directory-indexer 0.1.1 → 0.1.3

package/README.md

@@ -58,6 +58,8 @@ Add to your MCP configuration:
 
 Your AI assistant will automatically start the MCP server and can now search your indexed files.
 
+**Advanced:** For organizing content into focused search areas, see [Workspace Support](#workspace-support).
+
 ## 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.
@@ -197,6 +199,33 @@ Configure with custom endpoints and data directory:
 }
 ```
 
+### Workspace Support
+
+Organize content into workspaces for focused searches:
+
+```json
+{
+  "mcpServers": {
+    "directory-indexer": {
+      "command": "npx",
+      "args": ["directory-indexer@latest", "serve"],
+      "env": {
+        "WORKSPACE_CUSTOMER_CASES": "C:\\Users\\john\\Documents\\Support\\Cases,C:\\Users\\john\\Documents\\Incidents",
+        "WORKSPACE_ENGINEERING_DOCS": "C:\\Users\\john\\Code\\API,C:\\Users\\john\\Code\\Web",
+        "WORKSPACE_COMPANY_POLICIES": "C:\\Users\\john\\Documents\\Policies,C:\\Users\\john\\Documents\\Procedures"
+      }
+    }
+  }
+}
+```
+
+**How workspaces work:**
+- Define workspace environments with `WORKSPACE_NAME` format
+- Use comma-separated paths or JSON arrays: `["path1", "path2"]`
+- Search within specific workspaces: _"Find issues about authentication in customer cases workspace"_
+- Your AI assistant can filter results to relevant workspace content
+- Use `server_info` to see available workspaces and their statistics
+
 ### CLI Usage
 
 For advanced users who prefer command-line usage, see [CLI Documentation](./docs/design.md#cli-usage).

package/dist/cli.js

@@ -10,6 +10,139 @@ import { getIndexStatus } from "./storage.js";
 import { Server } from "@modelcontextprotocol/sdk/server/index.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import { ListToolsRequestSchema, CallToolRequestSchema } from "@modelcontextprotocol/sdk/types.js";
+function isIndexToolArgs(args) {
+  return typeof args === "object" && args !== null && typeof args.directory_path === "string";
+}
+function isSearchToolArgs(args) {
+  return typeof args === "object" && args !== null && typeof args.query === "string";
+}
+function isSimilarFilesToolArgs(args) {
+  return typeof args === "object" && args !== null && typeof args.file_path === "string";
+}
+function isGetContentToolArgs(args) {
+  return typeof args === "object" && args !== null && typeof args.file_path === "string";
+}
+function isGetChunkToolArgs(args) {
+  return typeof args === "object" && args !== null && typeof args.file_path === "string" && typeof args.chunk_id === "string";
+}
+async function handleIndexTool(args, config) {
+  if (!isIndexToolArgs(args)) {
+    throw new Error("directory_path is required");
+  }
+  const paths = args.directory_path.split(",").map((p) => p.trim());
+  const result = await indexDirectories(paths, config);
+  let responseText = `Indexed ${result.indexed} files, skipped ${result.skipped} files, ${result.failed} failed`;
+  if (result.errors.length > 0) {
+    responseText += `
+Errors: [
+`;
+    result.errors.forEach((error) => {
+      responseText += `  '${error}'
+`;
+    });
+    responseText += `]`;
+  }
+  return {
+    content: [
+      {
+        type: "text",
+        text: responseText
+      }
+    ]
+  };
+}
+async function validateWorkspace(workspace) {
+  if (!workspace) return { workspace };
+  const config = (await import("./config.js")).loadConfig();
+  const { getAvailableWorkspaces } = await import("./config.js");
+  const availableWorkspaces = getAvailableWorkspaces(config);
+  if (availableWorkspaces.includes(workspace)) {
+    return { workspace };
+  }
+  const message = availableWorkspaces.length > 0 ? `Note: Workspace '${workspace}' not found. Searching all content instead. Available workspaces: ${availableWorkspaces.join(", ")}. Use server_info tool to see workspace details.` : `Note: Workspace '${workspace}' not found and no workspaces are configured. Searching all indexed content.`;
+  return { workspace: void 0, message };
+}
+async function handleSearchTool(args) {
+  if (!isSearchToolArgs(args)) {
+    throw new Error("query is required");
+  }
+  const { workspace, message } = await validateWorkspace(args.workspace);
+  const results = await searchContent(args.query, { limit: args.limit || 10, workspace });
+  const response = message ? `${message}
+
+${JSON.stringify(results, null, 2)}` : JSON.stringify(results, null, 2);
+  return {
+    content: [{ type: "text", text: response }]
+  };
+}
+async function handleSimilarFilesTool(args) {
+  if (!isSimilarFilesToolArgs(args)) {
+    throw new Error("file_path is required");
+  }
+  const { workspace, message } = await validateWorkspace(args.workspace);
+  const results = await findSimilarFiles(args.file_path, args.limit || 10, workspace);
+  const response = message ? `${message}
+
+${JSON.stringify(results, null, 2)}` : JSON.stringify(results, null, 2);
+  return {
+    content: [{ type: "text", text: response }]
+  };
+}
+async function handleGetContentTool(args) {
+  if (!isGetContentToolArgs(args)) {
+    throw new Error("file_path is required");
+  }
+  const content = await getFileContent(args.file_path, args.chunks);
+  return {
+    content: [
+      {
+        type: "text",
+        text: content
+      }
+    ]
+  };
+}
+async function handleGetChunkTool(args) {
