directory-indexer 0.0.13 → 0.0.14

package/README.md

@@ -9,6 +9,55 @@
 
 Self-hosted semantic search for local files. Enable AI assistants to search your documents using vector embeddings and MCP integration.
 
+## Quick Start
+
+**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
+
+_Note: For native Qdrant and Ollama installation without Docker, see [Setup section](#setup)._
+
+**1. Start Qdrant vector database** _(skip if already running)_
+
+```bash
+docker run -d --name qdrant -p 127.0.0.1:6333:6333 -v qdrant_storage:/qdrant/storage qdrant/qdrant
+```
+
+**2. Start Ollama embedding service** _(skip if already running)_
+
+_Note: Docker Ollama won't use GPU acceleration. For better performance, consider [native installation](#2-embedding-provider)._
+
+```bash
+docker run -d --name ollama -p 127.0.0.1:11434:11434 -v ollama:/root/.ollama ollama/ollama
+
+# Pull the embedding model
+docker exec ollama ollama pull nomic-embed-text
+```
+
+**3. Index your directories**
+
+```bash
+npx directory-indexer index ~/Documents ~/Projects
+```
+
+**4. Configure AI assistant** _(Claude Desktop, Cursor, Cline, Roo Code, Zed etc.)_
+
+Add to your MCP configuration:
+
+```json
+{
+  "mcpServers": {
+    "directory-indexer": {
+      "command": "npx",
+      "args": ["directory-indexer", "serve"]
+    }
+  }
+}
+```
+
+Your AI assistant will automatically start the MCP server and can now search your indexed files.
+
 ## Setup
 
 Directory Indexer runs locally on your machine or server. It uses an embedding provider (such as Ollama) to create vector embeddings of your files and stores them in a Qdrant vector database for fast semantic search. Both services can run remotely if needed.
@@ -62,7 +111,10 @@ export OPENAI_API_KEY="your-api-key-here"
 Test your setup:
 
 ```bash
-# Check Qdrant
+# Check Qdrant Health
+curl http://localhost:6333/healthz
+
+# View collections
 curl http://localhost:6333/collections
 
 # Check Ollama
@@ -88,24 +140,42 @@ Configure with AI assistants (Claude Desktop, Cline, etc.) using npx:
 }
 ```
 
-Index your directories and start using with your AI assistant:
+Index your directories:
 
 ```bash
 # Index your directories first
 npx directory-indexer index /home/user/projects/docs /home/user/work/reports
-
-# Start MCP server (usually done automatically by your AI assistant)
-npx directory-indexer serve
 ```
 
+**How it works:**
+
+1. **MCP server starts automatically** - When your AI assistant connects, it launches the MCP server in the background
+2. **Indexing runs independently** - You can index files before, during, or after MCP setup
+3. **Search immediately available** - Your AI assistant can search files as soon as they're indexed
+
+**Key point:** You don't need to wait for indexing to complete before using the MCP server. Index files as needed, and your AI assistant will immediately have access to search them.
+
 ### Using with AI Assistant
 
 Once configured, your AI assistant can search your indexed documents semantically:
 
+**Search by concept:**
+
 - _"Find API authentication examples"_
-- _"Show me incidents similar to this outage report"_
+- _"Show me error handling patterns"_
+- _"Find configuration for Redis"_
+
+**Find similar content:**
+
+- _"Show me incidents similar to this outage report"_ _(when you have an incident file open)_
+- _"Find documentation like this API guide"_ _(when viewing an API doc)_
+- _"What files are similar to my deployment script?"_
+
+**Troubleshoot issues:**
+
 - _"Find troubleshooting guides on SQL deadlocks"_
-- _"What files contain database configuration?"_
+- _"Show me solutions for timeout errors"_
+- _"Find debugging tips for performance issues"_
 
 ### Custom Configuration
 
@@ -133,7 +203,7 @@ For advanced users who prefer command-line usage, see [CLI Documentation](./docs
 
 ## Configuration
 
-Environment variables for MCP configuration:
+Environment variables (all optional):
 
 ```bash
 # Data directory (default: ~/.directory-indexer)
@@ -142,6 +212,10 @@ export DIRECTORY_INDEXER_DATA_DIR="/opt/ai-knowledge-base"
 # Service endpoints (defaults shown)
 export QDRANT_ENDPOINT="http://localhost:6333"
 export OLLAMA_ENDPOINT="http://localhost:11434"
+
+# Optional API keys
+export OPENAI_API_KEY="your-key-here"
+export QDRANT_API_KEY="your-key-here"
 ```
 
 For all configuration options, see [Environment Variables](./docs/design.md#environment-variables).
@@ -160,28 +234,6 @@ For all configuration options, see [Environment Variables](./docs/design.md#envi
 - **[Contributing](docs/CONTRIBUTING.md)**: Development setup and guidelines
 - **[Design](docs/design.md)**: Architecture and technical decisions
 
-## Usage Examples
-
-Once indexed, try these queries with your AI assistant:
-
-**Search by concept:**
-
-- _"Find API authentication examples"_
-- _"Show me error handling patterns"_
-- _"Find configuration for Redis"_
-
-**Find similar content:**
-
-- _"Show me incidents similar to this outage report"_ _(when you have an incident file open)_
-- _"Find documentation like this API guide"_ _(when viewing an API doc)_
-- _"What files are similar to my deployment script?"_
-
-**Troubleshoot issues:**
-
-- _"Find troubleshooting guides on SQL deadlocks"_
-- _"Show me solutions for timeout errors"_
-- _"Find debugging tips for performance issues"_
-
 ## License
 
