath);
@@ -3571,8 +3849,11 @@ async function ensureIndexFresh(rootDir, options = {}) {
       },
       getIntrospection: (filepath) => introspection.getFile(filepath)
     };
-    for (const filepath of currentFiles) {
+    const totalFiles = currentFiles.length;
+    for (let i = 0;i < currentFiles.length; i++) {
+      const filepath = currentFiles[i];
       const relativePath = path12.relative(rootDir, filepath);
+      const progress = `[${i + 1}/${totalFiles}]`;
       try {
         const stats = await fs6.stat(filepath);
         const lastModified = stats.mtime.toISOString();
@@ -3581,9 +3862,7 @@ async function ensureIndexFresh(rootDir, options = {}) {
           totalUnchanged++;
           continue;
         }
-        if (verbose) {
-          console.log(`  Indexing: ${relativePath}`);
-        }
+        logger.progress(`  ${progress} Indexing: ${relativePath}`);
         const content = await fs6.readFile(filepath, "utf-8");
         introspection.addFile(relativePath, content);
         const fileIndex = await module.indexFile(relativePath, content, ctx);
@@ -3596,11 +3875,11 @@ async function ensureIndexFresh(rootDir, options = {}) {
           totalIndexed++;
         }
       } catch (error) {
-        if (verbose) {
-          console.error(`  Error indexing ${relativePath}:`, error);
-        }
+        logger.clearProgress();
+        logger.error(`  ${progress} Error indexing ${relativePath}: ${error}`);
       }
     }
+    logger.clearProgress();
     if (totalIndexed > 0 || totalRemoved > 0) {
       manifest.lastUpdated = new Date().toISOString();
       await writeModuleManifest(rootDir, module.id, manifest, config);
@@ -3624,7 +3903,7 @@ async function ensureIndexFresh(rootDir, options = {}) {
     unchanged: totalUnchanged
   };
 }
-async function indexWithModule(rootDir, files, module, config, verbose, introspection) {
+async function indexWithModule(rootDir, files, module, config, verbose, introspection, logger) {
   const result = {
     moduleId: module.id,
     indexed: 0,
@@ -3632,6 +3911,30 @@ async function indexWithModule(rootDir, files, module, config, verbose, introspe
     errors: 0
   };
   const manifest = await loadModuleManifest(rootDir, module.id, config);
+  const indexPath = getModuleIndexPath(rootDir, module.id, config);
+  const currentFileSet = new Set(files.map((f) => path12.relative(rootDir, f)));
+  const filesToRemove = [];
+  for (const filepath of Object.keys(manifest.files)) {
+    if (!currentFileSet.has(filepath)) {
+      filesToRemove.push(filepath);
+    }
+  }
+  if (filesToRemove.length > 0) {
+    logger.info(`  Removing ${filesToRemove.length} stale entries...`);
+    for (const filepath of filesToRemove) {
+      logger.debug(`    Removing: ${filepath}`);
+      const indexFilePath = path12.join(indexPath, filepath.replace(/\.[^.]+$/, ".json"));
+      try {
+        await fs6.unlink(indexFilePath);
+      } catch {}
+      const symbolicFilePath = path12.join(indexPath, "symbolic", filepath.replace(/\.[^.]+$/, ".json"));
+      try {
+        await fs6.unlink(symbolicFilePath);
+      } catch {}
+      delete manifest.files[filepath];
+    }
+    await cleanupEmptyDirectories(indexPath);
+  }
   const ctx = {
     rootDir,
     config,
@@ -3646,29 +3949,26 @@ async function indexWithModule(rootDir, files, module, config, verbose, introspe
     },
     getIntrospection: (filepath) => introspection.getFile(filepath)
   };
-  for (const filepath of files) {
+  const totalFiles = files.length;
+  for (let i = 0;i < files.length; i++) {
+    const filepath = files[i];
     const relativePath = path12.relative(rootDir, filepath);