+  if (!isGetChunkToolArgs(args)) {
+    throw new Error("file_path and chunk_id are required");
+  }
+  const content = await getChunkContent(args.file_path, args.chunk_id);
+  return {
+    content: [
+      {
+        type: "text",
+        text: content
+      }
+    ]
+  };
+}
+async function handleServerInfoTool(version) {
+  const status = await getIndexStatus();
+  return {
+    content: [
+      {
+        type: "text",
+        text: JSON.stringify({
+          name: "directory-indexer",
+          version,
+          status
+        }, null, 2)
+      }
+    ]
+  };
+}
+function formatErrorResponse(error) {
+  const errorMessage = error instanceof Error ? error.message : "Unknown error";
+  return {
+    content: [
+      {
+        type: "text",
+        text: `Error: ${errorMessage}`
+      }
+    ],
+    isError: true
+  };
+}
 const __dirname$1 = dirname(fileURLToPath(import.meta.url));
 const packageJsonPath$1 = join(__dirname$1, "../package.json");
 const packageJson$1 = JSON.parse(readFileSync(packageJsonPath$1, "utf-8"));
@@ -64,11 +197,11 @@ How it works:
 - Returns files ranked by relevance score
 
 Examples:
-- "database configuration" - finds config files, documentation about DB setup
-- "error handling patterns" - finds code files with exception handling
-- "authentication implementation" - finds auth-related code and docs
-- "API documentation" - finds API guides, endpoint definitions
-- "deployment scripts" - finds CI/CD configs, deployment automation
+- "database configuration and connection pooling setup" - finds config files, documentation about DB setup
+- "comprehensive error handling patterns and exception management" - finds code files with exception handling
+- "JWT authentication implementation and session management" - finds auth-related code and docs
+- "REST API documentation and endpoint specifications" - finds API guides, endpoint definitions
+- "Docker deployment scripts and CI/CD pipeline configuration" - finds deployment automation
 
 Returns files with similarity scores and chunk information. Use get_content to retrieve full file content or get_chunk to retrieve specific chunk content by chunk ID.
 - Groups results by file to avoid duplicates from multiple matching sections
@@ -80,9 +213,9 @@ Response format:
 - Average similarity score calculated across all matching chunks per file
 
 Example queries:
-- "error handling patterns" (finds try/catch, error classes, logging)
-- "database migration scripts" (finds SQL, schema changes, migration files)
-- "authentication middleware" (finds auth logic, JWT handling, middleware functions)`,
+- "error handling patterns and exception management strategies" (finds try/catch, error classes, logging)
+- "database migration scripts and schema versioning approaches" (finds SQL, schema changes, migration files)
+- "authentication middleware and JWT token validation logic" (finds auth logic, JWT handling, middleware functions)`,
     inputSchema: {
       type: "object",
       properties: {
@@ -94,6 +227,10 @@ Example queries:
           type: "number",
           description: "Maximum number of files to return (default: 10). Each file may contain multiple matching chunks.",
           default: 10
+        },
+        workspace: {
+          type: "string",
+          description: "Optional workspace name to filter search results. Only files within the workspace directories will be searched. IMPORTANT: Use server_info tool first to discover available workspace names - using invalid workspace names will result in empty results."
         }
       },
       required: ["query"]
@@ -132,6 +269,10 @@ Returns file paths with similarity scores. Use get_content to read full files or
           type: "number",
           description: "Maximum number of similar files to return (default: 10). Results are sorted by similarity score.",
           default: 10
+        },
+        workspace: {
+          type: "string",
+          description: "Optional workspace name to filter results. Only files within the workspace directories will be considered. IMPORTANT: Use server_info tool first to discover available workspace names - using invalid workspace names will result in empty results."
         }
       },
       required: ["file_path"]
@@ -216,6 +357,7 @@ Returns chunk content as text. Use this with chunk IDs from search results to ge
     description: `Get information about server status and indexed content. Shows what directories and files are available for search.
 
 When to use this tool:
+- REQUIRED: Check available workspace names before using workspace parameter in search or similar_files tools
 - Check what content is already indexed before performing searches
 - Verify system is working properly
 - See indexing statistics and status
@@ -225,14 +367,16 @@ How it works:
 - Reports total indexed directories, files, and chunks
 - Shows database size and last indexing time
 - Lists all indexed directories with file counts
+- Lists all configured workspaces with their paths and file counts
 - Reports any errors or issues
 
 Examples:
+- Check workspaces before searching: "What workspaces are available?"
 - Check before searching: "What content is indexed?"
 - Verify after indexing: "Did the indexing complete successfully?"
 - Monitor system: "How many files are searchable?"
