directory-indexer 0.2.2 → 0.3.0

package/dist/storage.js

@@ -1,6 +1,25 @@
 import Database from "better-sqlite3";
 import { ensureDirectory } from "./utils.js";
 import { dirname } from "path";
+function escapeLike(value) {
+  return value.replace(/\\/g, "\\\\").replace(/%/g, "\\%").replace(/_/g, "\\_");
+}
+function directoryLikeClause(column, dirPath) {
+  const escaped = escapeLike(dirPath);
+  return {
+    clause: `(${column} = ? OR ${column} LIKE ? ESCAPE '\\' OR ${column} LIKE ? ESCAPE '\\')`,
+    params: [dirPath, `${escaped}/%`, `${escaped}\\%`]
+  };
+}
+const openStorageInstances = /* @__PURE__ */ new Set();
+function closeAllStorage() {
+  for (const instance of openStorageInstances) {
+    try {
+      instance.close();
+    } catch {
+    }
+  }
+}
 class StorageError extends Error {
   constructor(message, cause) {
     super(message);
@@ -221,6 +240,7 @@ class SQLiteStorage {
   constructor(config) {
     this.config = config;
     this.db = this.initializeDatabase();
+    openStorageInstances.add(this);
   }
   db;
   initializeDatabase() {
@@ -250,6 +270,8 @@ class SQLiteStorage {
         CREATE INDEX IF NOT EXISTS idx_files_hash ON files(hash);
         CREATE INDEX IF NOT EXISTS idx_directories_path ON directories(path);
       `);
+      db.pragma("journal_mode = WAL");
+      db.pragma("busy_timeout = 5000");
       return db;
     } catch (error) {
       throw new StorageError(`Failed to initialize SQLite database`, error);
@@ -327,10 +349,15 @@ class SQLiteStorage {
       throw new StorageError(`Failed to delete file record`, error);
     }
   }
+  getDirectories() {
+    const rows = this.db.prepare("SELECT path FROM directories").all();
+    return rows.map((row) => row.path);
+  }
   async getFilesByDirectory(directoryPath) {
     try {
-      const stmt = this.db.prepare("SELECT * FROM files WHERE path LIKE ?");
-      const rows = stmt.all(`${directoryPath}%`);
+      const { clause, params } = directoryLikeClause("path", directoryPath);
+      const stmt = this.db.prepare(`SELECT * FROM files WHERE ${clause}`);
+      const rows = stmt.all(...params);
       return rows.map((row) => ({
         id: row.id,
         path: row.path,
@@ -345,7 +372,16 @@ class SQLiteStorage {
       throw new StorageError(`Failed to get files by directory`, error);
     }
   }
+  deleteDirectory(path) {
+    this.db.prepare("DELETE FROM directories WHERE path = ?").run(path);
+  }
+  deleteFilesByDirectory(directoryPath) {
+    const { clause, params } = directoryLikeClause("path", directoryPath);
+    const result = this.db.prepare(`DELETE FROM files WHERE ${clause}`).run(...params);
+    return result.changes;
+  }
   close() {
+    openStorageInstances.delete(this);
     this.db.close();
   }
 }
@@ -603,22 +639,23 @@ async function getIndexStatus() {
       }
     });
     const directoriesDetailStmt = sqlite.db.prepare(`
-      SELECT 
+      SELECT
         d.path,
         d.status,
         d.indexed_at,
-        (SELECT COUNT(*) FROM files f WHERE f.path LIKE d.path || '%') as files_count,
-        (SELECT COALESCE(SUM(json_array_length(f.chunks_json)), 0) FROM files f WHERE f.path LIKE d.path || '%' AND f.chunks_json IS NOT NULL) as chunks_count
+        (SELECT COUNT(*) FROM files f WHERE f.path = d.path OR f.path LIKE REPLACE(d.path, '\\', '\\\\') || '/%' ESCAPE '\\' OR f.path LIKE REPLACE(d.path, '\\', '\\\\') || '\\%' ESCAPE '\\') as files_count,
+        (SELECT COALESCE(SUM(json_array_length(f.chunks_json)), 0) FROM files f WHERE (f.path = d.path OR f.path LIKE REPLACE(d.path, '\\', '\\\\') || '/%' ESCAPE '\\' OR f.path LIKE REPLACE(d.path, '\\', '\\\\') || '\\%' ESCAPE '\\') AND f.chunks_json IS NOT NULL) as chunks_count
       FROM directories d
       ORDER BY d.indexed_at DESC
     `);
     const directoryDetails = directoriesDetailStmt.all();
     const directories = directoryDetails.map((row) => {
+      const { clause, params } = directoryLikeClause("path", row.path);
       const errorsByDirStmt = sqlite.db.prepare(`
-        SELECT errors_json FROM files 
-        WHERE path LIKE ? || '%' AND errors_json IS NOT NULL
+        SELECT errors_json FROM files
+        WHERE ${clause} AND errors_json IS NOT NULL
       `);
-      const dirErrors = errorsByDirStmt.all(row.path);
+      const dirErrors = errorsByDirStmt.all(...params);
       const dirErrorsList = [];
       dirErrors.forEach((errorRow) => {
         try {
@@ -677,6 +714,7 @@ export {
   StorageError,
   clearDatabase,
   clearVectorCollection,
+  closeAllStorage,
   getIndexStatus,
   getResetPreview,
   initDatabase,

package/dist/storage.js.map

@@ -1 +1 @@
-{"version":3,"file":"storage.js","sources":["../src/storage.ts"],"sourcesContent":["import Database from 'better-sqlite3';\nimport { Config } from './config.js';\nimport { FileInfo, ChunkInfo, ensureDirectory } from './utils.js';\nimport { dirname } from 'path';\n\nexport interface DirectoryRecord {\n  id: number;\n  path: string;\n  status: 'pending' | 'indexing' | 'completed' | 'failed';\n  indexedAt: Date;\n}\n\nexport interface FileRecord {\n  id: number;\n  path: string;\n  size: number;\n  modifiedTime: Date;\n  hash: string;\n  parentDirs: string[];\n  chunks: ChunkInfo[];\n  errors?: string[];\n}\n\nexport interface QdrantPoint {\n  id: string | number;\n  vector: number[];\n  payload: {\n    filePath: string;\n    chunkId: string;\n    fileHash: string;\n    content: string;\n    parentDirectories: string[];\n  };\n  score?: number;\n}\n\nexport class StorageError extends Error {\n  constructor(message: string, public override cause?: Error) {\n    super(message);\n    this.name = 'StorageError';\n  }\n}\n\nexport class QdrantClient {\n  constructor(private config: Config) {}\n\n  async healthCheck(): Promise<boolean> {\n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/healthz`);\n      return response.ok;\n    } catch {\n      return false;\n    }\n  }\n\n  async createCollection(): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const checkResponse = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}`);\n      if (checkResponse.ok) {\n        return;\n      }\n\n      const createResponse = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}`, {\n        method: 'PUT',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify({\n          vectors: {\n            size: 768,\n            distance: 'Cosine'\n          }\n        })\n      });\n\n      if (!createResponse.ok) {\n        throw new Error(`Failed to create collection: ${createResponse.statusText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to create Qdrant collection`, error as Error);\n    }\n  }\n\n  async upsertPoints(points: QdrantPoint[]): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points`, {\n        method: 'PUT',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify({ points })\n      });\n\n      if (!response.ok) {\n        const errorText = await response.text();\n        throw new Error(`Failed to upsert points: ${response.status} ${response.statusText} - ${errorText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to upsert points to Qdrant`, error as Error);\n    }\n  }\n\n  async searchPoints(vector: number[], limit: number = 10, filter?: Record<string, unknown>): Promise<QdrantPoint[]> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const searchBody: Record<string, unknown> = {\n        vector,\n        limit,\n        with_payload: true\n      };\n      \n      if (filter) {\n        searchBody.filter = filter;\n      }\n      \n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points/search`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify(searchBody)\n      });\n\n      if (!response.ok) {\n        const errorBody = await response.text();\n        throw new Error(`Failed to search points: ${response.statusText} - ${errorBody}`);\n      }\n\n      const data = await response.json();\n      return data.result.map((item: { id: string | number; vector: number[]; payload: Record<string, unknown>; score: number }) => ({\n        id: item.id,\n        vector: item.vector,\n        payload: item.payload,\n        score: item.score\n      }));\n    } catch (error) {\n      throw new StorageError(`Failed to search points in Qdrant`, error as Error);\n    }\n  }\n\n  async deletePoints(ids: (string | number)[]): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points/delete`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify({ points: ids })\n      });\n\n      if (!response.ok) {\n        throw new Error(`Failed to delete points: ${response.statusText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to delete points from Qdrant`, error as Error);\n    }\n  }\n\n  async deletePointsByFilePath(filePath: string): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points/delete`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify({\n          filter: {\n            must: [\n              {\n                key: 'filePath',\n                match: { value: filePath }\n              }\n            ]\n          }\n        })\n      });\n\n      if (!response.ok) {\n        const errorText = await response.text();\n        throw new Error(`Failed to delete points by file path: ${response.status} ${response.statusText} - ${errorText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to delete points by file path from Qdrant`, error as Error);\n    }\n  }\n\n  async countPoints(filter?: Record<string, unknown>): Promise<number> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const countBody: Record<string, unknown> = { exact: true };\n      if (filter) {\n        countBody.filter = filter;\n      }\n\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points/count`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify(countBody)\n      });\n\n      if (!response.ok) {\n        throw new Error(`Failed to count points: ${response.statusText}`);\n      }\n\n      const data = await response.json();\n      return data.result.count;\n    } catch (error) {\n      throw new StorageError(`Failed to count points in Qdrant`, error as Error);\n    }\n  }\n\n  async scrollPoints(filter?: Record<string, unknown>, limit: number = 1000): Promise<QdrantPoint[]> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const scrollBody: Record<string, unknown> = {\n        limit,\n        with_payload: true,\n        with_vector: false\n      };\n      if (filter) {\n        scrollBody.filter = filter;\n      }\n\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points/scroll`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify(scrollBody)\n      });\n\n      if (!response.ok) {\n        throw new Error(`Failed to scroll points: ${response.statusText}`);\n      }\n\n      const data = await response.json();\n      return data.result.points.map((item: { id: string | number; payload: Record<string, unknown> }) => ({\n        id: item.id,\n        vector: [],\n        payload: item.payload,\n        score: 0\n      }));\n    } catch (error) {\n      throw new StorageError(`Failed to scroll points in Qdrant`, error as Error);\n    }\n  }\n\n  async getCollectionInfo(): Promise<{ vectors_count?: number } | null> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}`);\n      \n      if (!response.ok) {\n        if (response.status === 404) {\n          return null;\n        }\n        throw new Error(`Failed to get collection info: ${response.statusText}`);\n      }\n\n      const data = await response.json();\n      return {\n        vectors_count: data.result?.points_count || data.result?.vectors_count || 0\n      };\n    } catch (error) {\n      throw new StorageError(`Failed to get collection info from Qdrant`, error as Error);\n    }\n  }\n\n  async deleteCollection(): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}`, {\n        method: 'DELETE',\n        headers: this.config.storage.qdrantApiKey ? {\n          'api-key': this.config.storage.qdrantApiKey\n        } : {}\n      });\n\n      if (!response.ok && response.status !== 404) {\n        throw new Error(`Failed to delete collection: ${response.statusText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to delete collection from Qdrant`, error as Error);\n    }\n  }\n}\n\nexport class SQLiteStorage {\n  public db: Database.Database;\n\n  constructor(private config: Config) {\n    this.db = this.initializeDatabase();\n  }\n\n  private initializeDatabase(): Database.Database {\n    try {\n      ensureDirectory(dirname(this.config.storage.sqlitePath));\n      \n      const db = new Database(this.config.storage.sqlitePath);\n      \n      db.exec(`\n        CREATE TABLE IF NOT EXISTS directories (\n          id INTEGER PRIMARY KEY,\n          path TEXT UNIQUE NOT NULL,\n          status TEXT DEFAULT 'pending',\n          indexed_at INTEGER DEFAULT 0\n        );\n\n        CREATE TABLE IF NOT EXISTS files (\n          id INTEGER PRIMARY KEY,\n          path TEXT UNIQUE NOT NULL,\n          size INTEGER NOT NULL,\n          modified_time INTEGER NOT NULL,\n          hash TEXT NOT NULL,\n          parent_dirs TEXT NOT NULL,\n          chunks_json TEXT,\n          errors_json TEXT\n        );\n\n        CREATE INDEX IF NOT EXISTS idx_files_path ON files(path);\n        CREATE INDEX IF NOT EXISTS idx_files_hash ON files(hash);\n        CREATE INDEX IF NOT EXISTS idx_directories_path ON directories(path);\n      `);\n\n      return db;\n    } catch (error) {\n      throw new StorageError(`Failed to initialize SQLite database`, error as Error);\n    }\n  }\n\n  async getDirectory(path: string): Promise<DirectoryRecord | null> {\n    try {\n      const stmt = this.db.prepare('SELECT * FROM directories WHERE path = ?');\n      const row = stmt.get(path) as { id: number; path: string; status: 'pending' | 'indexing' | 'completed' | 'failed'; indexed_at: number } | undefined;\n      \n      if (!row) return null;\n      \n      return {\n        id: row.id,\n        path: row.path,\n        status: row.status,\n        indexedAt: new Date(row.indexed_at)\n      };\n    } catch (error) {\n      throw new StorageError(`Failed to get directory record`, error as Error);\n    }\n  }\n\n  async upsertDirectory(path: string, status: DirectoryRecord['status']): Promise<void> {\n    try {\n      const stmt = this.db.prepare(`\n        INSERT OR REPLACE INTO directories (path, status, indexed_at)\n        VALUES (?, ?, ?)