 MIT

package/dist/cli.js

@@ -296,21 +296,62 @@ async function main() {
     try {
       await loadConfig({ verbose: options.verbose });
       const status = await getIndexStatus();
-      console.log("Indexing Status:");
-      console.log(`  Directories indexed: ${status.directoriesIndexed}`);
-      console.log(`  Files indexed: ${status.filesIndexed}`);
-      console.log(`  Total chunks: ${status.chunksIndexed}`);
-      console.log(`  Database size: ${status.databaseSize}`);
-      console.log(`  Last indexed: ${status.lastIndexed || "Never"}`);
+      console.log("Directory Indexer Status Report");
+      console.log("=====================================");
+      console.log("");
+      console.log("OVERVIEW:");
+      console.log(`  • ${status.directoriesIndexed} directories have been indexed`);
+      console.log(`  • ${status.filesIndexed} files processed for semantic search`);
+      console.log(`  • ${status.chunksIndexed} text chunks available for AI search`);
+      console.log(`  • Database storage: ${status.databaseSize}`);
+      console.log(`  • Most recent indexing: ${status.lastIndexed || "No indexing performed yet"}`);
       if (status.errors.length > 0) {
-        console.log(`  Errors: ${status.errors.length}`);
+        console.log(`  • Processing errors encountered: ${status.errors.length}`);
         if (options.verbose) {
-          console.log("  Recent errors:");
+          console.log("");
+          console.log("RECENT ERRORS:");
           status.errors.slice(0, 5).forEach((error) => {
-            console.log(`    - ${error}`);
+            console.log(`  - ${error}`);
           });
         }
       }
+      console.log("");
+      console.log("INDEXED DIRECTORIES:");
+      if (status.directories.length === 0) {
+        console.log("  No directories have been indexed yet.");
+        console.log('  Run "directory-indexer index <path>" to start indexing.');
+      } else {
+        status.directories.forEach((dir) => {
+          console.log("");
+          console.log(`  Directory: ${dir.path}`);
+          console.log(`    • Indexing status: ${dir.status}`);
+          console.log(`    • Files processed: ${dir.filesCount}`);
+          console.log(`    • Searchable chunks: ${dir.chunksCount}`);
+          console.log(`    • Last indexed: ${dir.lastIndexed || "Never completed"}`);
+          if (dir.errors.length > 0) {
+            console.log(`    • Files with errors: ${dir.errors.length}`);
+            if (options.verbose) {
+              console.log("    • Recent errors:");
+              dir.errors.slice(0, 3).forEach((error) => {
+                console.log(`      - ${error}`);
+              });
+            }
+          }
+        });
+      }
+      if (!status.qdrantConsistency.isConsistent) {
+        console.log("");
+        console.log("SYSTEM STATUS:");
+        status.qdrantConsistency.issues.forEach((issue) => {
+          console.log(`  • ${issue}`);
+        });
+        console.log("");
+        console.log("ℹ️  Note: Status messages above may be normal during setup or active indexing.");
+      } else {
+        console.log("");
+        console.log("SYSTEM STATUS:");
+        console.log("  • All systems operational - ready for AI-powered search");
+      }
     } catch (error) {
       console.error("Error getting status:", error);
       process.exit(1);