 
-Returns server version, indexing statistics, directory list, and any errors. Use this to understand what content is available for search and similar_files tools.`,
+Returns server version, indexing statistics, directory list, workspace information, and any errors. IMPORTANT: Always use this tool first to discover available workspace names when you need to search within specific workspaces.`,
     inputSchema: {
       type: "object",
       properties: {},
@@ -261,106 +405,23 @@ async function startMcpServer(config) {
     const { name, arguments: args } = request.params;
     try {
       switch (name) {
-        case "index": {
-          if (!args || typeof args.directory_path !== "string") {
-            throw new Error("directory_path is required");
-          }
-          const paths = args.directory_path.split(",").map((p) => p.trim());
-          const result = await indexDirectories(paths, config);
-          return {
-            content: [
-              {
-                type: "text",
-                text: `Indexed ${result.indexed} files, skipped ${result.skipped} files, ${result.errors.length} errors`
-              }
-            ]
-          };
-        }
-        case "search": {
-          if (!args || typeof args.query !== "string") {
-            throw new Error("query is required");
-          }
-          const results = await searchContent(args.query, { limit: args.limit || 10 });
-          return {
-            content: [
-              {
-                type: "text",
-                text: JSON.stringify(results, null, 2)
-              }
-            ]
-          };
-        }
-        case "similar_files": {
-          if (!args || typeof args.file_path !== "string") {
-            throw new Error("file_path is required");
-          }
-          const results = await findSimilarFiles(args.file_path, args.limit || 10);
-          return {
-            content: [
-              {
-                type: "text",
-                text: JSON.stringify(results, null, 2)
-              }
-            ]
-          };
-        }
-        case "get_content": {
-          if (!args || typeof args.file_path !== "string") {
-            throw new Error("file_path is required");
-          }
-          const content = await getFileContent(args.file_path, args.chunks);
-          return {
-            content: [
-              {
-                type: "text",
-                text: content
-              }
-            ]
-          };
-        }
-        case "get_chunk": {
-          if (!args || typeof args.file_path !== "string" || typeof args.chunk_id !== "string") {
-            throw new Error("file_path and chunk_id are required");
-          }
-          const content = await getChunkContent(args.file_path, args.chunk_id);
-          return {
-            content: [
-              {
-                type: "text",
-                text: content
-              }
-            ]
-          };
-        }
-        case "server_info": {
-          const status = await getIndexStatus();
-          return {
-            content: [
-              {
-                type: "text",
-                text: JSON.stringify({
-                  name: "directory-indexer",
-                  version: VERSION$1,
-                  status
-                }, null, 2)
-              }
-            ]
-          };
-        }
+        case "index":
+          return await handleIndexTool(args, config);
+        case "search":
+          return await handleSearchTool(args);
+        case "similar_files":
+          return await handleSimilarFilesTool(args);
+        case "get_content":
+          return await handleGetContentTool(args);
+        case "get_chunk":
+          return await handleGetChunkTool(args);
+        case "server_info":
+          return await handleServerInfoTool(VERSION$1);
         default:
           throw new Error(`Unknown tool: ${name}`);
       }
     } catch (error) {
-      const errorMessage = error instanceof Error ? error.message : "Unknown error";
-      return {
-        content: [
-          {
-            type: "text",
-            text: `Error: ${errorMessage}`
-          }
-        ],
-        isError: true
-      };
+      return formatErrorResponse(error);
     }
   });
   const transport = new StdioServerTransport();
@@ -381,9 +442,13 @@ async function main() {
       const config = await loadConfig({ verbose: options.verbose });
       console.log(`Indexing ${paths.length} ${paths.length === 1 ? "directory" : "directories"}: ${paths.join(", ")}`);
       const result = await indexDirectories(paths, config);
-      console.log(`Indexed ${result.indexed} files, skipped ${result.skipped} files, ${result.errors.length} errors`);
-      if (result.errors.length > 0 && config.verbose) {
-        console.log("Errors:", result.errors);
+      console.log(`Indexed ${result.indexed} files, skipped ${result.skipped} files, ${result.failed} failed`);
+      if (result.errors.length > 0) {
+        console.log(`Errors: [`);
+        result.errors.forEach((error) => {
+          console.log(`  '${error}'`);
+        });
+        console.log(`]`);
       }
     } catch (error) {
       console.error("Error indexing directories:", error);

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, getChunkContent } 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 to make their files searchable. Processes files to create vector embeddings for semantic search.\n\nWhen to use this tool:\n- User specifically requests indexing a directory as a knowledge base\n- Adding new documentation, code repositories, or file collections to search\n- Updating index when many files have changed\n\nHow it works:\n- Recursively scans directories for supported file types\n- Extracts text content and splits into chunks\n- Generates vector embeddings for semantic similarity\n- Stores in database for fast retrieval\n\nExamples:\n- Index documentation: \"/home/user/docs/project-wiki\"\n- Index codebase: \"/home/user/projects/api-server\"\n- Index multiple directories: \"/home/user/docs,/home/user/configs\"\n\nIndexing can take several minutes for large directories. Most users will already have directories indexed and can directly use search tool. Use server_info to check current indexing status first.`,\n    inputSchema: {\n      type: 'object',\n      properties: {\n        directory_path: {\n          type: 'string',\n          description: 'Comma-separated list of absolute directory paths to index. Must be absolute paths since MCP server runs independently. Examples: \"/home/user/projects\" (Unix) or \"C:\\\\Users\\\\user\\\\projects\" (Windows)'\n        }\n      },\n      required: ['directory_path']\n    }\n  },\n  {\n    name: 'search',\n    description: `Search indexed files using natural language queries. Finds files containing content semantically similar to the query.