\n      `);\n      \n      stmt.run(path, status, Date.now());\n    } catch (error) {\n      throw new StorageError(`Failed to upsert directory record`, error as Error);\n    }\n  }\n\n  async getFile(path: string): Promise<FileRecord | null> {\n    try {\n      const stmt = this.db.prepare('SELECT * FROM files WHERE path = ?');\n      const row = stmt.get(path) as { id: number; path: string; size: number; modified_time: number; hash: string; parent_dirs: string; chunks_json: string | null; errors_json: string | null } | undefined;\n      \n      if (!row) return null;\n      \n      return {\n        id: row.id,\n        path: row.path,\n        size: row.size,\n        modifiedTime: new Date(row.modified_time * 1000),\n        hash: row.hash,\n        parentDirs: JSON.parse(row.parent_dirs),\n        chunks: row.chunks_json ? JSON.parse(row.chunks_json) : [],\n        errors: row.errors_json ? JSON.parse(row.errors_json) : undefined\n      };\n    } catch (error) {\n      throw new StorageError(`Failed to get file record`, error as Error);\n    }\n  }\n\n  async upsertFile(fileInfo: FileInfo, chunks: ChunkInfo[] = [], errors: string[] = []): Promise<void> {\n    try {\n      const stmt = this.db.prepare(`\n        INSERT OR REPLACE INTO files (path, size, modified_time, hash, parent_dirs, chunks_json, errors_json)\n        VALUES (?, ?, ?, ?, ?, ?, ?)\n      `);\n      \n      stmt.run(\n        fileInfo.path,\n        fileInfo.size,\n        fileInfo.modifiedTime.getTime(),\n        fileInfo.hash,\n        JSON.stringify(fileInfo.parentDirs),\n        chunks.length > 0 ? JSON.stringify(chunks) : null,\n        errors.length > 0 ? JSON.stringify(errors) : null\n      );\n    } catch (error) {\n      throw new StorageError(`Failed to upsert file record`, error as Error);\n    }\n  }\n\n  async deleteFile(path: string): Promise<void> {\n    try {\n      const stmt = this.db.prepare('DELETE FROM files WHERE path = ?');\n      stmt.run(path);\n    } catch (error) {\n      throw new StorageError(`Failed to delete file record`, error as Error);\n    }\n  }\n\n  async getFilesByDirectory(directoryPath: string): Promise<FileRecord[]> {\n    try {\n      const stmt = this.db.prepare('SELECT * FROM files WHERE path LIKE ?');\n      const rows = stmt.all(`${directoryPath}%`) as { id: number; path: string; size: number; modified_time: number; hash: string; parent_dirs: string; chunks_json: string | null; errors_json: string | null }[];\n      \n      return rows.map(row => ({\n        id: row.id,\n        path: row.path,\n        size: row.size,\n        modifiedTime: new Date(row.modified_time * 1000),\n        hash: row.hash,\n        parentDirs: JSON.parse(row.parent_dirs),\n        chunks: row.chunks_json ? JSON.parse(row.chunks_json) : [],\n        errors: row.errors_json ? JSON.parse(row.errors_json) : undefined\n      }));\n    } catch (error) {\n      throw new StorageError(`Failed to get files by directory`, error as Error);\n    }\n  }\n\n  close(): void {\n    this.db.close();\n  }\n}\n\nexport async function initializeStorage(config: Config): Promise<{ sqlite: SQLiteStorage; qdrant: QdrantClient }> {\n  const sqlite = new SQLiteStorage(config);\n  const qdrant = new QdrantClient(config);\n  \n  await qdrant.createCollection();\n  \n  return { sqlite, qdrant };\n}\n\nexport async function initDatabase(dbPath: string): Promise<Database.Database> {\n  return new Database(dbPath);\n}\n\nexport interface ResetStats {\n  sqliteExists: boolean;\n  sqliteSize?: string;\n  qdrantCollectionExists: boolean;\n  qdrantVectorCount?: number;\n}\n\nexport interface ResetResult {\n  sqliteDeleted: boolean;\n  qdrantDeleted: boolean;\n  warnings: string[];\n}\n\nexport async function getResetPreview(config: Config): Promise<ResetStats> {\n  const stats: ResetStats = {\n    sqliteExists: false,\n    qdrantCollectionExists: false\n  };\n\n  if (await import('fs').then(fs => fs.existsSync(config.storage.sqlitePath))) {\n    stats.sqliteExists = true;\n    try {\n      const fileStats = await import('fs').then(fs => fs.statSync(config.storage.sqlitePath));\n      const sizeInMB = (fileStats.size / (1024 * 1024)).toFixed(1);\n      stats.sqliteSize = `${sizeInMB} MB`;\n    } catch {\n      stats.sqliteSize = 'unknown size';\n    }\n  }\n\n  try {\n    const qdrant = new QdrantClient(config);\n    const isHealthy = await qdrant.healthCheck();\n    \n    if (isHealthy) {\n      const collectionInfo = await qdrant.getCollectionInfo();\n      if (collectionInfo) {\n        stats.qdrantCollectionExists = true;\n        stats.qdrantVectorCount = collectionInfo.vectors_count || 0;\n      }\n    }\n  } catch {\n    // Qdrant unavailable\n  }\n\n  return stats;\n}\n\nexport async function clearDatabase(config: Config): Promise<boolean> {\n  try {\n    if (!await import('fs').then(fs => fs.existsSync(config.storage.sqlitePath))) {\n      return true; // Already clean\n    }\n    \n    await import('fs/promises').then(fs => fs.unlink(config.storage.sqlitePath));\n    return true;\n  } catch (error) {\n    throw new StorageError(`Failed to delete SQLite database: ${error instanceof Error ? error.message : 'Unknown error'}`, error as Error);\n  }\n}\n\nexport async function clearVectorCollection(config: Config): Promise<boolean> {\n  try {\n    const qdrant = new QdrantClient(config);\n    const isHealthy = await qdrant.healthCheck();\n    \n    if (!isHealthy) {\n      throw new StorageError(`Qdrant unavailable at ${config.storage.qdrantEndpoint}`);\n    }\n    \n    const collectionInfo = await qdrant.getCollectionInfo();\n    if (collectionInfo) {\n      await qdrant.deleteCollection();\n    }\n    \n    return true;\n  } catch (error) {\n    throw new StorageError(`Failed to reset Qdrant collection: ${error instanceof Error ? error.message : 'Unknown error'}`, error as Error);\n  }\n}\n\nexport interface DirectoryStatus {\n  path: string;\n  status: string;\n  filesCount: number;\n  chunksCount: number;\n  lastIndexed: string | null;\n  errors: string[];\n}\n\nexport interface WorkspaceStatus {\n  name: string;\n  paths: string[];\n  isValid: boolean;\n  filesCount: number;\n  chunksCount: number;\n  health: {\n    status: 'healthy' | 'warning' | 'error';\n    issues: string[];\n    recommendations: string[];\n  };\n}\n\nexport interface IndexStatus {\n  directoriesIndexed: number;\n  filesIndexed: number;\n  chunksIndexed: number;\n  databaseSize: string;\n  lastIndexed: string | null;\n  errors: string[];\n  directories: DirectoryStatus[];\n  workspaces: WorkspaceStatus[];\n  workspaceHealth: {\n    healthy: number;\n    warnings: number;\n    errors: number;\n    criticalIssues: string[];\n    recommendations: string[];\n  };\n  qdrantConsistency: {\n    isConsistent: boolean;\n    issues: string[];\n  };\n}\n\nasync function calculateWorkspaceStatistics(sqlite: SQLiteStorage, config: Config): Promise<WorkspaceStatus[]> {\n  const { getAvailableWorkspaces, getWorkspacePaths } = await import('./config.js');\n  const workspaces: WorkspaceStatus[] = [];\n  \n  // Get all indexed directories for comparison\n  const directoriesStmt = sqlite.db.prepare('SELECT path, status FROM directories');\n  const indexedDirectories = directoriesStmt.all() as { path: string; status: string }[];\n  const indexedDirectoryPaths = indexedDirectories.map(d => d.path);\n  \n  // Get Qdrant client for efficient workspace filtering\n  const qdrant = new QdrantClient(config);\n  \n  for (const workspaceName of getAvailableWorkspaces(config)) {\n    const workspacePaths = getWorkspacePaths(config, workspaceName);\n    const workspaceConfig = config.workspaces[workspaceName];\n    \n    let filesCount = 0;\n    let chunksCount = 0;\n    \n    if (workspacePaths.length > 0) {\n      try {\n        // Build workspace filter using same logic as search\n        const workspaceFilter = {\n          must: [\n            {\n              key: \"parentDirectories\",\n              match: { any: workspacePaths }\n            }\n          ]\n        };\n        \n        // Get chunk count efficiently using Qdrant\n        chunksCount = await qdrant.countPoints(workspaceFilter);\n        \n        // Get unique file paths using Qdrant scroll\n        const points = await qdrant.scrollPoints(workspaceFilter, 10000);\n        const uniqueFilePaths = new Set(points.map(p => p.payload.filePath));\n        filesCount = uniqueFilePaths.size;\n        \n      } catch {\n        // Fallback to 0 if Qdrant is unavailable\n        filesCount = 0;\n        chunksCount = 0;\n      }\n    }\n    \n    // Check workspace health\n    const health = analyzeWorkspaceHealth(workspacePaths, workspaceConfig.isValid, filesCount, indexedDirectoryPaths);\n    \n    workspaces.push({\n      name: workspaceName,\n      paths: workspacePaths,\n      isValid: workspaceConfig.isValid,\n      filesCount,\n      chunksCount,\n      health\n    });\n  }\n  \n  return workspaces;\n}\n\nfunction analyzeWorkspaceHealth(\n  workspacePaths: string[], \n  isValid: boolean, \n  filesCount: number, \n  indexedDirectoryPaths: string[]\n): { status: 'healthy' | 'warning' | 'error'; issues: string[]; recommendations: string[] } {\n  const issues: string[] = [];\n  const recommendations: string[] = [];\n  \n  // Check if workspace paths exist and are valid\n  if (!isValid) {\n    issues.push('One or more workspace directories do not exist on the filesystem');\n    recommendations.push('Verify workspace directory paths exist and are accessible');\n  }\n  \n  // Check if workspace paths are indexed\n  const unindexedPaths: string[] = [];\n  const partiallyIndexedPaths: string[] = [];\n  \n  for (const workspacePath of workspacePaths) {\n    // Check if this exact path is indexed\n    const exactMatch = indexedDirectoryPaths.includes(workspacePath);\n    \n    if (exactMatch) {\n      // Perfect match - workspace directory is directly indexed\n      continue;\n    }\n    \n    // Check if workspace path is covered by a parent directory that is indexed\n    const isChildOfIndexed = indexedDirectoryPaths.some(indexedPath => {\n      // Workspace path must start with indexed path and be a subdirectory\n      return workspacePath.startsWith(indexedPath + '/') || workspacePath.startsWith(indexedPath + '\\\\');\n    });\n    \n    if (isChildOfIndexed) {\n      partiallyIndexedPaths.push(workspacePath);\n    } else {\n      unindexedPaths.push(workspacePath);\n    }\n  }\n  \n  // Report unindexed paths\n  if (unindexedPaths.length > 0) {\n    issues.push(`Workspace directories not indexed: ${unindexedPaths.join(', ')}`);\n    recommendations.push(`Run indexing on these directories: ${unindexedPaths.join(', ')}`);\n  }\n  \n  // Report partially indexed paths (where parent directory is indexed)\n  if (partiallyIndexedPaths.length > 0) {\n    issues.push(`Workspace directories indexed as part of parent directory: ${partiallyIndexedPaths.join(', ')}`);\n    recommendations.push('Consider indexing workspace directories directly for better organization');\n  }\n  \n  // Check if workspace is empty (no files found)\n  if (isValid && filesCount === 0 && unindexedPaths.length === 0) {\n    issues.push('Workspace contains no indexed files');\n    recommendations.push('Verify the workspace directory contains files and re-index if necessary');\n  }\n  \n  // Determine overall health status\n  let status: 'healthy' | 'warning' | 'error';\n  if (!isValid || unindexedPaths.length > 0) {\n    status = 'error';\n  } else if (issues.length > 0) {\n    status = 'warning';\n  } else {\n    status = 'healthy';\n  }\n  \n  return { status, issues, recommendations };\n}\n\nfunction calculateWorkspaceHealthSummary(workspaces: WorkspaceStatus[]): {\n  healthy: number;\n  warnings: number; \n  errors: number;\n  criticalIssues: string[];\n  recommendations: string[];\n} {\n  let healthy = 0;\n  let warnings = 0;\n  let errors = 0;\n  const criticalIssues: string[] = [];\n  const recommendations: string[] = [];\n  \n  for (const workspace of workspaces) {\n    switch (workspace.health.status) {\n      case 'healthy':\n        healthy++;\n        break;\n      case 'warning':\n        warnings++;\n        break;\n      case 'error':\n        errors++;\n        criticalIssues.push(`${workspace.name}: ${workspace.health.issues.join(', ')}`);\n        break;\n    }\n    \n    // Collect unique recommendations\n    for (const rec of workspace.health.recommendations) {\n      if (!recommendations.includes(rec)) {\n        recommendations.push(rec);\n      }\n    }\n  }\n  \n  return {\n    healthy,\n    warnings,\n    errors,\n    criticalIssues,\n    recommendations\n  };\n}\n\nasync function checkQdrantConsistency(sqlite: SQLiteStorage, config: Config): Promise<{ isConsistent: boolean; issues: string[] }> {\n  const issues: string[] = [];\n  \n  try {\n    const qdrant = new QdrantClient(config);\n    const isHealthy = await qdrant.healthCheck();\n    \n    if (!isHealthy) {\n      issues.push('Qdrant vector database is not running or accessible');\n      return { isConsistent: false, issues };\n    }\n    \n    const filesWithChunksStmt = sqlite.db.prepare('SELECT COUNT(*) as count FROM files WHERE chunks_json IS NOT NULL');\n    const filesWithChunks = filesWithChunksStmt.get() as { count: number };\n    \n    const totalChunksStmt = sqlite.db.prepare('SELECT SUM(json_array_length(chunks_json)) as count FROM files WHERE chunks_json IS NOT NULL');\n    const totalChunks = totalChunksStmt.get() as { count: number | null };\n    \n    if (filesWithChunks.count > 0 && (totalChunks.count || 0) === 0) {\n      issues.push('Files exist but no chunks found - possible data corruption');\n    }\n    \n    const collectionName = config.storage.qdrantCollection;\n    try {\n      const response = await fetch(`${config.storage.qdrantEndpoint}/collections/${collectionName}`);\n      if (!response.ok) {\n        issues.push(`Vector collection '${collectionName}' not found (normal during first-time setup)`);\n        return { isConsistent: false, issues };\n      }\n      \n      const collectionInfo = await response.json();\n      const qdrantPointCount = collectionInfo.result?.points_count || 0;\n      const sqliteChunkCount = totalChunks.count || 0;\n      \n      if (Math.abs(qdrantPointCount - sqliteChunkCount) > 0) {\n        if (qdrantPointCount > sqliteChunkCount) {\n          issues.push(`Extra vectors in database: ${qdrantPointCount} vectors vs ${sqliteChunkCount} indexed chunks (normal during cleanup)`);\n        } else {\n          issues.push(`Missing vectors: ${sqliteChunkCount} indexed chunks vs ${qdrantPointCount} vectors (normal during indexing)`);\n        }\n      }\n    } catch (error) {\n      issues.push(`Cannot verify vector database status: ${error}`);\n    }\n    \n  } catch (error) {\n    issues.push(`Database status check failed: ${error}`);\n  }\n  \n  return {\n    isConsistent: issues.length === 0,\n    issues\n  };\n}\n\nexport async function getIndexStatus(): Promise<IndexStatus> {\n  const config = await import('./config.js').then(m => m.loadConfig());\n  const sqlite = new SQLiteStorage(config);\n  \n  try {\n    const directoriesStmt = sqlite.db.prepare('SELECT COUNT(*) as count FROM directories WHERE status = ?');\n    const directoriesCount = directoriesStmt.get('completed') as { count: number };\n    \n    const filesStmt = sqlite.db.prepare('SELECT COUNT(*) as count FROM files');\n    const filesCount = filesStmt.get() as { count: number };\n    \n    const chunksStmt = sqlite.db.prepare('SELECT SUM(json_array_length(chunks_json)) as count FROM files WHERE chunks_json IS NOT NULL');\n    const chunksCount = chunksStmt.get() as { count: number | null };\n    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+{"version":3,"file":"storage.js","sources":["../src/storage.ts"],"sourcesContent":["import Database from 'better-sqlite3';\nimport { Config } from './config.js';\nimport { FileInfo, ChunkInfo, ensureDirectory } from './utils.js';\nimport { dirname } from 'path';\n\n/**\n * Escape special characters in a string for use in a SQL LIKE pattern.\n * Escapes %, _, and \\ using \\ as the escape character.\n */\nfunction escapeLike(value: string): string {\n  return value.replace(/\\\\/g, '\\\\\\\\').replace(/%/g, '\\\\%').replace(/_/g, '\\\\_');\n}\n\n/**\n * Build a SQL WHERE clause that matches files within a directory,\n * handling both `/` and `\\` as path separators so queries work\n * regardless of how paths were stored.\n *\n * Returns [clause, ...params] where clause uses `?` placeholders.\n */\nfunction directoryLikeClause(column: string, dirPath: string): { clause: string; params: string[] } {\n  const escaped = escapeLike(dirPath);\n  return {\n    clause: `(${column} = ? OR ${column} LIKE ? ESCAPE '\\\\' OR ${column} LIKE ? ESCAPE '\\\\')`,\n    params: [dirPath, `${escaped}/%`, `${escaped}\\\\%`]\n  };\n}\n\n// Registry of all open SQLiteStorage instances for graceful shutdown\nconst openStorageInstances = new Set<SQLiteStorage>();\n\n/**\n * Close all open SQLiteStorage instances. Called during graceful shutdown.\n */\nexport function closeAllStorage(): void {\n  for (const instance of openStorageInstances) {\n    try {\n      instance.close();\n    } catch {\n      // Ignore errors during shutdown cleanup\n    }\n  }\n}\n\nexport interface DirectoryRecord {\n  id: number;\n  path: string;\n  status: 'pending' | 'indexing' | 'completed' | 'failed';\n  indexedAt: Date;\n}\n\nexport interface FileRecord {\n  id: number;\n  path: string;\n  size: number;\n  modifiedTime: Date;\n  hash: string;\n  parentDirs: string[];\n  chunks: ChunkInfo[];\n  errors?: string[];\n}\n\nexport interface QdrantPoint {\n  id: string | number;\n  vector: number[];\n  payload: {\n    filePath: string;\n    chunkId: string;\n    fileHash: string;\n    content: string;\n    parentDirectories: string[];\n  };\n  score?: number;\n}\n\nexport class StorageError extends Error {\n  constructor(message: string, public override cause?: Error) {\n    super(message);\n    this.name = 'StorageError';\n  }\n}\n\nexport class QdrantClient {\n  constructor(private config: Config) {}\n\n  async healthCheck(): Promise<boolean> {\n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/healthz`);\n      return response.ok;\n    } catch {\n      return false;\n    }\n  }\n\n  async createCollection(): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const checkResponse = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}`);\n      if (checkResponse.ok) {\n        return;\n      }\n\n      const createResponse = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}`, {\n        method: 'PUT',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify({\n          vectors: {\n            size: 768,\n            distance: 'Cosine'\n          }\n        })\n      });\n\n      if (!createResponse.ok) {\n        throw new Error(`Failed to create collection: ${createResponse.statusText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to create Qdrant collection`, error as Error);\n    }\n  }\n\n  async upsertPoints(points: QdrantPoint[]): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points`, {\n        method: 'PUT',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify({ points })\n      });\n\n      if (!response.ok) {\n        const errorText = await response.text();\n        throw new Error(`Failed to upsert points: ${response.status} ${response.statusText} - ${errorText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to upsert points to Qdrant`, error as Error);\n    }\n  }\n\n  async searchPoints(vector: number[], limit: number = 10, filter?: Record<string, unknown>): Promise<QdrantPoint[]> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const searchBody: Record<string, unknown> = {\n        vector,\n        limit,\n        with_payload: true\n      };\n      \n      if (filter) {\n        searchBody.filter = filter;\n      }\n      \n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points/search`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify(searchBody)\n      });\n\n      if (!response.ok) {\n        const errorBody = await response.text();\n        throw new Error(`Failed to search points: ${response.statusText} - ${errorBody}`);\n      }\n\n      const data = await response.json();\n      return data.result.map((item: { id: string | number; vector: number[]; payload: Record<string, unknown>; score: number }) => ({\n        id: item.id,\n        vector: item.vector,\n        payload: item.payload,\n        score: item.score\n      }));\n    } catch (error) {\n      throw new StorageError(`Failed to search points in Qdrant`, error as Error);\n    }\n  }\n\n  async deletePoints(ids: (string | number)[]): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points/delete`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify({ points: ids })\n      });\n\n      if (!response.ok) {\n        throw new Error(`Failed to delete points: ${response.statusText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to delete points from Qdrant`, error as Error);\n    }\n  }\n\n  async deletePointsByFilePath(filePath: string): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points/delete`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify({\n          filter: {\n            must: [\n              {\n                key: 'filePath',\n                match: { value: filePath }\n              }\n            ]\n          }\n        })\n      });\n\n      if (!response.ok) {\n        const errorText = await response.text();\n        throw new Error(`Failed to delete points by file path: ${response.status} ${response.statusText} - ${errorText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to