directory-indexer 0.2.2 → 1.0.0

package/README.md

@@ -14,7 +14,7 @@ Self-hosted semantic search for local files. Give your AI assistant access to se
 **Prerequisites:**
 
 - **[Docker](https://docs.docker.com/get-docker/)** - For running Qdrant and Ollama _(skip if you already have them running natively)_
-- **[Node.js 18+](https://nodejs.org/en/download/)** - Required for running directory-indexer
+- **[Node.js 18+](https://nodejs.org/en/download/)** - Required for running directory-indexer (the v1.x line targets Node 18 LTS compatibility)
 
 _Note: For native Qdrant and Ollama installation without Docker, see [Setup section](#setup)._
 

package/dist/cli-handlers.js

@@ -1,5 +1,5 @@
 import { indexDirectories } from "./indexing.js";
-import { searchContent, findSimilarFiles, getFileContent } from "./search.js";
+import { getFileContent, searchContent, findSimilarFiles } from "./search.js";
 import { loadConfig } from "./config.js";
 import { getIndexStatus } from "./storage.js";
 import { startMcpServer } from "./mcp.js";

package/dist/cli.js

@@ -4,8 +4,8 @@ import { fileURLToPath } from "url";
 import { readFileSync } from "fs";
 import { dirname, join } from "path";
 import { handleIndex, handleSearch, handleSimilar, handleGet, handleServe, handleReset, handleStatus } from "./cli-handlers.js";
-const __dirname = dirname(fileURLToPath(import.meta.url));
-const packageJsonPath = join(__dirname, "../package.json");
+const __dirname$1 = dirname(fileURLToPath(import.meta.url));
+const packageJsonPath = join(__dirname$1, "../package.json");
 const packageJson = JSON.parse(readFileSync(packageJsonPath, "utf-8"));
 const VERSION = packageJson.version;
 async function main() {