package/dist/cli.js.map

@@ -1 +1 @@
-{"version":3,"file":"cli.js","sources":["../src/mcp.ts","../src/cli.ts"],"sourcesContent":["import { Server } from '@modelcontextprotocol/sdk/server/index.js';\nimport { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';\nimport { \n  CallToolRequestSchema, \n  ListToolsRequestSchema,\n  Tool\n} from '@modelcontextprotocol/sdk/types.js';\nimport { readFileSync } from 'fs';\nimport { join, dirname } from 'path';\nimport { fileURLToPath } from 'url';\nimport { Config } from './config.js';\nimport { indexDirectories } from './indexing.js';\nimport { searchContent, findSimilarFiles, getFileContent } from './search.js';\nimport { getIndexStatus } from './storage.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\nconst MCP_TOOLS: Tool[] = [\n  {\n    name: 'index',\n    description: 'Index directories for semantic search',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        directory_path: {\n          type: 'string',\n          description: 'Comma-separated list of directory paths to index'\n        }\n      },\n      required: ['directory_path']\n    }\n  },\n  {\n    name: 'search',\n    description: 'Search indexed content semantically',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        query: {\n          type: 'string',\n          description: 'Search query'\n        },\n        limit: {\n          type: 'number',\n          description: 'Maximum number of results (default: 10)',\n          default: 10\n        }\n      },\n      required: ['query']\n    }\n  },\n  {\n    name: 'similar_files',\n    description: 'Find files similar to a given file',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        file_path: {\n          type: 'string',\n          description: 'Path to the file to find similar files for'\n        },\n        limit: {\n          type: 'number',\n          description: 'Maximum number of results (default: 10)',\n          default: 10\n        }\n      },\n      required: ['file_path']\n    }\n  },\n  {\n    name: 'get_content',\n    description: 'Get file content',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        file_path: {\n          type: 'string',\n          description: 'Path to the file to retrieve'\n        },\n        chunks: {\n          type: 'string',\n          description: 'Optional chunk range (e.g., \"2-5\")'\n        }\n      },\n      required: ['file_path']\n    }\n  },\n  {\n    name: 'server_info',\n    description: 'Get server information and status',\n    inputSchema: {\n      type: 'object',\n      properties: {}\n    }\n  }\n];\n\nexport async function startMcpServer(config: Config): Promise<void> {\n  const server = new Server(\n    {\n      name: 'directory-indexer',\n      version: VERSION\n    },\n    {\n      capabilities: {\n        tools: {}\n      }\n    }\n  );\n\n  server.setRequestHandler(ListToolsRequestSchema, async () => {\n    return {\n      tools: MCP_TOOLS\n    };\n  });\n\n  server.setRequestHandler(CallToolRequestSchema, async (request) => {\n    const { name, arguments: args } = request.params;\n\n    try {\n      switch (name) {\n        case 'index': {\n          if (!args || typeof args.directory_path !== 'string') {\n            throw new Error('directory_path is required');\n          }\n          const paths = args.directory_path.split(',').map((p: string) => p.trim());\n          const result = await indexDirectories(paths, config);\n          return {\n            content: [\n              {\n                type: 'text',\n                text: `Indexed ${result.indexed} files, skipped ${result.skipped} files, ${result.errors.length} errors`\n              }\n            ]\n          };\n        }\n\n        case 'search': {\n          if (!args || typeof args.query !== 'string') {\n            throw new Error('query is required');\n          }\n          const results = await searchContent(args.query, { limit: (args.limit as number) || 10 });\n          return {\n            content: [\n              {\n                type: 'text',\n                text: JSON.stringify(results, null, 2)\n              }\n            ]\n          };\n        }\n\n        case 'similar_files': {\n          if (!args || typeof args.file_path !== 'string') {\n            throw new Error('file_path is required');\n          }\n          const results = await findSimilarFiles(args.file_path, (args.limit as number) || 10);\n          return {\n            content: [\n              {\n                type: 'text',\n                text: JSON.stringify(results, null, 2)\n              }\n            ]\n          };\n        }\n\n        case 'get_content': {\n          if (!args || typeof args.file_path !== 'string') {\n            throw new Error('file_path is required');\n          }\n          const content = await getFileContent(args.file_path, args.chunks as string);\n          return {\n            content: [\n              {\n                type: 'text',\n                text: content\n              }\n            ]\n          };\n        }\n\n        case 'server_info': {\n          const status = await getIndexStatus();\n          return {\n            content: [\n              {\n                type: 'text',\n                text: JSON.stringify({\n                  name: 'directory-indexer',\n                  version: VERSION,\n                  status: status\n                }, null, 2)\n              }\n            ]\n          };\n        }\n\n        default:\n          throw new Error(`Unknown tool: ${name}`);\n      }\n    } catch (error) {\n      const errorMessage = error instanceof Error ? error.message : 'Unknown error';\n      return {\n        content: [\n          {\n            type: 'text',\n            text: `Error: ${errorMessage}`\n          }\n        ],\n        isError: true\n      };\n    }\n  });\n\n  const transport = new StdioServerTransport();\n  await server.connect(transport);\n  \n  if (config.verbose) {\n    console.error('MCP server started successfully');\n  }\n}","#!/usr/bin/env node\n\nimport { Command } from 'commander';\nimport { fileURLToPath } from 'url';\nimport { readFileSync } from 'fs';\nimport { join, dirname } from 'path';\nimport { indexDirectories } from './indexing.js';\nimport { searchContent, findSimilarFiles, getFileContent } from './search.js';\nimport { loadConfig } from './config.js';\nimport { getIndexStatus } from './storage.js';\nimport { startMcpServer } from './mcp.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        const config = await loadConfig({ verbose: options.verbose });\n        console.log(`Indexing ${paths.length} directories...`);\n        const result = await indexDirectories(paths, config);\n        console.log(`Indexed ${result.indexed} files, skipped ${result.skipped} files, ${result.errors.length} errors`);\n        if (result.errors.length > 0 && config.verbose) {\n          console.log('Errors:', result.errors);\n        }\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('-v, --verbose', 'Enable verbose logging')\n    .action(async (query: string, options) => {\n      try {\n        await loadConfig({ verbose: options.verbose });\n        const results = await searchContent(query, { limit: parseInt(options.limit) });\n        \n        if (results.length === 0) {\n          console.log('No results found');\n          return;\n        }\n\n        console.log(`Found ${results.length} results:\\n`);\n        results.forEach((result, index) => {\n          console.log(`${index + 1}. ${result.filePath}`);\n          console.log(`   Score: ${result.score.toFixed(3)}`);\n          if (result.content) {\n            console.log(`   Content: ${result.content.substring(0, 150)}...`);\n          }\n          console.log();\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 loadConfig({ verbose: options.verbose });\n        const results = await findSimilarFiles(filePath, parseInt(options.limit));\n        \n        if (results.length === 0) {\n          console.log('No similar files found');\n          return;\n        }\n\n        console.log(`Found ${results.length} similar files:\\n`);\n        results.forEach((result, index) => {\n          console.log(`${index + 1}. ${result.filePath}`);\n          console.log(`   Similarity: ${result.score.toFixed(3)}`);\n          console.log();\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 loadConfig({ verbose: options.verbose });\n        const content = await getFileContent(filePath, options.chunks);\n        console.log(content);\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        const config = await loadConfig({ verbose: options.verbose });\n        await startMcpServer(config);\n      } catch (error) {\n        console.error('Error starting MCP server:', 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 loadConfig({ verbose: options.verbose });\n        const status = await getIndexStatus();\n        \n        console.log('Indexing Status:');\n        console.log(`  Directories indexed: ${status.directoriesIndexed}`);\n        console.log(`  Files indexed: ${status.filesIndexed}`);\n        console.log(`  Total chunks: ${status.chunksIndexed}`);\n        console.log(`  Database size: ${status.databaseSize}`);\n        console.log(`  Last indexed: ${status.lastIndexed || 'Never'}`);\n        \n        if (status.errors.length > 0) {\n          console.log(`  Errors: ${status.errors.length}`);\n          if (options.verbose) {\n            console.log('  Recent errors:');\n            status.errors.slice(0, 5).forEach(error => {\n              console.log(`    - ${error}`);\n            });\n          }\n        }\n      } catch (error) {\n        console.error('Error getting status:', error);\n        process.exit(1);\n      }\n    });\n\n  await program.parseAsync();\n}\n\n// Main function is already exported 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description: 'Path to the file to find similar files for'\n        },\n        limit: {\n          type: 'number',\n          description: 'Maximum number of results (default: 10)',\n          default: 10\n        }\n      },\n      required: ['file_path']\n    }\n  },\n  {\n    name: 'get_content',\n    description: 'Get file content',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        file_path: {\n          type: 'string',\n          description: 'Path to the file to retrieve'\n        },\n        chunks: {\n          type: 'string',\n          description: 'Optional chunk range (e.g., \"2-5\")'\n        }\n      },\n      required: ['file_path']\n    }\n  },\n  {\n    name: 'server_info',\n    description: 'Get server information and status',\n    inputSchema: {\n      type: 'object',\n      properties: {}\n    }\n  }\n];\n\nexport async function startMcpServer(config: Config): Promise<void> {\n  const server = new Server(\n    {\n      name: 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${result.filePath}`);\n          console.log(`   Similarity: ${result.score.toFixed(3)}`);\n          console.log();\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 loadConfig({ verbose: options.verbose });\n        const content = await getFileContent(filePath, options.chunks);\n        console.log(content);\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        const config = await loadConfig({ verbose: options.verbose });\n        await startMcpServer(config);\n      } catch (error) {\n        console.error('Error starting MCP server:', 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 loadConfig({ verbose: options.verbose });\n        const status = await getIndexStatus();\n        \n        console.log('Directory Indexer Status Report');\n        console.log('=====================================');\n        console.log('');\n        console.log('OVERVIEW:');\n        console.log(`  • ${status.directoriesIndexed} directories have been indexed`);\n        console.log(`  • ${status.filesIndexed} files processed for semantic search`);\n        console.log(`  • ${status.chunksIndexed} text chunks 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console.log('');\n          console.log('ℹ️  Note: Status messages above may be normal during setup or active indexing.');\n        } else {\n          console.log('');\n          console.log('SYSTEM STATUS:');\n          console.log('  • All systems operational - ready for AI-powered search');\n        }\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