\n\nWhen to use this tool:\n- Find documentation, guides, or explanations about specific topics\n- Locate code files implementing certain functionality or patterns\n- Discover configuration files, scripts, or settings related to a topic\n- Search for files covering specific concepts or technologies\n\nHow it works:\n- Converts query to vector embedding using semantic similarity\n- Searches all indexed file chunks for relevant content\n- Groups results by file and calculates average relevance scores\n- Returns files ranked by relevance score\n\nExamples:\n- \"database configuration\" - finds config files, documentation about DB setup\n- \"error handling patterns\" - finds code files with exception handling\n- \"authentication implementation\" - finds auth-related code and docs\n- \"API documentation\" - finds API guides, endpoint definitions\n- \"deployment scripts\" - finds CI/CD configs, deployment automation\n\nReturns files with similarity scores and chunk information. Use get_content to retrieve full file content or get_chunk to retrieve specific chunk content by chunk ID.\n- Groups results by file to avoid duplicates from multiple matching sections\n\nResponse format:\n- Returns lightweight metadata including file paths, relevance scores, and chunk IDs\n- Use 'get_chunk' or 'get_content' tools to fetch actual content from search results\n- Chunks are sorted by relevance score within each file\n- Average similarity score calculated across all matching chunks per file\n\nExample queries:\n- \"error handling patterns\" (finds try/catch, error classes, logging)\n- \"database migration scripts\" (finds SQL, schema changes, migration files)\n- \"authentication middleware\" (finds auth logic, JWT handling, middleware functions)`,\n    inputSchema: {\n      type: 'object',\n      properties: {\n        query: {\n          type: 'string',\n          description: 'Natural language search query describing what you are looking for. Can be concepts, functionality, or specific technical terms.'\n        },\n        limit: {\n          type: 'number',\n          description: 'Maximum number of files to return (default: 10). Each file may contain multiple matching chunks.',\n          default: 10\n        }\n      },\n      required: ['query']\n    }\n  },\n  {\n    name: 'similar_files',\n    description: `Find files with content similar to a reference file. Uses semantic similarity to find related documents, code files, or any text content.\n\nWhen to use this tool:\n- Find documentation similar to a specific guide or README\n- Locate related code files, configuration files, or scripts\n- Discover alternative implementations or approaches\n- Find files covering similar topics or concepts\n\nHow it works:\n- Analyzes the semantic content of the reference file\n- Compares against all indexed files using vector similarity\n- Returns files ranked by content similarity score\n\nExamples:\n- Given \"deployment-guide.md\" - finds other deployment docs, CI/CD guides, infrastructure setup\n- Given \"troubleshooting.md\" - finds other troubleshooting guides, FAQ files, error documentation\n- Given \"config.yaml\" - finds other configuration files, settings, environment setups\n- Given \"auth.py\" - finds other authentication modules, security code, middleware\n\nReturns file paths with similarity scores. Use get_content to read full files or get_chunk for specific sections.`,\n    inputSchema: {\n      type: 'object',\n      properties: {\n        file_path: {\n          type: 'string',\n          description: 'Absolute or relative path to the reference file. This file must have been previously indexed.'\n        },\n        limit: {\n          type: 'number',\n          description: 'Maximum number of similar files to return (default: 10). Results are sorted by similarity score.',\n          default: 10\n        }\n      },\n      required: ['file_path']\n    }\n  },\n  {\n    name: 'get_content',\n    description: `Retrieve the full content of a file or specific chunks. Reads files directly from the filesystem.\n\nWhen to use this tool:\n- Get complete file content after finding files through search\n- Read documentation, code files, or configuration files for analysis\n- Extract specific sections of large files using chunk ranges\n- Access any text-based file content\n\nHow it works:\n- Reads files directly from filesystem (not from search index)\n- Returns entire file by default\n- Can return specific chunk ranges for indexed files\n- Preserves original formatting and content\n\nExamples:\n- Get full file: file_path=\"/home/user/docs/api.md\"\n- Get specific chunks: file_path=\"/home/user/code/main.py\", chunks=\"2-5\"\n- Get single chunk: file_path=\"/home/user/config.json\", chunks=\"1\"\n\nReturns file content as text. Use this after search or similar_files to read actual content.`,\n    inputSchema: {\n      type: 'object',\n      properties: {\n        file_path: {\n          type: 'string',\n          description: 'Absolute or relative path to the file to retrieve. File must be readable and text-based.'\n        },\n        chunks: {\n          type: 'string',\n          description: 'Optional chunk range specification. Examples: \"3\" (single chunk), \"2-5\" (chunks 2 through 5), \"1-3\" (first three chunks). Only works for indexed files.'\n        }\n      },\n      required: ['file_path']\n    }\n  },\n  {\n    name: 'get_chunk',\n    description: `Retrieve content of a specific chunk from an indexed file. Gets exact text segments identified during search.\n\nWhen to use this tool:\n- Get specific relevant sections after performing a search\n- Access only the most pertinent parts of large files\n- Retrieve content from high-scoring chunks identified in search results\n- Avoid reading entire files when only specific sections are needed\n\nHow it works:\n- Files are split into overlapping text chunks during indexing\n- Each chunk has a sequential ID (\"0\", \"1\", \"2\", etc.)\n- Search results include chunk IDs for relevant sections\n- Returns the exact content that was semantically matched\n\nExamples:\n- After search returns chunk \"3\" from \"api-docs.md\" with high score\n- Get chunk content: file_path=\"/docs/api-docs.md\", chunk_id=\"3\"\n- Returns the specific text segment that matched your query\n\nReturns chunk content as text. Use this with chunk IDs from search results to get precise content sections.