package/dist/cli.js.map

@@ -1 +1 @@
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.argument('<paths...>', 'Directory paths to index')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (paths: string[], options) => {\n      try {\n        await handleIndex(paths, options);\n      } catch (error) {\n        console.error('Error indexing directories:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('search')\n    .description('Search indexed content semantically')\n    .argument('<query>', 'Search query')\n    .option('-l, --limit <number>', 'Maximum number of results', '10')\n    .option('-c, --show-chunks', 'Show individual chunk scores and IDs')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (query: string, options) => {\n      try {\n        await handleSearch(query, {\n          limit: parseInt(options.limit),\n          showChunks: options.showChunks,\n          verbose: options.verbose\n        });\n      } catch (error) {\n        console.error('Error searching content:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('similar')\n    .description('Find files similar to a given file')\n    .argument('<file>', 'File path to find similar files for')\n    .option('-l, --limit <number>', 'Maximum number of results', '10')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (filePath: string, options) => {\n      try {\n        await handleSimilar(filePath, {\n          limit: parseInt(options.limit),\n          verbose: options.verbose\n        });\n      } catch (error) {\n        console.error('Error finding similar files:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('get')\n    .description('Get file content')\n    .argument('<file>', 'File path to retrieve')\n    .option('-c, --chunks <range>', 'Chunk range (e.g., \"2-5\")')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (filePath: string, options) => {\n      try {\n        await handleGet(filePath, options);\n      } catch (error) {\n        console.error('Error getting file content:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('serve')\n    .description('Start MCP server')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (options) => {\n      try {\n        await handleServe(options);\n      } catch (error) {\n        console.error('Error starting MCP server:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('reset')\n    .description('Reset directory-indexer data (database and vector collection)')\n    .option('--force', 'Skip confirmation prompt')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (options) => {\n      try {\n        await handleReset(options);\n      } catch (error) {\n        if (error instanceof Error && error.message === 'Reset cancelled by user') {\n          console.log('\\nReset cancelled.');\n          process.exit(0);\n        }\n        console.error('Error during reset:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('status')\n    .description('Show indexing status')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (options) => {\n      try {\n        await handleStatus(options);\n      } catch (error) {\n        console.error('Error getting status:', error);\n        process.exit(1);\n      }\n    });\n\n  await program.parseAsync();\n}\n\n// Main function is already exported 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+{"version":3,"file":"cli.js","sources":["../src/cli.ts"],"sourcesContent":["#!/usr/bin/env node\n\nimport { Command } from 'commander';\nimport { fileURLToPath } from 'url';\nimport { readFileSync } from 'fs';\nimport { join, dirname } from 'path';\nimport { \n  handleIndex, \n  handleSearch, \n  handleSimilar, \n  handleGet, \n  handleServe, \n  handleReset, \n  handleStatus \n} from './cli-handlers.js';\n\n// Read version from package.json\nconst __dirname = dirname(fileURLToPath(import.meta.url));\nconst packageJsonPath = join(__dirname, '../package.json');\nconst packageJson = JSON.parse(readFileSync(packageJsonPath, 'utf-8'));\nconst VERSION = packageJson.version;\n\nexport async function main() {\n  const program = new Command();\n  \n  program\n    .name('directory-indexer')\n    .description('AI-powered directory indexing with semantic search')\n    .version(VERSION);\n\n  program\n    .command('index')\n    .description('Index directories for semantic search')\n    .argument('<paths...>', 'Directory paths to index')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (paths: string[], options) => {\n      try {\n        await handleIndex(paths, options);\n      } catch (error) {\n        console.error('Error indexing directories:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('search')\n    .description('Search indexed content semantically')\n    .argument('<query>', 'Search query')\n    .option('-l, --limit <number>', 'Maximum number of results', '10')\n    .option('-c, --show-chunks', 'Show individual chunk scores and IDs')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (query: string, options) => {\n      try {\n        await handleSearch(query, {\n          limit: parseInt(options.limit),\n          showChunks: options.showChunks,\n          verbose: options.verbose\n        });\n      } catch (error) {\n        console.error('Error searching content:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('similar')\n    .description('Find files similar to a given file')\n    .argument('<file>', 'File path to find similar files for')\n    .option('-l, --limit <number>', 'Maximum number of results', '10')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (filePath: string, options) => {\n      try {\n        await handleSimilar(filePath, {\n          limit: parseInt(options.limit),\n          verbose: options.verbose\n        });\n      } catch (error) {\n        console.error('Error finding similar files:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('get')\n    .description('Get file content')\n    .argument('<file>', 'File path to retrieve')\n    .option('-c, --chunks <range>', 'Chunk range (e.g., \"2-5\")')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (filePath: string, options) => {\n      try {\n        await handleGet(filePath, options);\n      } catch (error) {\n        console.error('Error getting file content:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('serve')\n    .description('Start MCP server')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (options) => {\n      try {\n        await handleServe(options);\n      } catch (error) {\n        console.error('Error starting MCP server:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('reset')\n    .description('Reset directory-indexer data (database and vector collection)')\n    .option('--force', 'Skip confirmation prompt')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (options) => {\n      try {\n        await handleReset(options);\n      } catch (error) {\n        if (error instanceof Error && error.message === 'Reset cancelled by user') {\n          console.log('\\nReset cancelled.');\n          process.exit(0);\n        }\n        console.error('Error during reset:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('status')\n    .description('Show indexing status')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (options) => {\n      try {\n        await handleStatus(options);\n      } catch (error) {\n        console.error('Error getting status:', error);\n        process.exit(1);\n      }\n    });\n\n  await program.parseAsync();\n}\n\n// Main function is already exported 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package/dist/config.js

@@ -12,14 +12,14 @@ const WorkspaceSchema = z.object({
 const ConfigSchema = z.object({
   storage: z.object({
     sqlitePath: z.string(),
-    qdrantEndpoint: z.string().url(),
+    qdrantEndpoint: z.url(),
     qdrantCollection: z.string(),
     qdrantApiKey: z.string().optional()
   }),
   embedding: z.object({
     provider: z.enum(["ollama", "openai", "mock"]),
     model: z.string(),
-    endpoint: z.string().url()
+    endpoint: z.url()
   }),
   indexing: z.object({
     chunkSize: z.number().positive(),
@@ -30,7 +30,7 @@ const ConfigSchema = z.object({
   }),
   dataDir: z.string(),
   verbose: z.boolean(),
-  workspaces: z.record(WorkspaceSchema)
+  workspaces: z.record(z.string(), WorkspaceSchema)
 });
 class ConfigError extends Error {
   constructor(message, cause) {
@@ -109,7 +109,7 @@ function loadConfig(options = {}) {
     return ConfigSchema.parse(config);
   } catch (error) {
     if (error instanceof z.ZodError) {
-      const messages = error.errors.map((e) => `${e.path.join(".")}: ${e.message}`);
+      const messages = error.issues.map((e) => `${e.path.join(".")}: ${e.message}`);
       throw new ConfigError(`Configuration validation failed: ${messages.join(", ")}`, error);
     }
     throw new ConfigError("Failed to load configuration", error);