@@ -30,11 +30,14 @@ class ConfigError extends Error {
 }
 function loadConfig(options = {}) {
   const dataDir = process.env.DIRECTORY_INDEXER_DATA_DIR || join(homedir(), ".directory-indexer");
+  const isTest = process.env.NODE_ENV === "test" || process.env.VITEST === "true";
+  const dbFileName = isTest ? "test-data.db" : "data.db";
+  const defaultCollection = isTest ? "directory-indexer-test" : "directory-indexer";
   const config = {
     storage: {
-      sqlitePath: join(dataDir, "data.db"),
+      sqlitePath: join(dataDir, dbFileName),
       qdrantEndpoint: process.env.QDRANT_ENDPOINT || "http://localhost:6333",
-      qdrantCollection: process.env.DIRECTORY_INDEXER_QDRANT_COLLECTION || "directory-indexer"
+      qdrantCollection: process.env.DIRECTORY_INDEXER_QDRANT_COLLECTION || defaultCollection
     },
     embedding: {
       provider: process.env.EMBEDDING_PROVIDER || "ollama",

package/dist/config.js.map

@@ -1 +1 @@
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package/dist/embedding.js.map

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+{"version":3,"file":"embedding.js","sources":["../src/embedding.ts"],"sourcesContent":["import { Config } from './config.js';\n\nexport interface EmbeddingProvider {\n  name: string;\n  dimensions: number;\n  generateEmbedding(text: string): Promise<number[]>;\n  generateEmbeddings(texts: string[]): Promise<number[][]>;\n}\n\nexport interface EmbeddingConfig {\n  model: string;\n  endpoint: string;\n  dimensions: number;\n}\n\nexport class EmbeddingError extends Error {\n  constructor(message: string, public override cause?: Error) {\n    super(message);\n    this.name = 'EmbeddingError';\n  }\n}\n\nclass MockEmbeddingProvider implements EmbeddingProvider {\n  name = 'mock';\n  \n  constructor(private config: EmbeddingConfig) {}\n  \n  get dimensions(): number {\n    return this.config.dimensions;\n  }\n  \n  async generateEmbedding(text: string): Promise<number[]> {\n    const hash = this.hashString(text);\n    return Array.from({ length: this.dimensions }, (_, i) => \n      Math.sin(hash + i) * 0.1\n    );\n  }\n  \n  async generateEmbeddings(texts: string[]): Promise<number[][]> {\n    return Promise.all(texts.map(text => this.generateEmbedding(text)));\n  }\n  \n  private hashString(str: string): number {\n    let hash = 0;\n    for (let i = 0; i < str.length; i++) {\n      const char = str.charCodeAt(i);\n      hash = ((hash << 5) - hash) + char;\n      hash = hash & hash;\n    }\n    return Math.abs(hash);\n  }\n}\n\nclass OllamaEmbeddingProvider implements EmbeddingProvider {\n  name = 'ollama';\n  dimensions = 768;\n  \n  constructor(private config: EmbeddingConfig) {}\n  \n  async generateEmbedding(text: string): Promise<number[]> {\n    try {\n      const response = await fetch(`${this.config.endpoint}/api/embeddings`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify({\n          model: this.config.model,\n          prompt: text\n        })\n      });\n      \n      if (!response.ok) {\n        throw new Error(`Ollama API error: ${response.statusText}`);\n      }\n      \n      const data = await response.json();\n      return data.embedding;\n    } catch (error) {\n      throw new EmbeddingError(`Failed to generate Ollama embedding`, error as Error);\n    }\n  }\n  \n  async generateEmbeddings(texts: string[]): Promise<number[][]> {\n    return Promise.all(texts.map(text => this.generateEmbedding(text)));\n  }\n}\n\nclass OpenAIEmbeddingProvider implements EmbeddingProvider {\n  name = 'openai';\n  dimensions = 1536;\n  \n  constructor(private config: EmbeddingConfig) {}\n  \n  async generateEmbedding(text: string): Promise<number[]> {\n    try {\n      const response = await fetch('https://api.openai.com/v1/embeddings', {\n        method: 'POST',\n        headers: {\n          'Content-Type': 'application/json',\n          'Authorization': `Bearer ${process.env.OPENAI_API_KEY}`\n        },\n        body: JSON.stringify({\n          model: this.config.model,\n          input: text\n        })\n      });\n      \n      if (!response.ok) {\n        throw new Error(`OpenAI API error: ${response.statusText}`);\n      }\n      \n      const data = await response.json();\n      return data.data[0].embedding;\n    } catch (error) {\n      throw new EmbeddingError(`Failed to generate OpenAI embedding`, error as Error);\n    }\n  }\n  \n  async generateEmbeddings(texts: string[]): Promise<number[][]> {\n    try {\n      const response = await fetch('https://api.openai.com/v1/embeddings', {\n        method: 'POST',\n        headers: {\n          'Content-Type': 'application/json',\n          'Authorization': `Bearer ${process.env.OPENAI_API_KEY}`\n        },\n        body: JSON.stringify({\n          model: this.config.model,\n          input: texts\n        })\n      });\n      \n      if (!response.ok) {\n        throw new Error(`OpenAI API error: ${response.statusText}`);\n      }\n      \n      const data = await response.json();\n      return data.data.map((item: { embedding: number[] }) => item.embedding);\n    } catch (error) {\n      throw new EmbeddingError(`Failed to generate OpenAI embeddings`, error as Error);\n    }\n  }\n}\n\nexport function createEmbeddingProvider(provider: string, config: EmbeddingConfig): EmbeddingProvider {\n  switch (provider) {\n    case 'mock':\n      return new MockEmbeddingProvider(config);\n    case 'ollama':\n      return new OllamaEmbeddingProvider(config);\n    case 'openai':\n      return new OpenAIEmbeddingProvider(config);\n    default:\n      throw new EmbeddingError(`Unknown embedding provider: ${provider}`);\n  }\n}\n\nexport async function generateEmbedding(text: string, config: Config): Promise<number[]> {\n  const provider = createEmbeddingProvider(config.embedding.provider, {\n    model: config.embedding.model,\n    endpoint: config.embedding.endpoint,\n    dimensions: config.embedding.provider === 'mock' ? 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package/dist/indexing.js