`,\n    inputSchema: {\n      type: 'object',\n      properties: {\n        file_path: {\n          type: 'string',\n          description: 'Absolute or relative path to the indexed file containing the desired chunk.'\n        },\n        chunk_id: {\n          type: 'string',\n          description: 'ID of the specific chunk to retrieve. This is typically obtained from search results and is a sequential string like \"0\", \"1\", \"2\", etc.'\n        }\n      },\n      required: ['file_path', 'chunk_id']\n    }\n  },\n  {\n    name: 'server_info',\n    description: `Get information about server status and indexed content. Shows what directories and files are available for search.\n\nWhen to use this tool:\n- Check what content is already indexed before performing searches\n- Verify system is working properly\n- See indexing statistics and status\n- Understand scope of available searchable content\n\nHow it works:\n- Reports total indexed directories, files, and chunks\n- Shows database size and last indexing time\n- Lists all indexed directories with file counts\n- Reports any errors or issues\n\nExamples:\n- Check before searching: \"What content is indexed?\"\n- Verify after indexing: \"Did the indexing complete successfully?\"\n- Monitor system: \"How many files are searchable?\"\n\nReturns server version, indexing statistics, directory list, and any errors. Use this to understand what content is available for search and similar_files tools.`,\n    inputSchema: {\n      type: 'object',\n      properties: {},\n      additionalProperties: false\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 'get_chunk': {\n          if (!args || typeof args.file_path !== 'string' || typeof args.chunk_id !== 'string') {\n            throw new Error('file_path and chunk_id are required');\n          }\n          const content = await getChunkContent(args.file_path, args.chunk_id);\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} ${paths.length === 1 ? 'directory' : 'directories'}: ${paths.join(', ')}`);\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('-c, --show-chunks', 'Show individual chunk scores and IDs')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (query: string, options) => {\n      try {\n        await 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: ${result.score.toFixed(3)} (${result.matchingChunks} chunks)`);\n          \n          if (options.showChunks && result.chunks.length > 0) {\n            console.log(`   Chunks:`);\n            result.chunks.forEach(chunk => {\n              console.log(`     - Chunk ${chunk.chunkId}: ${chunk.score.toFixed(3)}`);\n            });\n          }\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('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 available for AI search`);\n        console.log(`  • Database storage: ${status.databaseSize}`);\n        console.log(`  • Most recent indexing: ${status.lastIndexed || 'No indexing performed yet'}`);\n        \n        if (status.errors.length > 0) {\n          console.log(`  • Processing errors encountered: ${status.errors.length}`);\n          if (options.verbose) {\n            console.log('');\n            console.log('RECENT ERRORS:');\n            status.errors.slice(0, 5).forEach(error => {\n              console.log(`  - ${error}`);\n            });\n          }\n        }\n        \n        console.log('');\n        console.log('INDEXED DIRECTORIES:');\n        if (status.directories.length === 0) {\n          console.log('  No directories have been indexed yet.');\n          console.log('  Run \"directory-indexer index <path>\" to start indexing.');\n        } else {\n          status.directories.forEach(dir => {\n            console.log('');\n            console.log(`  Directory: ${dir.path}`);\n            console.log(`    • Indexing status: ${dir.status}`);\n            console.log(`    • Files processed: ${dir.filesCount}`);\n            console.log(`    • Searchable chunks: ${dir.chunksCount}`);\n            console.log(`    • Last indexed: ${dir.lastIndexed || 'Never completed'}`);\n            if (dir.errors.length > 0) {\n              console.log(`    • Files with errors: ${dir.errors.length}`);\n              if (options.verbose) {\n                console.log('    • Recent errors:');\n                dir.errors.slice(0, 3).forEach(error => {\n                  console.log(`      - ${error}`);\n                });\n              }\n            }\n          });\n        }\n        \n        if (!status.qdrantConsistency.isConsistent) {\n          console.log('');\n          console.log('SYSTEM STATUS:');\n          status.qdrantConsistency.issues.forEach(issue => {\n            console.log(`  • ${issue}`);\n          });\n          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      } 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+{"version":3,"file":"cli.js","sources":["../src/mcp-handlers.ts","../src/mcp.ts","../src/cli.ts"],"sourcesContent":["import { Config } from './config.js';\nimport { indexDirectories } from './indexing.js';\nimport { searchContent, findSimilarFiles, getFileContent, getChunkContent } from './search.js';\nimport { getIndexStatus } from './storage.js';\nimport { CallToolResult } from '@modelcontextprotocol/sdk/types.js';\n\n// Type-safe interfaces for MCP tool arguments\ninterface IndexToolArgs {\n  directory_path: string;\n}\n\ninterface SearchToolArgs {\n  query: string;\n  limit?: number;\n  workspace?: string;\n}\n\ninterface SimilarFilesToolArgs {\n  file_path: string;\n  limit?: number;\n  workspace?: string;\n}\n\ninterface GetContentToolArgs {\n  file_path: string;\n  chunks?: string;\n}\n\ninterface GetChunkToolArgs {\n  file_path: string;\n  chunk_id: string;\n}\n\n// Type guard functions\nfunction isIndexToolArgs(args: unknown): args is IndexToolArgs {\n  return typeof args === 'object' && args !== null && \n         typeof (args as IndexToolArgs).directory_path === 'string';\n}\n\nfunction isSearchToolArgs(args: unknown): args is SearchToolArgs {\n  return typeof args === 'object' && args !== null && \n         typeof (args as SearchToolArgs).query === 'string';\n}\n\nfunction isSimilarFilesToolArgs(args: unknown): args is SimilarFilesToolArgs {\n  return typeof args === 'object' && args !== null && \n         typeof (args as SimilarFilesToolArgs).file_path === 'string';\n}\n\nfunction isGetContentToolArgs(args: unknown): args is GetContentToolArgs {\n  return typeof args === 'object' && args !== null && \n         typeof (args as GetContentToolArgs).file_path === 'string';\n}\n\nfunction isGetChunkToolArgs(args: unknown): args is GetChunkToolArgs {\n  return typeof args === 'object' && args !