package/dist/config.js.map

@@ -1 +1 @@
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'test-data.db' : 'data.db';\n  const defaultCollection = isTest ? 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+{"version":3,"file":"config.js","sources":["../src/config.ts"],"sourcesContent":["import { homedir } from 'os';\nimport { join } from 'path';\nimport { existsSync, statSync } from 'fs';\nimport { z } from 'zod';\nimport { normalizePath } from './utils';\n\nconst WorkspaceSchema = z.object({\n  paths: z.array(z.string()),\n  isValid: z.boolean(),\n  filesCount: z.number().optional(),\n  chunksCount: z.number().optional(),\n});\n\nconst ConfigSchema = z.object({\n  storage: z.object({\n    sqlitePath: z.string(),\n    qdrantEndpoint: z.url(),\n    qdrantCollection: z.string(),\n    qdrantApiKey: z.string().optional(),\n  }),\n  embedding: z.object({\n    provider: z.enum(['ollama', 'openai', 'mock']),\n    model: z.string(),\n    endpoint: z.url(),\n  }),\n  indexing: z.object({\n    chunkSize: z.number().positive(),\n    chunkOverlap: z.number().nonnegative(),\n    maxFileSize: z.number().positive(),\n    ignorePatterns: z.array(z.string()),\n    respectGitignore: z.boolean(),\n  }),\n  dataDir: z.string(),\n  verbose: z.boolean(),\n  workspaces: z.record(z.string(), WorkspaceSchema),\n});\n\nexport type Config = z.infer<typeof ConfigSchema>;\nexport type WorkspaceConfig = z.infer<typeof WorkspaceSchema>;\n\nexport class ConfigError extends Error {\n  constructor(message: string, public override cause?: Error) {\n    super(message);\n    this.name = 'ConfigError';\n  }\n}\n\nfunction parseWorkspaces(env: Record<string, string | undefined>): Record<string, WorkspaceConfig> {\n  const workspaces: Record<string, WorkspaceConfig> = {};\n  \n  for (const [key, value] of Object.entries(env)) {\n    if (key.startsWith('WORKSPACE_') && value) {\n      const name = key.replace('WORKSPACE_', '').toLowerCase();\n      \n      // Parse paths from comma-separated string or JSON array\n      let paths: string[];\n      try {\n        // Try parsing as JSON array first\n        paths = JSON.parse(value);\n        if (!Array.isArray(paths)) {\n          throw new Error('Not an array');\n        }\n      } catch {\n        // Fall back to comma-separated string\n        paths = value.split(',').map(p => p.trim()).filter(p => p.length > 0);\n      }\n      \n      // Normalize paths for consistent comparison\n      const normalizedPaths = paths.map(normalizePath);\n      \n      // Validate that paths exist and are directories\n      const isValid = normalizedPaths.every(path => {\n        try {\n          return existsSync(path) && statSync(path).isDirectory();\n        } catch {\n          return false;\n        }\n      });\n      \n      workspaces[name] = {\n        paths: normalizedPaths,\n        isValid,\n      };\n    }\n  }\n  \n  return workspaces;\n}\n\nexport function getWorkspacePaths(config: Config, workspace: string): string[] {\n  const workspaceConfig = config.workspaces[workspace];\n  return workspaceConfig?.paths || [];\n}\n\nexport function getAvailableWorkspaces(config: Config): string[] {\n  return Object.keys(config.workspaces);\n}\n\nexport function loadConfig(options: { verbose?: boolean } = {}): Config {\n  const dataDir = process.env.DIRECTORY_INDEXER_DATA_DIR || join(homedir(), '.directory-indexer');\n  \n  // Use separate database file and collection for tests to avoid contaminating main data\n  const isTest = process.env.NODE_ENV === 'test' || process.env.VITEST === 'true';\n  const dbFileName = isTest ? 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package/dist/indexing.js