@@ -86,6 +86,31 @@ async function getFileMetadata(filePath) {
     throw new IndexingError(`Failed to get file metadata`, error);
   }
 }
+async function shouldReprocessFile(filePath, existingRecord, config) {
+  try {
+    const fs2 = await import("fs/promises");
+    const currentStats = await fs2.stat(filePath);
+    const existingModTime = new Date(existingRecord.modifiedTime);
+    if (currentStats.mtime <= existingModTime) {
+      return false;
+    }
+    const currentFileInfo = await getFileInfo(filePath);
+    return currentFileInfo.hash !== existingRecord.hash;
+  } catch (modtimeError) {
+    if (config.verbose) {
+      console.log(`Warning: Could not check modification time for ${filePath}:`, modtimeError);
+    }
+    try {
+      const currentFileInfo = await getFileInfo(filePath);
+      return currentFileInfo.hash !== existingRecord.hash;
+    } catch (hashError) {
+      if (config.verbose) {
+        console.log(`Warning: Could not compute hash for ${filePath}:`, hashError);
+      }
+      return true;
+    }
+  }
+}
 async function indexDirectories(paths, config) {
   let indexed = 0;
   let skipped = 0;
@@ -97,9 +122,19 @@ async function indexDirectories(paths, config) {
   const { sqlite, qdrant } = await initializeStorage(config);
   for (const path of paths) {
     try {
+      await sqlite.upsertDirectory(path, "indexing");
       const files = await scanDirectory(path, scanOptions);
       for (const file of files) {
         try {
+          const existingFile = await sqlite.getFile(file.path);
+          if (existingFile) {
+            const needsReprocessing = await shouldReprocessFile(file.path, existingFile, config);
+            if (!needsReprocessing) {
+              skipped++;
+              continue;
+            }
+            await qdrant.deletePointsByFileHash(existingFile.hash);
+          }
           const content = await promises.readFile(file.path, "utf-8");
           const chunks = chunkText(content, config.indexing.chunkSize, config.indexing.chunkOverlap);
           await sqlite.upsertFile(file, chunks);
@@ -123,13 +158,16 @@ async function indexDirectories(paths, config) {
           }
           indexed++;
         } catch (error) {
-          skipped++;
           const errorMessage = error instanceof Error ? error.message : String(error);
           const causeMessage = error instanceof Error && error.cause ? `: ${error.cause.message}` : "";
           errors.push(`Failed to process ${file.path}: ${errorMessage}${causeMessage}`);
         }
       }
+      const directoryErrors = errors.filter((err) => err.includes(path));
+      const directoryStatus = directoryErrors.length > 0 ? "failed" : "completed";
+      await sqlite.upsertDirectory(path, directoryStatus);
     } catch (error) {
+      await sqlite.upsertDirectory(path, "failed");
       errors.push(`Failed to scan directory ${path}: ${error.message}`);
     }
   }