== null && \n         typeof (args as GetChunkToolArgs).file_path === 'string' &&\n         typeof (args as GetChunkToolArgs).chunk_id === 'string';\n}\n\nexport async function handleIndexTool(args: unknown, config: Config): Promise<CallToolResult> {\n  if (!isIndexToolArgs(args)) {\n    throw new Error('directory_path is required');\n  }\n  \n  const paths = args.directory_path.split(',').map((p: string) => p.trim());\n  const result = await indexDirectories(paths, config);\n  \n  let responseText = `Indexed ${result.indexed} files, skipped ${result.skipped} files, ${result.failed} failed`;\n  \n  if (result.errors.length > 0) {\n    responseText += `\\nErrors: [\\n`;\n    result.errors.forEach(error => {\n      responseText += `  '${error}'\\n`;\n    });\n    responseText += `]`;\n  }\n  \n  return {\n    content: [\n      {\n        type: 'text',\n        text: responseText\n      }\n    ]\n  };\n}\n\nasync function validateWorkspace(workspace?: string): Promise<{ workspace?: string; message?: string }> {\n  if (!workspace) return { workspace };\n  \n  const config = (await import('./config.js')).loadConfig();\n  const { getAvailableWorkspaces } = await import('./config.js');\n  const availableWorkspaces = getAvailableWorkspaces(config);\n  \n  if (availableWorkspaces.includes(workspace)) {\n    return { workspace };\n  }\n  \n  // Invalid workspace - search all content with informative message\n  const message = availableWorkspaces.length > 0\n    ? `Note: Workspace '${workspace}' not found. Searching all content instead. Available workspaces: ${availableWorkspaces.join(', ')}. Use server_info tool to see workspace details.`\n    : `Note: Workspace '${workspace}' not found and no workspaces are configured. Searching all indexed content.`;\n  \n  return { workspace: undefined, message };\n}\n\nexport async function handleSearchTool(args: unknown): Promise<CallToolResult> {\n  if (!isSearchToolArgs(args)) {\n    throw new Error('query is required');\n  }\n  \n  const { workspace, message } = await validateWorkspace(args.workspace);\n  const results = await searchContent(args.query, { limit: args.limit || 10, workspace });\n  \n  const response = message \n    ? `${message}\\n\\n${JSON.stringify(results, null, 2)}`\n    : JSON.stringify(results, null, 2);\n  \n  return {\n    content: [{ type: 'text', text: response }]\n  };\n}\n\nexport async function handleSimilarFilesTool(args: unknown): Promise<CallToolResult> {\n  if (!isSimilarFilesToolArgs(args)) {\n    throw new Error('file_path is required');\n  }\n  \n  const { workspace, message } = await validateWorkspace(args.workspace);\n  const results = await findSimilarFiles(args.file_path, args.limit || 10, workspace);\n  \n  const response = message \n    ? `${message}\\n\\n${JSON.stringify(results, null, 2)}`\n    : JSON.stringify(results, null, 2);\n  \n  return {\n    content: [{ type: 'text', text: response }]\n  };\n}\n\nexport async function handleGetContentTool(args: unknown): Promise<CallToolResult> {\n  if (!isGetContentToolArgs(args)) {\n    throw new Error('file_path is required');\n  }\n  \n  const content = await getFileContent(args.file_path, args.chunks);\n  \n  return {\n    content: [\n      {\n        type: 'text',\n        text: content\n      }\n    ]\n  };\n}\n\nexport async function handleGetChunkTool(args: unknown): Promise<CallToolResult> {\n  if (!isGetChunkToolArgs(args)) {\n    throw new Error('file_path and chunk_id are required');\n  }\n  \n  const content = await getChunkContent(args.file_path, args.chunk_id);\n  \n  return {\n    content: [\n      {\n        type: 'text',\n        text: content\n      }\n    ]\n  };\n}\n\nexport async function handleServerInfoTool(version: string): Promise<CallToolResult> {\n  const status = await getIndexStatus();\n  \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\nexport function formatErrorResponse(error: unknown): CallToolResult {\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}","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 { \n  handleIndexTool, \n  handleSearchTool, \n  handleSimilarFilesTool, \n  handleGetContentTool, \n  handleGetChunkTool, \n  handleServerInfoTool,\n  formatErrorResponse\n} from './mcp-handlers.js';\n\n// Read version from package.json\nconst __dirname = dirname(fileURLToPath(import.meta.url));\nconst packageJsonPath = join(__dirname, '../package.json');\nconst packageJson = JSON.parse(readFileSync(packageJsonPath, 'utf-8'));\nconst VERSION = packageJson.version;\n\nconst MCP_TOOLS: Tool[] = [\n  {\n    name: 'index',\n    description: `Index directories to make their files searchable. Processes files to create vector embeddings for semantic search.\n\nWhen to use this tool:\n- User specifically requests indexing a directory as a knowledge base\n- Adding new documentation, code repositories, or file collections to search\n- Updating index when many files have changed\n\nHow it works:\n- Recursively scans directories for supported file types\n- Extracts text content and splits into chunks\n- Generates vector embeddings for semantic similarity\n- Stores in database for fast retrieval\n\nExamples:\n- Index documentation: \"/home/user/docs/project-wiki\"\n- Index codebase: \"/home/user/projects/api-server\"\n- Index multiple directories: \"/home/user/docs,/home/user/configs\"\n\nIndexing can take several minutes for large directories. Most users will already have directories indexed and can directly use search tool. Use server_info to check current indexing status first.`,\n    inputSchema: {\n      type: 'object',\n      properties: {\n        directory_path: {\n          type: 'string',\n          description: 'Comma-separated list of absolute directory paths to index. Must be absolute paths since MCP server runs independently. Examples: \"/home/user/projects\" (Unix) or \"C:\\\\Users\\\\user\\\\projects\" (Windows)'\n        }\n      },\n      required: ['directory_path']\n    }\n  },\n  {\n    name: 'search',\n    description: `Search indexed files using natural language queries. Finds files containing content semantically similar to the query.