@@ -1,9 +1,10 @@
 import { promises } from "fs";
 import { join } from "path";
-import { normalizePath, getFileInfo, shouldIgnoreFile, isDirectory, isFile, isSupportedFileType } from "./utils.js";
+import { getFileInfo, normalizePath, shouldIgnoreFile, isDirectory, isFile, isSupportedFileType } from "./utils.js";
 import { loadGitignoreRules } from "./gitignore.js";
 import { generateEmbedding } from "./embedding.js";
 import { initializeStorage } from "./storage.js";
+import { log } from "./logger.js";
 class IndexingError extends Error {
   constructor(message, cause) {
     super(message);
@@ -170,7 +171,14 @@ async function indexDirectories(paths, config) {
             }
             await qdrant.deletePointsByFilePath(file.path);
           }
-          const content = await promises.readFile(file.path, "utf-8");
+          const rawContent = await promises.readFile(file.path, "utf-8");
+          if (rawContent.includes("�")) {
+            log("warning", "Skipping non-UTF-8 file", { path: file.path });
+            await sqlite.upsertFile(file, [], ["Skipped: file appears to be non-UTF-8 encoded"]);
+            skipped++;
+            continue;
+          }
+          const content = rawContent.replace(/\r\n/g, "\n");
           const chunks = chunkText(content, config.indexing.chunkSize, config.indexing.chunkOverlap);
           await sqlite.upsertFile(file, chunks);
           for (let i = 0; i < chunks.length; i++) {

package/dist/indexing.js.map

@@ -1 +1 @@
-{"version":3,"file":"indexing.js","sources":["../src/indexing.ts"],"sourcesContent":["import { promises as fs } from 'fs';\nimport { join } from 'path';\nimport { Config } from './config.js';\nimport {\n  FileInfo,\n  ChunkInfo,\n  normalizePath,\n  getFileInfo,\n  shouldIgnoreFile,\n  isSupportedFileType,\n  isDirectory,\n  isFile\n} from './utils.js';\nimport { loadGitignoreRules } from './gitignore.js';\nimport { generateEmbedding } from './embedding.js';\nimport { initializeStorage, FileRecord } from './storage.js';\n\nexport interface ScanOptions {\n  ignorePatterns: string[];\n  maxFileSize: number;\n  respectGitignore: boolean;\n}\n\nexport interface IndexResult {\n  indexed: number;\n  skipped: number;\n  failed: number;\n  deleted: number;\n  errors: string[];\n}\n\nexport class IndexingError extends Error {\n  constructor(message: string, public override cause?: Error) {\n    super(message);\n    this.name = 'IndexingError';\n  }\n}\n\nexport function chunkText(content: string, chunkSize: number, overlap: number): ChunkInfo[] {\n  if (content.length <= chunkSize) {\n    return [{\n      id: '0',\n      content,\n      startIndex: 0,\n      endIndex: content.length\n    }];\n  }\n\n  const chunks: ChunkInfo[] = [];\n  let startIndex = 0;\n  let chunkId = 0;\n\n  while (startIndex < content.length) {\n    const endIndex = Math.min(startIndex + chunkSize, content.length);\n    const chunkContent = content.slice(startIndex, endIndex);\n\n    chunks.push({\n      id: chunkId.toString(),\n      content: chunkContent,\n      startIndex,\n      endIndex\n    });\n\n    chunkId++;\n    const nextStart = endIndex - overlap;\n\n    if (nextStart <= startIndex) {\n      startIndex = startIndex + Math.max(1, chunkSize - overlap);\n    } else {\n      startIndex = nextStart;\n    }\n\n    if (startIndex >= content.length) break;\n  }\n\n  return chunks;\n}\n\nexport async function scanDirectory(dirPath: string, options: ScanOptions): Promise<FileInfo[]> {\n  const files: FileInfo[] = [];\n  const visited = new Set<string>();\n  const basePath = normalizePath(dirPath);\n  \n  // Load gitignore rules for the root directory if enabled\n  const gitignoreFilter = options.respectGitignore ? 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package/dist/logger.js