+    const progress = `[${i + 1}/${totalFiles}]`;
     try {
       const stats = await fs6.stat(filepath);
       const lastModified = stats.mtime.toISOString();
       const existingEntry = manifest.files[relativePath];
       if (existingEntry && existingEntry.lastModified === lastModified) {
-        if (verbose) {
-          console.log(`  Skipped ${relativePath} (unchanged)`);
-        }
+        logger.debug(`  ${progress} Skipped ${relativePath} (unchanged)`);
         result.skipped++;
         continue;
       }
       const content = await fs6.readFile(filepath, "utf-8");
       introspection.addFile(relativePath, content);
-      if (verbose) {
-        console.log(`  Processing ${relativePath}...`);
-      }
+      logger.progress(`  ${progress} Processing: ${relativePath}`);
       const fileIndex = await module.indexFile(relativePath, content, ctx);
       if (!fileIndex) {
-        if (verbose) {
-          console.log(`  Skipped ${relativePath} (no chunks)`);
-        }
+        logger.debug(`  ${progress} Skipped ${relativePath} (no chunks)`);
         result.skipped++;
         continue;
       }
@@ -3679,10 +3979,12 @@ async function indexWithModule(rootDir, files, module, config, verbose, introspe
       };
       result.indexed++;
     } catch (error) {
-      console.error(`  Error indexing ${relativePath}:`, error);
+      logger.clearProgress();
+      logger.error(`  ${progress} Error indexing ${relativePath}: ${error}`);
       result.errors++;
     }
   }
+  logger.clearProgress();
   manifest.lastUpdated = new Date().toISOString();
   await writeModuleManifest(rootDir, module.id, manifest, config);
   return result;
@@ -3738,26 +4040,27 @@ async function updateGlobalManifest(rootDir, modules, config) {
 }
 async function cleanupIndex(rootDir, options = {}) {
   const verbose = options.verbose ?? false;
+  const logger = options.logger ?? createLogger({ verbose });
   rootDir = path12.resolve(rootDir);
-  console.log(`Cleaning up index in: ${rootDir}`);
+  logger.info(`Cleaning up index in: ${rootDir}`);
   const config = await loadConfig(rootDir);
   await registerBuiltInModules();
   const enabledModules = registry.getEnabled(config);
   if (enabledModules.length === 0) {
-    console.log("No modules enabled.");
+    logger.info("No modules enabled.");
     return [];
   }
   const results = [];
   for (const module of enabledModules) {
-    console.log(`
+    logger.info(`
 [${module.name}] Checking for stale entries...`);
-    const result = await cleanupModuleIndex(rootDir, module.id, config, verbose);
+    const result = await cleanupModuleIndex(rootDir, module.id, config, logger);
     results.push(result);
-    console.log(`[${module.name}] Removed ${result.removed} stale entries, kept ${result.kept} valid entries`);
+    logger.info(`[${module.name}] Removed ${result.removed} stale entries, kept ${result.kept} valid entries`);
   }
   return results;
 }
-async function cleanupModuleIndex(rootDir, moduleId, config, verbose) {
+async function cleanupModuleIndex(rootDir, moduleId, config, logger) {
   const result = {
     moduleId,
     removed: 0,
@@ -3776,9 +4079,7 @@ async function cleanupModuleIndex(rootDir, moduleId, config, verbose) {
     } catch {
       filesToRemove.push(filepath);
       result.removed++;
-      if (verbose) {
-        console.log(`  Removing stale entry: ${filepath}`);
-      }
+      logger.debug(`  Removing stale entry: ${filepath}`);
     }
   }
   for (const filepath of filesToRemove) {
@@ -3874,9 +4175,15 @@ var init_indexer = __esm(() => {
   init_config2();
   init_registry();
   init_introspection2();
+  init_logger();
   init_watcher();
 });
 