\n\nWhen to use this tool:\n- Find documentation, guides, or explanations about specific topics\n- Locate code files implementing certain functionality or patterns\n- Discover configuration files, scripts, or settings related to a topic\n- Search for files covering specific concepts or technologies\n\nHow it works:\n- Converts query to vector embedding using semantic similarity\n- Searches all indexed file chunks for relevant content\n- Groups results by file and calculates average relevance scores\n- Returns files ranked by relevance score\n\nExamples:\n- \"database configuration and connection pooling setup\" - finds config files, documentation about DB setup\n- \"comprehensive error handling patterns and exception management\" - finds code files with exception handling\n- \"JWT authentication implementation and session management\" - finds auth-related code and docs\n- \"REST API documentation and endpoint specifications\" - finds API guides, endpoint definitions\n- \"Docker deployment scripts and CI/CD pipeline configuration\" - finds deployment automation\n\nReturns files with similarity scores and chunk information. Use get_content to retrieve full file content or get_chunk to retrieve specific chunk content by chunk ID.\n- Groups results by file to avoid duplicates from multiple matching sections\n\nResponse format:\n- Returns lightweight metadata including file paths, relevance scores, and chunk IDs\n- Use 'get_chunk' or 'get_content' tools to fetch actual content from search results\n- Chunks are sorted by relevance score within each file\n- Average similarity score calculated across all matching chunks per file\n\nExample queries:\n- \"error handling patterns and exception management strategies\" (finds try/catch, error classes, logging)\n- \"database migration scripts and schema versioning approaches\" (finds SQL, schema changes, migration files)\n- \"authentication middleware and JWT token validation logic\" (finds auth logic, JWT handling, middleware functions)`,\n    inputSchema: {\n      type: 'object',\n      properties: {\n        query: {\n          type: 'string',\n          description: 'Natural language search query describing what you are looking for. Can be concepts, functionality, or specific technical terms.'\n        },\n        limit: {\n          type: 'number',\n          description: 'Maximum number of files to return (default: 10). Each file may contain multiple matching chunks.',\n          default: 10\n        },\n        workspace: {\n          type: 'string',\n          description: 'Optional workspace name to filter search results. Only files within the workspace directories will be searched. IMPORTANT: Use server_info tool first to discover available workspace names - using invalid workspace names will result in empty results.'\n        }\n      },\n      required: ['query']\n    }\n  },\n  {\n    name: 'similar_files',\n    description: `Find files with content similar to a reference file. Uses semantic similarity to find related documents, code files, or any text content.\n\nWhen to use this tool:\n- Find documentation similar to a specific guide or README\n- Locate related code files, configuration files, or scripts\n- Discover alternative implementations or approaches\n- Find files covering similar topics or concepts\n\nHow it works:\n- Analyzes the semantic content of the reference file\n- Compares against all indexed files using vector similarity\n- Returns files ranked by content similarity score\n\nExamples:\n- Given \"deployment-guide.md\" - finds other deployment docs, CI/CD guides, infrastructure setup\n- Given \"troubleshooting.md\" - finds other troubleshooting guides, FAQ files, error documentation\n- Given \"config.yaml\" - finds other configuration files, settings, environment setups\n- Given \"auth.py\" - finds other authentication modules, security code, middleware\n\nReturns file paths with similarity scores. Use get_content to read full files or get_chunk for specific sections.`,\n    inputSchema: {\n      type: 'object',\n      properties: {\n        file_path: {\n          type: 'string',\n          description: 'Absolute or relative path to the reference file. This file must have been previously indexed.'\n        },\n        limit: {\n          type: 'number',\n          description: 'Maximum number of similar files to return (default: 10). Results are sorted by similarity score.',\n          default: 10\n        },\n        workspace: {\n          type: 'string',\n          description: 'Optional workspace name to filter results. Only files within the workspace directories will be considered. IMPORTANT: Use server_info tool first to discover available workspace names - using invalid workspace names will result in empty results.'\n        }\n      },\n      required: ['file_path']\n    }\n  },\n  {\n    name: 'get_content',\n    description: `Retrieve the full content of a file or specific chunks. Reads files directly from the filesystem.\n\nWhen to use this tool:\n- Get complete file content after finding files through search\n- Read documentation, code files, or configuration files for analysis\n- Extract specific sections of large files using chunk ranges\n- Access any text-based file content\n\nHow it works:\n- Reads files directly from filesystem (not from search index)\n- Returns entire file by default\n- Can return specific chunk ranges for indexed files\n- Preserves original formatting and content\n\nExamples:\n- Get full file: file_path=\"/home/user/docs/api.md\"\n- Get specific chunks: file_path=\"/home/user/code/main.py\", chunks=\"2-5\"\n- Get single chunk: file_path=\"/home/user/config.json\", chunks=\"1\"\n\nReturns file content as text. Use this after search or similar_files to read actual content.`,\n    inputSchema: {\n      type: 'object',\n      properties: {\n        file_path: {\n          type: 'string',\n          description: 'Absolute or relative path to the file to retrieve. File must be readable and text-based.'\n        },\n        chunks: {\n          type: 'string',\n          description: 'Optional chunk range specification. Examples: \"3\" (single chunk), \"2-5\" (chunks 2 through 5), \"1-3\" (first three chunks). Only works for indexed files.'\n        }\n      },\n      required: ['file_path']\n    }\n  },\n  {\n    name: 'get_chunk',\n    description: `Retrieve content of a specific chunk from an indexed file. Gets exact text segments identified during search.\n\nWhen to use this tool:\n- Get specific relevant sections after performing a search\n- Access only the most pertinent parts of large files\n- Retrieve content from high-scoring chunks identified in search results\n- Avoid reading entire files when only specific sections are needed\n\nHow it works:\n- Files are split into overlapping text chunks during indexing\n- Each chunk has a sequential ID (\"0\", \"1\", \"2\", etc.)\n- Search results include chunk IDs for relevant sections\n- Returns the exact content that was semantically matched\n\nExamples:\n- After search returns chunk \"3\" from \"api-docs.md\" with high score\n- Get chunk content: file_path=\"/docs/api-docs.md\", chunk_id=\"3\"\n- Returns the specific text segment that matched your query\n\nReturns chunk content as text. Use this with chunk IDs from search results to get precise content sections.