@@ -0,0 +1,43 @@
+const LEVEL_ORDER = {
+  debug: 0,
+  info: 1,
+  warning: 2,
+  error: 3
+};
+let currentLevel = "info";
+function setLogLevel(level) {
+  currentLevel = level;
+}
+function getLogLevel() {
+  return currentLevel;
+}
+function initLogLevel() {
+  const envLevel = process.env.LOG_LEVEL?.toLowerCase();
+  if (!envLevel) return;
+  if (envLevel in LEVEL_ORDER) {
+    currentLevel = envLevel;
+  } else {
+    process.stderr.write(
+      `Warning: invalid LOG_LEVEL "${process.env.LOG_LEVEL}", defaulting to "info"
+`
+    );
+    currentLevel = "info";
+  }
+}
+function log(level, message, data) {
+  if (LEVEL_ORDER[level] < LEVEL_ORDER[currentLevel]) return;
+  const entry = {
+    timestamp: (/* @__PURE__ */ new Date()).toISOString(),
+    level,
+    message,
+    ...data
+  };
+  process.stderr.write(JSON.stringify(entry) + "\n");
+}
+export {
+  getLogLevel,
+  initLogLevel,
+  log,
+  setLogLevel
+};
+//# sourceMappingURL=logger.js.map

package/dist/logger.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"logger.js","sources":["../src/logger.ts"],"sourcesContent":["export type LogLevel = 'debug' | 'info' | 'warning' | 'error';\n\nconst LEVEL_ORDER: Record<LogLevel, number> = {\n  debug: 0,\n  info: 1,\n  warning: 2,\n  error: 3,\n};\n\nlet currentLevel: LogLevel = 'info';\n\n/**\n * Set the minimum log level. Messages below this level are discarded.\n */\nexport function setLogLevel(level: LogLevel): void {\n  currentLevel = level;\n}\n\n/**\n * Get the current log level.\n */\nexport function getLogLevel(): LogLevel {\n  return currentLevel;\n}\n\n/**\n * Initialize the log level from the LOG_LEVEL environment variable.\n * Invalid values default to 'info' with a warning on stderr.\n */\nexport function initLogLevel(): void {\n  const envLevel = process.env.LOG_LEVEL?.toLowerCase();\n  if (!envLevel) return;\n\n  if (envLevel in LEVEL_ORDER) {\n    currentLevel = envLevel as LogLevel;\n  } else {\n    process.stderr.write(\n      `Warning: invalid LOG_LEVEL \"${process.env.LOG_LEVEL}\", defaulting to \"info\"\\n`\n    );\n    currentLevel = 'info';\n  }\n}\n\n/**\n * Write a structured JSON log line to stderr.\n * Never writes to stdout (reserved for the MCP protocol channel).\n */\nexport function log(level: LogLevel, message: string, data?: Record<string, unknown>): void {\n  if (LEVEL_ORDER[level] < LEVEL_ORDER[currentLevel]) return;\n\n  const entry: Record<string, unknown> = {\n    timestamp: new Date().toISOString(),\n    level,\n    message,\n    ...data,\n  };\n\n  process.stderr.write(JSON.stringify(entry) + '\\n');\n}\n"],"names":[],"mappings":"AAEA,MAAM,cAAwC;AAAA,EAC5C,OAAO;AAAA,EACP,MAAM;AAAA,EACN,SAAS;AAAA,EACT,OAAO;AACT;AAEA,IAAI,eAAyB;AAKtB,SAAS,YAAY,OAAuB;AACjD,iBAAe;AACjB;AAKO,SAAS,cAAwB;AACtC,SAAO;AACT;AAMO,SAAS,eAAqB;AACnC,QAAM,WAAW,QAAQ,IAAI,WAAW,YAAA;AACxC,MAAI,CAAC,SAAU;AAEf,MAAI,YAAY,aAAa;AAC3B,mBAAe;AAAA,EACjB,OAAO;AACL,YAAQ,OAAO;AAAA,MACb,+BAA+B,QAAQ,IAAI,SAAS;AAAA;AAAA,IAAA;AAEtD,mBAAe;AAAA,EACjB;AACF;AAMO,SAAS,IAAI,OAAiB,SAAiB,MAAsC;AAC1F,MAAI,YAAY,KAAK,IAAI,YAAY,YAAY,EAAG;AAEpD,QAAM,QAAiC;AAAA,IACrC,YAAW,oBAAI,KAAA,GAAO,YAAA;AAAA,IACtB;AAAA,IACA;AAAA,IACA,GAAG;AAAA,EAAA;AAGL,UAAQ,OAAO,MAAM,KAAK,UAAU,KAAK,IAAI,IAAI;AACnD;"}