+// src/types.ts
+var init_types = __esm(() => {
+  init_entities();
+});
+
 // src/app/search/index.ts
 var exports_search = {};
 __export(exports_search, {
@@ -3887,12 +4194,16 @@ import * as fs7 from "fs/promises";
 import * as path13 from "path";
 async function search(rootDir, query, options = {}) {
   rootDir = path13.resolve(rootDir);
+  const ensureFresh = options.ensureFresh ?? DEFAULT_SEARCH_OPTIONS.ensureFresh;
+  if (ensureFresh) {
+    await ensureIndexFresh(rootDir, { quiet: true });
+  }
   console.log(`Searching for: "${query}"`);
   const config = await loadConfig(rootDir);
   await registerBuiltInModules();
   const globalManifest = await loadGlobalManifest(rootDir, config);
   if (!globalManifest || globalManifest.modules.length === 0) {
-    console.log('No index found. Run "bun run index" first.');
+    console.log('No index found. Run "raggrep index" first.');
     return [];
   }
   const modulesToSearch = [];
@@ -4015,16 +4326,19 @@ function formatSearchResults(results) {
   return output;
 }
 var init_search = __esm(() => {
+  init_types();
   init_config2();
   init_registry();
+  init_indexer();
 });
 
 // src/app/cli/main.ts
 init_embeddings();
+init_logger();
 // package.json
 var package_default = {
   name: "raggrep",
-  version: "0.2.3",
+  version: "0.4.0",
   description: "Local filesystem-based RAG system for codebases - semantic search using local embeddings",
   type: "module",
   main: "./dist/index.js",
@@ -4198,13 +4512,15 @@ Examples:
         process.exit(0);
       }
       const { indexDirectory: indexDirectory2, watchDirectory: watchDirectory2 } = await Promise.resolve().then(() => (init_indexer(), exports_indexer));
+      const logger = createInlineLogger({ verbose: flags.verbose });
       console.log("RAGgrep Indexer");
       console.log(`================
 `);
       try {
         const results = await indexDirectory2(process.cwd(), {
           model: flags.model,
-          verbose: flags.verbose
+          verbose: flags.verbose,
+          logger
         });
         console.log(`
 ================`);
@@ -4289,9 +4605,11 @@ Examples:
         process.exit(1);
       }
       try {
+        const silentLogger = createSilentLogger();
         const freshStats = await ensureIndexFresh2(process.cwd(), {
           model: flags.model,
-          quiet: true
+          quiet: true,
+          logger: silentLogger
         });
         console.log("RAGgrep Search");
         console.log(`==============
@@ -4314,7 +4632,8 @@ Examples:
         const results = await search2(process.cwd(), query, {
           topK: flags.topK ?? 10,
           minScore: flags.minScore,
-          filePatterns
+          filePatterns,
+          ensureFresh: false
         });
         console.log(formatSearchResults2(results));
       } catch (error) {
@@ -4323,44 +4642,37 @@ Examples:
       }
       break;
     }
-    case "cleanup": {
+    case "reset": {
       if (flags.help) {
         console.log(`
-raggrep cleanup - Remove stale index entries for deleted files
+raggrep reset - Clear the index for the current directory
 
 Usage:
-  raggrep cleanup [options]
+  raggrep reset [options]
 
 Options:
-  -v, --verbose        Show detailed progress
   -h, --help           Show this help message
 
 Description:
-  Scans the index and removes entries for files that no longer exist.
-  Run this command after deleting files to clean up the index.
+  Completely removes the index for the current directory.
+  The next 'raggrep index' or 'raggrep query' will rebuild from scratch.
 
 Examples:
-  raggrep cleanup
-  raggrep cleanup --verbose
+  raggrep reset
 `);
         process.exit(0);
       }
-      const { cleanupIndex: cleanupIndex2 } = await Promise.resolve().then(() => (init_indexer(), exports_indexer));
-      console.log("RAGgrep Cleanup");
-      console.log(`===============
-`);
+      const { resetIndex: resetIndex2 } = await Promise.resolve().then(() => (init_indexer(), exports_indexer));
       try {
-        const results = await cleanupIndex2(process.cwd(), {
-          verbose: flags.verbose
-        });
-        console.log(`
-===============`);
-        console.log("Summary:");
-        for (const result of results) {
-          console.log(`  ${result.moduleId}: ${result.removed} removed, ${result.kept} kept`);
-        }
+        const result = await resetIndex2(process.cwd());
+        console.log("Index cleared successfully.");
+        console.log(`  Removed: ${result.indexDir}`);
       } catch (error) {
-        console.error("Error during cleanup:", error);
+        if (error instanceof Error && error.message.includes("No index found")) {
+          console.error("Error: No index found for this directory.");
+          process.exit(1);
+        }
+        console.error("Error during reset:", error);
         process.exit(1);
       }
       break;
@@ -4439,7 +4751,7 @@ Commands:
   index    Index the current directory
   query    Search the indexed codebase
   status   Show the current state of the index
-  cleanup  Remove stale index entries for deleted files
+  reset    Clear the index for the current directory
 
 Options:
   -h, --help     Show help for a command
@@ -4449,7 +4761,7 @@ Examples:
   raggrep index
   raggrep query "user login"
   raggrep status
-  raggrep cleanup
+  raggrep reset
 
 Run 'raggrep <command> --help' for more information.
 `);
@@ -4461,4 +4773,4 @@ Run 'raggrep <command> --help' for more information.
 }
 main();
 
-//# debugId=DB928D21A583DAC064756E2164756E21
+//# debugId=B729BEE1B814E8D564756E2164756E21