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 { generateEmbedding } from './embedding.js';\nimport { initializeStorage } from './storage.js';\n\nexport interface ScanOptions {\n  ignorePatterns: string[];\n  maxFileSize: number;\n}\n\nexport interface IndexResult {\n  indexed: number;\n  skipped: 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  \n  async function walkDirectory(currentPath: string): Promise<void> {\n    const normalizedPath = normalizePath(currentPath);\n    \n    if (visited.has(normalizedPath)) {\n      return;\n    }\n    visited.add(normalizedPath);\n    \n    try {\n      if (shouldIgnoreFile(normalizedPath, options.ignorePatterns)) {\n        return;\n      }\n      \n      if (await isDirectory(normalizedPath)) {\n        const entries = await fs.readdir(normalizedPath);\n        \n        for (const entry of entries) {\n          const fullPath = join(normalizedPath, entry);\n          await walkDirectory(fullPath);\n        }\n      } else if (await isFile(normalizedPath)) {\n        if (!isSupportedFileType(normalizedPath)) {\n          return;\n        }\n        \n        const stats = await fs.stat(normalizedPath);\n        if (stats.size > options.maxFileSize) {\n          return;\n        }\n        \n        const fileInfo = await getFileInfo(normalizedPath);\n        files.push(fileInfo);\n      }\n    } catch (error) {\n      throw new IndexingError(`Failed to scan directory: ${normalizedPath}`, error as Error);\n    }\n  }\n  \n  await walkDirectory(dirPath);\n  return files;\n}\n\nexport async function getFileMetadata(filePath: string): Promise<FileInfo> {\n  try {\n    return await getFileInfo(filePath);\n  } catch (error) {\n    throw new IndexingError(`Failed to get file metadata`, error as Error);\n  }\n}\n\nexport async function indexDirectories(paths: string[], config: Config): Promise<IndexResult> {\n  let indexed = 0;\n  let skipped = 0;\n  const errors: string[] = [];\n  \n  const scanOptions: ScanOptions = {\n    ignorePatterns: config.indexing.ignorePatterns,\n    maxFileSize: config.indexing.maxFileSize\n  };\n  \n  // Initialize storage\n  const { sqlite, qdrant } = await initializeStorage(config);\n  \n  for (const path of paths) {\n    try {\n      const files = await scanDirectory(path, scanOptions);\n      \n      for (const file of files) {\n        try {\n          const content = await fs.readFile(file.path, 'utf-8');\n          const chunks = chunkText(content, config.indexing.chunkSize, config.indexing.chunkOverlap);\n          \n          // Store file metadata in SQLite\n          await sqlite.upsertFile(file, chunks);\n          \n          // Generate embeddings and store in Qdrant\n          for (let i = 0; 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// Skip processing\n    }\n    \n    // If modtime suggests change, verify with hash\n    const currentFileInfo = await getFileInfo(filePath);\n    return currentFileInfo.hash !== existingRecord.hash;\n    \n  } catch (modtimeError) {\n    // Graceful fallback: skip modtime, use hash only\n    if (config.verbose) {\n      console.log(`Warning: Could not check modification time for ${filePath}:`, modtimeError);\n    }\n    try {\n      const currentFileInfo = await getFileInfo(filePath);\n      return currentFileInfo.hash !== existingRecord.hash;\n    } catch (hashError) {\n      // If we can't hash either, assume changed to be safe\n      if (config.verbose) {\n        console.log(`Warning: Could not compute hash for ${filePath}:`, hashError);\n      }\n      return true;\n    }\n  }\n}\n\nexport async function indexDirectories(paths: string[], config: Config): Promise<IndexResult> {\n  let indexed = 0;\n  let skipped = 0;\n  const errors: string[] = [];\n  \n  const scanOptions: ScanOptions = {\n    ignorePatterns: config.indexing.ignorePatterns,\n    maxFileSize: config.indexing.maxFileSize\n  };\n  \n  // Initialize storage\n  const { sqlite, qdrant } = await initializeStorage(config);\n  \n  for (const path of paths) {\n    try {\n      // Mark directory as indexing\n      await sqlite.upsertDirectory(path, 'indexing');\n      \n      const files = await scanDirectory(path, scanOptions);\n      \n      for (const file of files) {\n        try {\n          // Check if file already exists and needs reprocessing\n          const existingFile = await sqlite.getFile(file.path);\n          \n          if (existingFile) {\n            const needsReprocessing = await shouldReprocessFile(file.path, existingFile, config);\n            if (!needsReprocessing) {\n              skipped++;\n              continue; // Skip unchanged file\n            }\n            \n            // File changed - clean up old vectors first\n            await qdrant.deletePointsByFileHash(existingFile.hash);\n          }\n          \n          const content = await fs.readFile(file.path, 'utf-8');\n          const chunks = chunkText(content, config.indexing.chunkSize, config.indexing.chunkOverlap);\n          \n          // Store file metadata in SQLite\n          await sqlite.upsertFile(file, chunks);\n          \n          // Generate embeddings and store in Qdrant\n          for (let i = 0; i < chunks.length; i++) {\n            const chunk = chunks[i];\n            const embedding = await generateEmbedding(chunk.content, config);\n            // Generate a unique integer ID by combining hash and chunk index\n            const hashNum = parseInt(file.hash.slice(0, 8), 16);\n            const pointId = (hashNum % 1000000) * 1000 + parseInt(chunk.id);\n            const point = {\n              id: pointId,\n              vector: embedding,\n              payload: {\n                filePath: file.path,\n                chunkId: chunk.id,\n                fileHash: file.hash,\n                content: chunk.content,\n                parentDirectories: file.parentDirs\n              }\n            };\n            await qdrant.upsertPoints([point]);\n          }\n          \n          indexed++;\n        } catch (error) {\n          const errorMessage = error instanceof Error ? error.message : String(error);\n          const causeMessage = error instanceof Error && error.cause ? `: ${(error.cause as Error).message}` : '';\n          errors.push(`Failed to process ${file.path}: ${errorMessage}${causeMessage}`);\n        }\n      }\n      \n      // Mark directory as completed if no errors for this directory\n      const directoryErrors = errors.filter(err => err.includes(path));\n      const directoryStatus = directoryErrors.length > 0 ? 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package/dist/storage.js