package/dist/mcp-handlers.js

@@ -1,9 +1,46 @@
 import { indexDirectories } from "./indexing.js";
-import { searchContent, findSimilarFiles, getFileContent, getChunkContent } from "./search.js";
-import { getIndexStatus } from "./storage.js";
+import { getChunkContent, getFileContent, searchContent, findSimilarFiles } from "./search.js";
+import { initializeStorage, getIndexStatus, SQLiteStorage } from "./storage.js";
 import { validateIndexPrerequisites, validateSearchPrerequisites } from "./prerequisites.js";
+import { validatePathWithinIndexedDirs, resolveIndexedDirectories } from "./path-validation.js";
+import { log } from "./logger.js";
+import { resolve, sep } from "path";
+import { realpathSync } from "fs";
+let mcpServer = null;
+function setMcpServer(server) {
+  mcpServer = server;
+}
+function normalizeMutexKey(dirPath) {
+  let normalized;
+  try {
+    normalized = realpathSync(resolve(dirPath));
+  } catch {
+    normalized = resolve(dirPath);
+  }
+  while (normalized.length > 1 && normalized.endsWith(sep)) {
+    normalized = normalized.slice(0, -sep.length);
+  }
+  return normalized;
+}
+const indexingMutex = /* @__PURE__ */ new Map();
+let indexedDirsCache = /* @__PURE__ */ new Set();
+let indexedDirsCacheInitialized = false;
+function refreshIndexedDirsCache(storage) {
+  indexedDirsCache = resolveIndexedDirectories(storage);
+  indexedDirsCacheInitialized = true;
+}
+async function ensureIndexedDirsCache(config) {
+  if (!indexedDirsCacheInitialized) {
+    const sqlite = new SQLiteStorage(config);
+    try {
+      refreshIndexedDirsCache(sqlite);
+    } finally {
+      sqlite.close();
+    }
+  }
+}
 function isIndexToolArgs(args) {
-  return typeof args === "object" && args !== null && typeof args.directory_path === "string";
+  return typeof args === "object" && args !== null && Array.isArray(args.directory_paths);
 }
 function isSearchToolArgs(args) {
   return typeof args === "object" && args !== null && typeof args.query === "string";
@@ -17,32 +54,74 @@ function isGetContentToolArgs(args) {
 function isGetChunkToolArgs(args) {
   return typeof args === "object" && args !== null && typeof args.file_path === "string" && typeof args.chunk_id === "string";
 }
+function isDeleteIndexToolArgs(args) {
+  return typeof args === "object" && args !== null && typeof args.directory_path === "string";
+}
 async function handleIndexTool(args, config) {
   if (!isIndexToolArgs(args)) {
-    throw new Error("directory_path is required");
+    throw new Error("directory_paths is required and must be an array");
   }
   await validateIndexPrerequisites(config);
-  const paths = args.directory_path.split(",").map((p) => p.trim());
-  const result = await indexDirectories(paths, config);
-  let responseText = `Indexed ${result.indexed} files, skipped ${result.skipped} files, cleaned up ${result.deleted} deleted files, ${result.failed} failed`;
-  if (result.errors.length > 0) {
-    responseText += `
+  const paths = args.directory_paths.map((p) => p.trim());
+  const mutexKeys = paths.map(normalizeMutexKey);
+  log("info", "Index start", { directories: paths });
+  mcpServer?.sendLoggingMessage({ level: "info", data: { event: "index_start", directories: paths } });
+  for (const key of mutexKeys) {
+    const existing = indexingMutex.get(key);
+    if (existing) {
+      log("info", "Waiting for ongoing indexing", { directory: key });
+      await existing;
+    }
+  }
+  let resolveIndexing;
+  const indexingPromise = new Promise((resolve2) => {
+    resolveIndexing = resolve2;
+  });
+  for (const key of mutexKeys) {
+    indexingMutex.set(key, indexingPromise);
+  }
+  try {