delete points by file path from Qdrant`, error as Error);\n    }\n  }\n\n  async countPoints(filter?: Record<string, unknown>): Promise<number> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const countBody: Record<string, unknown> = { exact: true };\n      if (filter) {\n        countBody.filter = filter;\n      }\n\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points/count`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify(countBody)\n      });\n\n      if (!response.ok) {\n        throw new Error(`Failed to count points: ${response.statusText}`);\n      }\n\n      const data = await response.json();\n      return data.result.count;\n    } catch (error) {\n      throw new StorageError(`Failed to count points in Qdrant`, error as Error);\n    }\n  }\n\n  async scrollPoints(filter?: Record<string, unknown>, limit: number = 1000): Promise<QdrantPoint[]> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const scrollBody: Record<string, unknown> = {\n        limit,\n        with_payload: true,\n        with_vector: false\n      };\n      if (filter) {\n        scrollBody.filter = filter;\n      }\n\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points/scroll`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify(scrollBody)\n      });\n\n      if (!response.ok) {\n        throw new Error(`Failed to scroll points: ${response.statusText}`);\n      }\n\n      const data = await response.json();\n      return data.result.points.map((item: { id: string | number; payload: Record<string, unknown> }) => ({\n        id: item.id,\n        vector: [],\n        payload: item.payload,\n        score: 0\n      }));\n    } catch (error) {\n      throw new StorageError(`Failed to scroll points in Qdrant`, error as Error);\n    }\n  }\n\n  async getCollectionInfo(): Promise<{ vectors_count?: number } | null> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}`);\n      \n      if (!response.ok) {\n        if (response.status === 404) {\n          return null;\n        }\n        throw new Error(`Failed to get collection info: ${response.statusText}`);\n      }\n\n      const data = await response.json();\n      return {\n        vectors_count: data.result?.points_count || data.result?.vectors_count || 0\n      };\n    } catch (error) {\n      throw new StorageError(`Failed to get collection info from Qdrant`, error as Error);\n    }\n  }\n\n  async deleteCollection(): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}`, {\n        method: 'DELETE',\n        headers: this.config.storage.qdrantApiKey ? {\n          'api-key': this.config.storage.qdrantApiKey\n        } : {}\n      });\n\n      if (!response.ok && response.status !== 404) {\n        throw new Error(`Failed to delete collection: ${response.statusText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to delete collection from Qdrant`, error as Error);\n    }\n  }\n}\n\nexport class SQLiteStorage {\n  public db: Database.Database;\n\n  constructor(private config: Config) {\n    this.db = this.initializeDatabase();\n    openStorageInstances.add(this);\n  }\n\n  private initializeDatabase(): Database.Database {\n    try {\n      ensureDirectory(dirname(this.config.storage.sqlitePath));\n      \n      const db = new Database(this.config.storage.sqlitePath);\n      \n      db.exec(`\n        CREATE TABLE IF NOT EXISTS directories (\n          id INTEGER PRIMARY KEY,\n          path TEXT UNIQUE NOT NULL,\n          status TEXT DEFAULT 'pending',\n          indexed_at INTEGER DEFAULT 0\n        );\n\n        CREATE TABLE IF NOT EXISTS files (\n          id INTEGER PRIMARY KEY,\n          path TEXT UNIQUE NOT NULL,\n          size INTEGER NOT NULL,\n          modified_time INTEGER NOT NULL,\n          hash TEXT NOT NULL,\n          parent_dirs TEXT NOT NULL,\n          chunks_json TEXT,\n          errors_json TEXT\n        );\n\n        CREATE INDEX IF NOT EXISTS idx_files_path ON files(path);\n        CREATE INDEX IF NOT EXISTS idx_files_hash ON files(hash);\n        CREATE INDEX IF NOT EXISTS idx_directories_path ON directories(path);\n      `);\n\n      db.pragma('journal_mode = WAL');\n      db.pragma('busy_timeout = 5000');\n\n      return db;\n    } catch (error) {\n      throw new StorageError(`Failed to initialize SQLite database`, error as Error);\n    }\n  }\n\n  async getDirectory(path: string): Promise<DirectoryRecord | null> {\n    try {\n      const stmt = this.db.prepare('SELECT * FROM directories WHERE path = ?');\n      const row = stmt.get(path) as { id: number; path: string; status: 'pending' | 'indexing' | 'completed' | 'failed'; indexed_at: number } | undefined;\n      \n      if (!row) return null;\n      \n      return {\n        id: row.id,\n        path: row.path,\n        status: row.status,\n        indexedAt: new Date(row.indexed_at)\n      };\n    } catch (error) {\n      throw new StorageError(`Failed to get directory record`, error as Error);\n    }\n  }\n\n  async upsertDirectory(path: string, status: DirectoryRecord['status']): Promise<void> {\n    try {\n      const stmt = this.db.prepare(`\n        INSERT OR REPLACE INTO directories (path, status, indexed_at)\n        VALUES (?, ?, ?)\n      `);\n      \n      stmt.run(path, status, Date.now());\n    } catch (error) {\n      throw new StorageError(`Failed to upsert directory record`, error as Error);\n    }\n  }\n\n  async getFile(path: string): Promise<FileRecord | null> {\n    try {\n      const stmt = this.db.prepare('SELECT * FROM files WHERE path = ?');\n      const row = stmt.get(path) as { id: number; path: string; size: number; modified_time: number; hash: string; parent_dirs: string; chunks_json: string | null; errors_json: string | null } | undefined;\n      \n      if (!row) return null;\n      \n      return {\n        id: row.id,\n        path: row.path,\n        size: row.size,\n        modifiedTime: new Date(row.modified_time * 1000),\n        hash: row.hash,\n        parentDirs: JSON.parse(row.parent_dirs),\n        chunks: row.chunks_json ? JSON.parse(row.chunks_json) : [],\n        errors: row.errors_json ? JSON.parse(row.errors_json) : undefined\n      };\n    } catch (error) {\n      throw new StorageError(`Failed to get file record`, error as Error);\n    }\n  }\n\n  async upsertFile(fileInfo: FileInfo, chunks: ChunkInfo[] = [], errors: string[] = []): Promise<void> {\n    try {\n      const stmt = this.db.prepare(`\n        INSERT OR REPLACE INTO files (path, size, modified_time, hash, parent_dirs, chunks_json, errors_json)\n        VALUES (?, ?, ?, ?, ?, ?, ?)