@@ -14,7 +14,7 @@ class QdrantClient {
   }
   async healthCheck() {
     try {
-      const response = await fetch(`${this.config.storage.qdrantEndpoint}/health`);
+      const response = await fetch(`${this.config.storage.qdrantEndpoint}/healthz`);
       return response.ok;
     } catch {
       return false;
@@ -53,7 +53,8 @@ class QdrantClient {
         body: JSON.stringify({ points })
       });
       if (!response.ok) {
-        throw new Error(`Failed to upsert points: ${response.statusText}`);
+        const errorText = await response.text();
+        throw new Error(`Failed to upsert points: ${response.status} ${response.statusText} - ${errorText}`);
       }
     } catch (error) {
       throw new StorageError(`Failed to upsert points to Qdrant`, error);
@@ -100,6 +101,31 @@ class QdrantClient {
       throw new StorageError(`Failed to delete points from Qdrant`, error);
     }
   }
+  async deletePointsByFileHash(fileHash) {
+    const collectionName = this.config.storage.qdrantCollection;
+    try {
+      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points/delete`, {
+        method: "POST",
+        headers: { "Content-Type": "application/json" },
+        body: JSON.stringify({
+          filter: {
+            must: [
+              {
+                key: "fileHash",
+                match: { value: fileHash }
+              }
+            ]
+          }
+        })
+      });
+      if (!response.ok) {
+        const errorText = await response.text();
+        throw new Error(`Failed to delete points by file hash: ${response.status} ${response.statusText} - ${errorText}`);
+      }
+    } catch (error) {
+      throw new StorageError(`Failed to delete points by file hash from Qdrant`, error);
+    }
+  }
 }
 class SQLiteStorage {
   constructor(config) {
@@ -174,7 +200,7 @@ class SQLiteStorage {
         id: row.id,
         path: row.path,
         size: row.size,
-        modifiedTime: new Date(row.modified_time),
+        modifiedTime: new Date(row.modified_time * 1e3),
         hash: row.hash,
         parentDirs: JSON.parse(row.parent_dirs),
         chunks: row.chunks_json ? JSON.parse(row.chunks_json) : [],
@@ -219,7 +245,7 @@ class SQLiteStorage {
         id: row.id,
         path: row.path,
         size: row.size,
-        modifiedTime: new Date(row.modified_time),
+        modifiedTime: new Date(row.modified_time * 1e3),
         hash: row.hash,
         parentDirs: JSON.parse(row.parent_dirs),
         chunks: row.chunks_json ? JSON.parse(row.chunks_json) : [],
@@ -242,6 +268,50 @@ async function initializeStorage(config) {
 async function initDatabase(dbPath) {
   return new Database(dbPath);
 }
+async function checkQdrantConsistency(sqlite, config) {
+  const issues = [];
+  try {
+    const qdrant = new QdrantClient(config);
+    const isHealthy = await qdrant.healthCheck();
+    if (!isHealthy) {
+      issues.push("Qdrant vector database is not running or accessible");
+      return { isConsistent: false, issues };
+    }
+    const filesWithChunksStmt = sqlite.db.prepare("SELECT COUNT(*) as count FROM files WHERE chunks_json IS NOT NULL");
+    const filesWithChunks = filesWithChunksStmt.get();
+    const totalChunksStmt = sqlite.db.prepare("SELECT SUM(json_array_length(chunks_json)) as count FROM files WHERE chunks_json IS NOT NULL");
+    const totalChunks = totalChunksStmt.get();
+    if (filesWithChunks.count > 0 && (totalChunks.count || 0) === 0) {
+      issues.push("Files exist but no chunks found - possible data corruption");
+    }
+    const collectionName = config.storage.qdrantCollection;
+    try {
+      const response = await fetch(`${config.storage.qdrantEndpoint}/collections/${collectionName}`);
+      if (!response.ok) {
+        issues.push(`Vector collection '${collectionName}' not found (normal during first-time setup)`);
+        return { isConsistent: false, issues };
+      }
+      const collectionInfo = await response.json();
+      const qdrantPointCount = collectionInfo.result?.points_count || 0;
+      const sqliteChunkCount = totalChunks.count || 0;
+      if (Math.abs(qdrantPointCount - sqliteChunkCount) > 0) {
+        if (qdrantPointCount > sqliteChunkCount) {
+          issues.push(`Extra vectors in database: ${qdrantPointCount} vectors vs ${sqliteChunkCount} indexed chunks (normal during cleanup)`);
+        } else {
+          issues.push(`Missing vectors: ${sqliteChunkCount} indexed chunks vs ${qdrantPointCount} vectors (normal during indexing)`);
+        }
+      }
+    } catch (error) {
+      issues.push(`Cannot verify vector database status: ${error}`);
+    }
+  } catch (error) {
+    issues.push(`Database status check failed: ${error}`);
+  }
+  return {
+    isConsistent: issues.length === 0,
+    issues
+  };
+}
 async function getIndexStatus() {
   const config = await import("./config.js").then((m) => m.loadConfig());
   const sqlite = new SQLiteStorage(config);
@@ -252,7 +322,7 @@ async function getIndexStatus() {
     const filesCount = filesStmt.get();
     const chunksStmt = sqlite.db.prepare("SELECT SUM(json_array_length(chunks_json)) as count FROM files WHERE chunks_json IS NOT NULL");
     const chunksCount = chunksStmt.get();
-    const lastIndexedStmt = sqlite.db.prepare("SELECT MAX(indexed_at) as last_indexed FROM directories");
+    const lastIndexedStmt = sqlite.db.prepare("SELECT MAX(indexed_at) as last_indexed FROM directories WHERE indexed_at > 0");
     const lastIndexedResult = lastIndexedStmt.get();
     const errorsStmt = sqlite.db.prepare("SELECT errors_json FROM files WHERE errors_json IS NOT NULL");
     const errorRows = errorsStmt.all();
@@ -265,6 +335,44 @@ async function getIndexStatus() {
         allErrors.push("Failed to parse error JSON");
       }
     });
+    const directoriesDetailStmt = sqlite.db.prepare(`
+      SELECT 
+        d.path,
+        d.status,
+        d.indexed_at,
+        COUNT(f.id) as files_count,
+        COALESCE(SUM(json_array_length(f.chunks_json)), 0) as chunks_count
+      FROM directories d
+      LEFT JOIN files f ON f.parent_dirs LIKE '%' || d.path || '%'
+      GROUP BY d.id, d.path, d.status, d.indexed_at
+      ORDER BY d.indexed_at DESC
+    `);
+    const directoryDetails = directoriesDetailStmt.all();
+    const directories = directoryDetails.map((row) => {
+      const errorsByDirStmt = sqlite.db.prepare(`
+        SELECT errors_json FROM files 
+        WHERE parent_dirs LIKE '%' || ? || '%' AND errors_json IS NOT NULL
+      `);
+      const dirErrors = errorsByDirStmt.all(row.path);
+      const dirErrorsList = [];
+      dirErrors.forEach((errorRow) => {
+        try {
+          const errors = JSON.parse(errorRow.errors_json);
+          dirErrorsList.push(...errors);
+        } catch {
+          dirErrorsList.push("Failed to parse error JSON");
+        }
+      });
+      return {
+        path: row.path,
+        status: row.status,
+        filesCount: row.files_count,
+        chunksCount: row.chunks_count,
+        lastIndexed: row.indexed_at && row.indexed_at > 0 ? new Date(row.indexed_at).toISOString() : null,
+        errors: dirErrorsList
+      };
+    });
+    const qdrantConsistency = await checkQdrantConsistency(sqlite, config);
     const fs = await import("fs");
     let databaseSize = "0 KB";
     try {
@@ -286,7 +394,9 @@ async function getIndexStatus() {
       chunksIndexed: chunksCount.count || 0,
       databaseSize,
       lastIndexed: lastIndexedResult.last_indexed ? new Date(lastIndexedResult.last_indexed).toISOString() : null,
-      errors: allErrors
+      errors: allErrors,
+      directories,
+      qdrantConsistency
     };
   } finally {
     sqlite.close();