+    const result = await indexDirectories(paths, config);
+    const { sqlite } = await initializeStorage(config);
+    try {
+      refreshIndexedDirsCache(sqlite);
+    } finally {
+      sqlite.close();
+    }
+    log("info", "Index complete", { result });
+    mcpServer?.sendLoggingMessage({ level: "info", data: { event: "index_complete", result } });
+    let responseText = `Indexed ${result.indexed} files, skipped ${result.skipped} files, cleaned up ${result.deleted} deleted files, ${result.failed} failed`;
+    if (result.errors.length > 0) {
+      responseText += `
 Errors: [
 `;
-    result.errors.forEach((error) => {
-      responseText += `  '${error}'
+      result.errors.forEach((error) => {
+        responseText += `  '${error}'
 `;
-    });
-    responseText += `]`;
+      });
+      responseText += `]`;
+    }
+    return {
+      content: [
+        {
+          type: "text",
+          text: responseText
+        }
+      ]
+    };
+  } catch (error) {
+    const errorMessage = error instanceof Error ? error.message : String(error);
+    log("error", "Index error", { error: errorMessage, directories: paths });
+    mcpServer?.sendLoggingMessage({ level: "error", data: { event: "index_error", error: errorMessage } });
+    throw new Error(
+      `Indexing failed for ${paths.join(", ")}. Verify the directory exists and is readable. Use 'server_info' to check current status.`
+    );
+  } finally {
+    resolveIndexing();
+    for (const key of mutexKeys) {
+      indexingMutex.delete(key);
+    }
   }
-  return {
-    content: [
-      {
-        type: "text",
-        text: responseText
-      }
-    ]
-  };
 }
 async function validateWorkspace(workspace) {
   if (!workspace) return { workspace };
@@ -85,33 +164,59 @@ ${JSON.stringify(results, null, 2)}` : JSON.stringify(results, null, 2);
     content: [{ type: "text", text: response }]
   };
 }
-async function handleGetContentTool(args) {
+async function handleGetContentTool(args, config) {
   if (!isGetContentToolArgs(args)) {
     throw new Error("file_path is required");
   }
-  const content = await getFileContent(args.file_path, args.chunks);
-  return {
-    content: [
-      {
-        type: "text",
-        text: content
-      }
-    ]
-  };
+  const resolvedConfig = config || (await import("./config.js")).loadConfig();
+  await ensureIndexedDirsCache(resolvedConfig);
+  validatePathWithinIndexedDirs(args.file_path, indexedDirsCache);
+  try {
+    const content = await getFileContent(args.file_path, args.chunks);
+    return {
+      content: [
+        {
+          type: "text",
+          text: content
+        }
+      ]
+    };
+  } catch (error) {
+    const msg = error instanceof Error ? error.message : String(error);
+    if (msg.includes("ENOENT") || msg.toLowerCase().includes("not found") || msg.toLowerCase().includes("no such file")) {
+      throw new Error(
+        `File not found: ${args.file_path}. The file may have been moved or deleted. Use 'search' to find similar content.`
+      );
+    }
+    throw error;
+  }
 }
-async function handleGetChunkTool(args) {
+async function handleGetChunkTool(args, config) {
   if (!isGetChunkToolArgs(args)) {
     throw new Error("file_path and chunk_id are required");
   }
-  const content = await getChunkContent(args.file_path, args.chunk_id);
-  return {
-    content: [
-      {
-        type: "text",
-        text: content
-      }
-    ]
-  };
+  const resolvedConfig = config || (await import("./config.js")).loadConfig();
+  await ensureIndexedDirsCache(resolvedConfig);
+  validatePathWithinIndexedDirs(args.file_path, indexedDirsCache);
+  try {