\n      `);\n      \n      stmt.run(\n        fileInfo.path,\n        fileInfo.size,\n        fileInfo.modifiedTime.getTime(),\n        fileInfo.hash,\n        JSON.stringify(fileInfo.parentDirs),\n        chunks.length > 0 ? JSON.stringify(chunks) : null,\n        errors.length > 0 ? JSON.stringify(errors) : null\n      );\n    } catch (error) {\n      throw new StorageError(`Failed to upsert file record`, error as Error);\n    }\n  }\n\n  async deleteFile(path: string): Promise<void> {\n    try {\n      const stmt = this.db.prepare('DELETE FROM files WHERE path = ?');\n      stmt.run(path);\n    } catch (error) {\n      throw new StorageError(`Failed to delete file record`, error as Error);\n    }\n  }\n\n  getDirectories(): string[] {\n    const rows = this.db.prepare('SELECT path FROM directories').all() as { path: string }[];\n    return rows.map(row => row.path);\n  }\n\n  async getFilesByDirectory(directoryPath: string): Promise<FileRecord[]> {\n    try {\n      const { clause, params } = directoryLikeClause('path', directoryPath);\n      const stmt = this.db.prepare(`SELECT * FROM files WHERE ${clause}`);\n      const rows = stmt.all(...params) as { id: number; path: string; size: number; modified_time: number; hash: string; parent_dirs: string; chunks_json: string | null; errors_json: string | null }[];\n\n      return rows.map(row => ({\n        id: row.id,\n        path: row.path,\n        size: row.size,\n        modifiedTime: new Date(row.modified_time * 1000),\n        hash: row.hash,\n        parentDirs: JSON.parse(row.parent_dirs),\n        chunks: row.chunks_json ? JSON.parse(row.chunks_json) : [],\n        errors: row.errors_json ? JSON.parse(row.errors_json) : undefined\n      }));\n    } catch (error) {\n      throw new StorageError(`Failed to get files by directory`, error as Error);\n    }\n  }\n\n  deleteDirectory(path: string): void {\n    this.db.prepare('DELETE FROM directories WHERE path = ?').run(path);\n  }\n\n  deleteFilesByDirectory(directoryPath: string): number {\n    const { clause, params } = directoryLikeClause('path', directoryPath);\n    const result = this.db.prepare(`DELETE FROM files WHERE ${clause}`).run(...params);\n    return result.changes;\n  }\n\n  close(): void {\n    openStorageInstances.delete(this);\n    this.db.close();\n  }\n}\n\nexport async function initializeStorage(config: Config): Promise<{ sqlite: SQLiteStorage; qdrant: QdrantClient }> {\n  const sqlite = new SQLiteStorage(config);\n  const qdrant = new QdrantClient(config);\n  \n  await qdrant.createCollection();\n  \n  return { sqlite, qdrant };\n}\n\nexport async function initDatabase(dbPath: string): Promise<Database.Database> {\n  return new Database(dbPath);\n}\n\nexport interface ResetStats {\n  sqliteExists: boolean;\n  sqliteSize?: string;\n  qdrantCollectionExists: boolean;\n  qdrantVectorCount?: number;\n}\n\nexport interface ResetResult {\n  sqliteDeleted: boolean;\n  qdrantDeleted: boolean;\n  warnings: string[];\n}\n\nexport async function getResetPreview(config: Config): Promise<ResetStats> {\n  const stats: ResetStats = {\n    sqliteExists: false,\n    qdrantCollectionExists: false\n  };\n\n  if (await import('fs').then(fs => fs.existsSync(config.storage.sqlitePath))) {\n    stats.sqliteExists = true;\n    try {\n      const fileStats = await import('fs').then(fs => fs.statSync(config.storage.sqlitePath));\n      const sizeInMB = (fileStats.size / (1024 * 1024)).toFixed(1);\n      stats.sqliteSize = `${sizeInMB} MB`;\n    } catch {\n      stats.sqliteSize = 'unknown size';\n    }\n  }\n\n  try {\n    const qdrant = new QdrantClient(config);\n    const isHealthy = await qdrant.healthCheck();\n    \n    if (isHealthy) {\n      const collectionInfo = await qdrant.getCollectionInfo();\n      if (collectionInfo) {\n        stats.qdrantCollectionExists = true;\n        stats.qdrantVectorCount = collectionInfo.vectors_count || 0;\n      }\n    }\n  } catch {\n    // Qdrant unavailable\n  }\n\n  return stats;\n}\n\nexport async function clearDatabase(config: Config): Promise<boolean> {\n  try {\n    if (!await import('fs').then(fs => fs.existsSync(config.storage.sqlitePath))) {\n      return true; // Already clean\n    }\n    \n    await import('fs/promises').then(fs => fs.unlink(config.storage.sqlitePath));\n    return true;\n  } catch (error) {\n    throw new StorageError(`Failed to delete SQLite database: ${error instanceof Error ? error.message : 'Unknown error'}`, error as Error);\n  }\n}\n\nexport async function clearVectorCollection(config: Config): Promise<boolean> {\n  try {\n    const qdrant = new QdrantClient(config);\n    const isHealthy = await qdrant.healthCheck();\n    \n    if (!isHealthy) {\n      throw new StorageError(`Qdrant unavailable at ${config.storage.qdrantEndpoint}`);\n    }\n    \n    const collectionInfo = await qdrant.getCollectionInfo();\n    if (collectionInfo) {\n      await qdrant.deleteCollection();\n    }\n    \n    return true;\n  } catch (error) {\n    throw new StorageError(`Failed to reset Qdrant collection: ${error instanceof Error ? error.message : 'Unknown error'}`, error as Error);\n  }\n}\n\nexport interface DirectoryStatus {\n  path: string;\n  status: string;\n  filesCount: number;\n  chunksCount: number;\n  lastIndexed: string | null;\n  errors: string[];\n}\n\nexport interface WorkspaceStatus {\n  name: string;\n  paths: string[];\n  isValid: boolean;\n  filesCount: number;\n  chunksCount: number;\n  health: {\n    status: 'healthy' | 'warning' | 'error';\n    issues: string[];\n    recommendations: string[];\n  };\n}\n\nexport interface IndexStatus {\n  directoriesIndexed: number;\n  filesIndexed: number;\n  chunksIndexed: number;\n  databaseSize: string;\n  lastIndexed: string | null;\n  errors: string[];\n  directories: DirectoryStatus[];\n  workspaces: WorkspaceStatus[];\n  workspaceHealth: {\n    healthy: number;\n    warnings: number;\n    errors: number;\n    criticalIssues: string[];\n    recommendations: string[];\n  };\n  qdrantConsistency: {\n    isConsistent: boolean;\n    issues: string[];\n  };\n}\n\nasync function calculateWorkspaceStatistics(sqlite: SQLiteStorage, config: Config): Promise<WorkspaceStatus[]> {\n  const { getAvailableWorkspaces, getWorkspacePaths } = await import('./config.js');\n  const workspaces: WorkspaceStatus[] = [];\n  \n  // Get all indexed directories for comparison\n  const directoriesStmt = sqlite.db.prepare('SELECT path, status FROM directories');\n  const indexedDirectories = directoriesStmt.all() as { path: string; status: string }[];\n  const indexedDirectoryPaths = indexedDirectories.map(d => d.path);\n  \n  // Get Qdrant client for efficient workspace filtering\n  const qdrant = new QdrantClient(config);\n  \n  for (const workspaceName of getAvailableWorkspaces(config)) {\n    const workspacePaths = getWorkspacePaths(config, workspaceName);\n    const workspaceConfig = config.workspaces[workspaceName];\n    \n    let filesCount = 0;\n    let chunksCount = 0;\n    \n    if (workspacePaths.length > 0) {\n      try {\n        // Build workspace filter using same logic as search\n        const workspaceFilter = {\n          must: [\n            {\n              key: \"parentDirectories\",\n              match: { any: workspacePaths }\n            }\n          ]\n        };\n        \n        // Get chunk count efficiently using Qdrant\n        chunksCount = await qdrant.countPoints(workspaceFilter);\n        \n        // Get unique file paths using Qdrant scroll\n        const points = await qdrant.scrollPoints(workspaceFilter, 10000);\n        const uniqueFilePaths = new Set(points.map(p => p.payload.filePath));\n        filesCount = uniqueFilePaths.size;\n        \n      } catch {\n        // Fallback to 0 if Qdrant is unavailable\n        filesCount = 0;\n        chunksCount = 0;\n      }\n    }\n    \n    // Check workspace health\n    const health = analyzeWorkspaceHealth(workspacePaths, workspaceConfig.isValid, filesCount, indexedDirectoryPaths);\n    \n    workspaces.push({\n      name: workspaceName,\n      paths: workspacePaths,\n      isValid: workspaceConfig.isValid,\n      filesCount,\n      chunksCount,\n      health\n    });\n  }\n  \n  return workspaces;\n}\n\nfunction analyzeWorkspaceHealth(\n  workspacePaths: string[], \n  isValid: boolean, \n  filesCount: number, \n  indexedDirectoryPaths: string[]\n): { status: 'healthy' | 'warning' | 'error'; issues: string[]; recommendations: string[] } {\n  const issues: string[] = [];\n  const recommendations: string[] = [];\n  \n  // Check if workspace paths exist and are valid\n  if (!isValid) {\n    issues.push('One or more workspace directories do not exist on the filesystem');\n    recommendations.push('Verify workspace directory paths exist and are accessible');\n  }\n  \n  // Check if workspace paths are indexed\n  const unindexedPaths: string[] = [];\n  const partiallyIndexedPaths: string[] = [];\n  \n  for (const workspacePath of workspacePaths) {\n    // Check if this exact path is indexed\n    const exactMatch = indexedDirectoryPaths.includes(workspacePath);\n    \n    if (exactMatch) {\n      // Perfect match - workspace directory is directly indexed\n      continue;\n    }\n    \n    // Check if workspace path is covered by a parent directory that is indexed\n    const isChildOfIndexed = indexedDirectoryPaths.some(indexedPath => {\n      // Workspace path must start with indexed path and be a subdirectory\n      return workspacePath.startsWith(indexedPath + '/') || workspacePath.startsWith(indexedPath + '\\\\');\n    });\n    \n    if (isChildOfIndexed) {\n      partiallyIndexedPaths.push(workspacePath);\n    } else {\n      unindexedPaths.push(workspacePath);\n    }\n  }\n  \n  // Report unindexed paths\n  if (unindexedPaths.length > 0) {\n    issues.push(`Workspace directories not indexed: ${unindexedPaths.join(', ')}`);\n    recommendations.push(`Run indexing on these directories: ${unindexedPaths.join(', ')}`);\n  }\n  \n  // Report partially indexed paths (where parent directory is indexed)\n  if (partiallyIndexedPaths.length > 0) {\n    issues.push(`Workspace directories indexed as part of parent directory: ${partiallyIndexedPaths.join(', ')}`);\n    recommendations.push('Consider indexing workspace directories directly for better organization');\n  }\n  \n  // Check if workspace is empty (no files found)\n  if (isValid && filesCount === 0 && unindexedPaths.length === 0) {\n    issues.push('Workspace contains no indexed files');\n    recommendations.push('Verify the workspace directory contains files and re-index if necessary');\n  }\n  \n  // Determine overall health status\n  let status: 'healthy' | 'warning' | 'error';\n  if (!isValid || unindexedPaths.length > 0) {\n    status = 'error';\n  } else if (issues.length > 0) {\n    status = 'warning';\n  } else {\n    status = 'healthy';\n  }\n  \n  return { status, issues, recommendations };\n}\n\nfunction calculateWorkspaceHealthSummary(workspaces: WorkspaceStatus[]): {\n  healthy: number;\n  warnings: number; \n  errors: number;\n  criticalIssues: string[];\n  recommendations: string[];\n} {\n  let healthy = 0;\n  let warnings = 0;\n  let errors = 0;\n  const criticalIssues: string[] = [];\n  const recommendations: string[] = [];\n  \n  for (const workspace of workspaces) {\n    switch (workspace.health.status) {\n      case 'healthy':\n        healthy++;\n        break;\n      case 'warning':\n        warnings++;\n        break;\n      case 'error':\n        errors++;\n        criticalIssues.push(`${workspace.name}: ${workspace.health.issues.join(', ')}`);\n        break;\n    }\n    \n    // Collect unique recommendations\n    for (const rec of workspace.health.recommendations) {\n      if (!recommendations.includes(rec)) {\n        recommendations.push(rec);\n      }\n    }\n  }\n  \n  return {\n    healthy,\n    warnings,\n    errors,\n    criticalIssues,\n    recommendations\n  };\n}\n\nasync function checkQdrantConsistency(sqlite: SQLiteStorage, config: Config): Promise<{ isConsistent: boolean; issues: string[] }> {\n  const issues: string[] = [];\n  \n  try {\n    const qdrant = new QdrantClient(config);\n    const isHealthy = await qdrant.healthCheck();\n    \n    if (!isHealthy) {\n      issues.push('Qdrant vector database is not running or accessible');\n      return { isConsistent: false, issues };\n    }\n    \n    const filesWithChunksStmt = sqlite.db.prepare('SELECT COUNT(*) as count FROM files WHERE chunks_json IS NOT NULL');\n    const filesWithChunks = filesWithChunksStmt.get() as { count: number };\n    \n    const totalChunksStmt = sqlite.db.prepare('SELECT SUM(json_array_length(chunks_json)) as count FROM files WHERE chunks_json IS NOT NULL');\n    const totalChunks = totalChunksStmt.get() as { count: number | null };\n    \n    if (filesWithChunks.count > 0 && (totalChunks.count || 0) === 0) {\n      issues.push('Files exist but no chunks found - possible data corruption');\n    }\n    \n    const collectionName = config.storage.qdrantCollection;\n    try {\n      const response = await fetch(`${config.storage.qdrantEndpoint}/collections/${collectionName}`);\n      if (!response.ok) {\n        issues.push(`Vector collection '${collectionName}' not found (normal during first-time setup)`);\n        return { isConsistent: false, issues };\n      }\n      \n      const collectionInfo = await response.json();\n      const qdrantPointCount = collectionInfo.result?.points_count || 0;\n      const sqliteChunkCount = totalChunks.count || 0;\n      \n      if (Math.abs(qdrantPointCount - 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package/dist/utils.js

@@ -106,6 +106,8 @@ function isSupportedFileType(filePath) {
     ".java",
     ".cpp",
     ".c",
+    ".pl",
+    ".pm",
     ".json",
     ".yaml",
     ".yml",

package/dist/utils.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "directory-indexer",
-  "version": "0.2.2",
+  "version": "0.3.0",
   "description": "AI-powered directory indexing with semantic search for MCP servers",
   "main": "dist/cli.js",
   "bin": {
@@ -42,29 +42,33 @@
   "engines": {
     "node": ">=18.0.0"
   },
+  "publishConfig": {
+    "provenance": true,
+    "access": "public"
+  },
   "files": [
     "dist/",
     "bin/"
   ],
   "dependencies": {
-    "@modelcontextprotocol/sdk": "^0.6.0",
+    "@modelcontextprotocol/sdk": "^1.27.1",
     "better-sqlite3": "^11.5.0",
     "commander": "^12.1.0",
     "ignore": "^7.0.5",
     "mime-types": "^2.1.35",
-    "zod": "^3.23.8"
+    "zod": "^3.25.0"
   },
   "devDependencies": {
     "@types/better-sqlite3": "^7.6.11",
     "@types/mime-types": "^2.1.4",
     "@types/node": "^22.10.1",
-    "@typescript-eslint/eslint-plugin": "^8.15.0",
-    "@typescript-eslint/parser": "^8.15.0",
+    "@typescript-eslint/eslint-plugin": "^8.53.0",
+    "@typescript-eslint/parser": "^8.53.0",
     "@vitest/coverage-v8": "^3.2.4",
-    "eslint": "^9.15.0",
-    "tmp": "^0.2.3",
-    "typescript": "^5.7.2",
-    "vite": "^6.0.3",
+    "eslint": "^9.39.2",
+    "tmp": "^0.2.4",
+    "typescript": "^5.9.3",
+    "vite": "^6.4.1",
     "vitest": "^3.2.4"
   }
-}
+}