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    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(`${this.config.storage.qdrantEndpoint}/health`);\n      return response.ok;\n    } catch {\n      return false;\n    }\n  }\n\n  async createCollection(): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const checkResponse = await fetch(`${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        throw new Error(`Failed to upsert points: ${response.statusText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to upsert points to Qdrant`, error as Error);\n    }\n  }\n\n  async searchPoints(vector: number[], limit: number = 10): Promise<QdrantPoint[]> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points/search`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify({\n          vector,\n          limit,\n          with_payload: true\n        })\n      });\n\n      if (!response.ok) {\n        throw new Error(`Failed to search points: ${response.statusText}`);\n      }\n\n      const data = await response.json();\n      return data.result.map((item: any) => ({\n        id: item.id,\n        vector: item.vector,\n        payload: item.payload,\n        score: item.score\n      }));\n    } catch (error) {\n      throw new StorageError(`Failed to search points in Qdrant`, error as Error);\n    }\n  }\n\n  async deletePoints(ids: string[]): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${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\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 any;\n      \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\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    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} - ${errorText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to upsert points to Qdrant`, error as Error);\n    }\n  }\n\n  async searchPoints(vector: number[], limit: number = 10): Promise<QdrantPoint[]> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${this.config.storage.qdrantEndpoint}/collections/${collectionName}/points/search`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify({\n          vector,\n          limit,\n          with_payload: true\n        })\n      });\n\n      if (!response.ok) {\n        throw new Error(`Failed to search points: ${response.statusText}`);\n      }\n\n      const data = await response.json();\n      return data.result.map((item: { id: string | number; vector: number[]; payload: Record<string, unknown>; score: number }) => ({\n        id: item.id,\n        vector: item.vector,\n        payload: item.payload,\n        score: item.score\n      }));\n    } catch (error) {\n      throw new StorageError(`Failed to search points in Qdrant`, error as Error);\n    }\n  }\n\n  async deletePoints(ids: (string | number)[]): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${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: ${response.statusText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to delete points from Qdrant`, error as Error);\n    }\n  }\n\n  async deletePointsByFileHash(fileHash: string): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const response = await fetch(`${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: 'fileHash',\n                match: { value: fileHash }\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 hash: ${response.status} ${response.statusText} - ${errorText}`);\n      }\n    } catch (error) {\n      throw new StorageError(`Failed to delete points by file hash 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 DirectoryStatus {\n  path: string;\n  status: string;\n  filesCount: number;\n  chunksCount: number;\n  lastIndexed: string | null;\n  errors: string[];\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  qdrantConsistency: {\n    isConsistent: boolean;\n    issues: string[];\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    \n    const lastIndexedStmt = sqlite.db.prepare('SELECT MAX(indexed_at) as last_indexed FROM directories WHERE indexed_at > 0');\n    const lastIndexedResult = lastIndexedStmt.get() as { last_indexed: number | null };\n    \n    const errorsStmt = sqlite.db.prepare('SELECT errors_json FROM files WHERE errors_json IS NOT NULL');\n    const errorRows = errorsStmt.all() as { errors_json: string }[];\n    \n    const allErrors: string[] = [];\n    errorRows.forEach(row => {\n      try {\n        const errors = JSON.parse(row.errors_json);\n        allErrors.push(...errors);\n      } catch {\n        allErrors.push('Failed to parse error JSON');\n      }\n    });\n    \n    const directoriesDetailStmt = sqlite.db.prepare(`\n      SELECT \n        d.path,\n        d.status,\n        d.indexed_at,\n        COUNT(f.id) as files_count,\n        COALESCE(SUM(json_array_length(f.chunks_json)), 0) as chunks_count\n      FROM directories d\n      LEFT JOIN files f ON f.parent_dirs LIKE '%' || d.path || '%'\n      GROUP BY d.id, d.path, d.status, d.indexed_at\n      ORDER BY d.indexed_at DESC\n    `);\n    const directoryDetails = directoriesDetailStmt.all() as { id: number; path: string; status: 'pending' | 'indexing' | 'completed' | 'failed'; indexed_at: number; files_count: number; chunks_count: number }[];\n    \n    const directories: DirectoryStatus[] = directoryDetails.map(row => {\n      const errorsByDirStmt = sqlite.db.prepare(`\n        SELECT errors_json FROM files \n        WHERE parent_dirs LIKE '%' || ? || '%' AND errors_json IS NOT NULL\n      `);\n      const dirErrors = errorsByDirStmt.all(row.path) as { errors_json: string }[];\n      \n      const dirErrorsList: string[] = [];\n      dirErrors.forEach(errorRow => {\n        try {\n          const errors = JSON.parse(errorRow.errors_json);\n          dirErrorsList.push(...errors);\n        } catch {\n          dirErrorsList.push('Failed to parse error JSON');\n        }\n      });\n      \n      return {\n        path: row.path,\n        status: row.status,\n        filesCount: row.files_count,\n        chunksCount: row.chunks_count,\n        lastIndexed: row.indexed_at && row.indexed_at > 0 ? new Date(row.indexed_at).toISOString() : null,\n        errors: dirErrorsList\n      };\n    });\n    \n    const qdrantConsistency = await checkQdrantConsistency(sqlite, config);\n    \n    const fs = await import('fs');\n    let databaseSize = '0 KB';\n    try {\n      const stats = fs.statSync(config.storage.sqlitePath);\n      const sizeInBytes = stats.size;\n      if (sizeInBytes > 1024 * 1024) {\n        databaseSize = `${(sizeInBytes / (1024 * 1024)).toFixed(2)} MB`;\n      } else if (sizeInBytes > 1024) {\n        databaseSize = `${(sizeInBytes / 1024).toFixed(2)} KB`;\n      } else {\n        databaseSize = `${sizeInBytes} bytes`;\n      }\n    } catch {\n      databaseSize = 'Unknown';\n    }\n    \n    return {\n      directoriesIndexed: directoriesCount.count,\n      filesIndexed: filesCount.count,\n      chunksIndexed: chunksCount.count || 0,\n      databaseSize,\n      lastIndexed: lastIndexedResult.last_indexed ? new Date(lastIndexedResult.last_indexed).toISOString() : null,\n      errors: allErrors,\n      directories,\n      qdrantConsistency\n    };\n  } finally {\n    sqlite.close();\n  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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "directory-indexer",
-  "version": "0.0.13",
+  "version": "0.0.14",
   "description": "AI-powered directory indexing with semantic search for MCP servers",
   "main": "dist/cli.js",
   "bin": {
@@ -18,7 +18,8 @@
     "lint": "eslint src tests --ext .ts",
     "typecheck": "tsc --noEmit",
     "clean": "rimraf dist",
-    "prepare": "npm run build"
+    "prepare": "npm run build",
+    "cli": "node bin/directory-indexer.js"
   },
   "keywords": [
     "mcp",