+    const content = await getChunkContent(args.file_path, args.chunk_id);
+    return {
+      content: [
+        {
+          type: "text",
+          text: content
+        }
+      ]
+    };
+  } catch (error) {
+    const msg = error instanceof Error ? error.message : String(error);
+    if (msg.includes("ENOENT") || msg.toLowerCase().includes("not found") || msg.toLowerCase().includes("no such file")) {
+      throw new Error(
+        `File not found: ${args.file_path}. The file may have been moved or deleted. Use 'search' to find similar content.`
+      );
+    }
+    throw error;
+  }
 }
 async function handleServerInfoTool(version) {
   const status = await getIndexStatus();
@@ -128,8 +233,73 @@ async function handleServerInfoTool(version) {
     ]
   };
 }
+async function handleDeleteIndexTool(args, config) {
+  if (!isDeleteIndexToolArgs(args)) {
+    throw new Error("directory_path is required");
+  }
+  const dirPath = args.directory_path.trim();
+  const mutexKey = normalizeMutexKey(dirPath);
+  const existing = indexingMutex.get(mutexKey);
+  if (existing) {
+    log("info", "Waiting for ongoing indexing before delete", { directory: dirPath });
+    await existing;
+  }
+  let resolveDelete;
+  const deletePromise = new Promise((r) => {
+    resolveDelete = r;
+  });
+  indexingMutex.set(mutexKey, deletePromise);
+  const { sqlite, qdrant } = await initializeStorage(config);
+  try {
+    const directory = await sqlite.getDirectory(dirPath);
+    if (!directory) {
+      throw new Error(
+        `Directory '${dirPath}' is not indexed. Use 'server_info' to see indexed directories.`
+      );
+    }
+    const files = await sqlite.getFilesByDirectory(dirPath);
+    const vectorErrors = [];
+    for (const file of files) {
+      try {
+        await qdrant.deletePointsByFilePath(file.path);
+      } catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        log("warning", "Failed to delete Qdrant points for file", {
+          path: file.path,
+          error: msg
+        });
+        vectorErrors.push(`${file.path}: ${msg}`);
+      }
+    }
+    if (vectorErrors.length > 0) {
+      throw new Error(
+        `Aborting delete: failed to remove vector embeddings for ${vectorErrors.length} file(s). SQLite rows were NOT deleted to avoid orphaned vectors.
+` + vectorErrors.join("\n")
+      );
+    }
+    const deletedFiles = sqlite.deleteFilesByDirectory(dirPath);
+    sqlite.deleteDirectory(dirPath);
+    refreshIndexedDirsCache(sqlite);
+    const chunksCount = files.reduce((sum, f) => sum + (f.chunks?.length || 0), 0);
+    log("info", "Index deleted", { directory: dirPath, files: deletedFiles, chunks: chunksCount });
+    mcpServer?.sendLoggingMessage({ level: "info", data: { event: "index_deleted", directory: dirPath } });
+    return {
+      content: [
+        {
+          type: "text",
+          text: `Deleted index for ${dirPath}: removed ${deletedFiles} files and ${chunksCount} chunks`
+        }
+      ]
+    };
+  } finally {
+    resolveDelete();
+    indexingMutex.delete(mutexKey);
+    sqlite.close();
+  }
+}
 function formatErrorResponse(error) {
   const errorMessage = error instanceof Error ? error.message : "Unknown error";
+  log("error", "Tool error", { error: errorMessage });
   return {
     content: [
       {
@@ -142,11 +312,14 @@ function formatErrorResponse(error) {
 }
 export {
   formatErrorResponse,
+  handleDeleteIndexTool,
   handleGetChunkTool,
   handleGetContentTool,
   handleIndexTool,
   handleSearchTool,
   handleServerInfoTool,
-  handleSimilarFilesTool
+  handleSimilarFilesTool,
+  refreshIndexedDirsCache,
+  setMcpServer
 };
 //# sourceMappingURL=mcp-handlers.js.map