`,\n    inputSchema: {\n      type: 'object',\n      properties: {\n        file_path: {\n          type: 'string',\n          description: 'Absolute or relative path to the indexed file containing the desired chunk.'\n        },\n        chunk_id: {\n          type: 'string',\n          description: 'ID of the specific chunk to retrieve. This is typically obtained from search results and is a sequential string like \"0\", \"1\", \"2\", etc.'\n        }\n      },\n      required: ['file_path', 'chunk_id']\n    }\n  },\n  {\n    name: 'server_info',\n    description: `Get information about server status and indexed content. Shows what directories and files are available for search.\n\nWhen to use this tool:\n- REQUIRED: Check available workspace names before using workspace parameter in search or similar_files tools\n- Check what content is already indexed before performing searches\n- Verify system is working properly\n- See indexing statistics and status\n- Understand scope of available searchable content\n\nHow it works:\n- Reports total indexed directories, files, and chunks\n- Shows database size and last indexing time\n- Lists all indexed directories with file counts\n- Lists all configured workspaces with their paths and file counts\n- Reports any errors or issues\n\nExamples:\n- Check workspaces before searching: \"What workspaces are available?\"\n- Check before searching: \"What content is indexed?\"\n- Verify after indexing: \"Did the indexing complete successfully?\"\n- Monitor system: \"How many files are searchable?\"\n\nReturns server version, indexing statistics, directory list, workspace information, and any errors. IMPORTANT: Always use this tool first to discover available workspace names when you need to search within specific workspaces.`,\n    inputSchema: {\n      type: 'object',\n      properties: {},\n      additionalProperties: false\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          return await handleIndexTool(args, config);\n        \n        case 'search':\n          return await handleSearchTool(args);\n        \n        case 'similar_files':\n          return await handleSimilarFilesTool(args);\n        \n        case 'get_content':\n          return await handleGetContentTool(args);\n        \n        case 'get_chunk':\n          return await handleGetChunkTool(args);\n        \n        case 'server_info':\n          return await handleServerInfoTool(VERSION);\n        \n        default:\n          throw new Error(`Unknown tool: ${name}`);\n      }\n    } catch (error) {\n      return formatErrorResponse(error);\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} ${paths.length === 1 ? 'directory' : 'directories'}: ${paths.join(', ')}`);\n        const result = await indexDirectories(paths, config);\n        console.log(`Indexed ${result.indexed} files, skipped ${result.skipped} files, ${result.failed} failed`);\n        if (result.errors.length > 0) {\n          console.log(`Errors: [`);\n          result.errors.forEach(error => {\n            console.log(`  '${error}'`);\n          });\n          console.log(`]`);\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('-c, --show-chunks', 'Show individual chunk scores and IDs')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (query: string, options) => {\n      try {\n        await 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: ${result.score.toFixed(3)} (${result.matchingChunks} chunks)`);\n          \n          if (options.showChunks && result.chunks.length > 0) {\n            console.log(`   Chunks:`);\n            result.chunks.forEach(chunk => {\n              console.log(`     - Chunk ${chunk.chunkId}: ${chunk.score.toFixed(3)}`);\n            });\n          }\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('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 available for AI search`);\n        console.log(`  • Database storage: ${status.databaseSize}`);\n        console.log(`  • Most recent indexing: ${status.lastIndexed || 'No indexing performed yet'}`);\n        \n        if (status.errors.length > 0) {\n          console.log(`  • Processing errors encountered: ${status.errors.length}`);\n          if (options.verbose) {\n            console.log('');\n            console.log('RECENT ERRORS:');\n            status.errors.slice(0, 5).forEach(error => {\n              console.log(`  - ${error}`);\n            });\n          }\n        }\n        \n        console.log('');\n        console.log('INDEXED DIRECTORIES:');\n        if (status.directories.length === 0) {\n          console.log('  No directories have been indexed yet.');\n          console.log('  Run \"directory-indexer index <path>\" to start indexing.');\n        } else {\n          status.directories.forEach(dir => {\n            console.log('');\n            console.log(`  Directory: ${dir.path}`);\n            console.log(`    • Indexing status: ${dir.status}`);\n            console.log(`    • Files processed: ${dir.filesCount}`);\n            console.log(`    • Searchable chunks: ${dir.chunksCount}`);\n            console.log(`    • Last indexed: ${dir.lastIndexed || 'Never completed'}`);\n            if (dir.errors.length > 0) {\n              console.log(`    • Files with errors: ${dir.errors.length}`);\n              if (options.verbose) {\n                console.log('    • Recent errors:');\n                dir.errors.slice(0, 3).forEach(error => {\n                  console.log(`      - ${error}`);\n                });\n              }\n            }\n          });\n        }\n        \n        if (!status.qdrantConsistency.isConsistent) {\n          console.log('');\n          console.log('SYSTEM STATUS:');\n          status.qdrantConsistency.issues.forEach(issue => {\n            console.log(`  • ${issue}`);\n          });\n          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

@@ -1,6 +1,14 @@
 import { homedir } from "os";
 import { join } from "path";
+import { existsSync, statSync } from "fs";
 import { z } from "zod";
+import { normalizePath } from "./utils.js";
+const WorkspaceSchema = z.object({
+  paths: z.array(z.string()),
+  isValid: z.boolean(),
+  filesCount: z.number().optional(),
+  chunksCount: z.number().optional()
+});
 const ConfigSchema = z.object({
   storage: z.object({
     sqlitePath: z.string(),
@@ -19,7 +27,8 @@ const ConfigSchema = z.object({
     ignorePatterns: z.array(z.string())
   }),
   dataDir: z.string(),
-  verbose: z.boolean()
+  verbose: z.boolean(),
+  workspaces: z.record(WorkspaceSchema)
 });
 class ConfigError extends Error {
   constructor(message, cause) {
@@ -28,11 +37,55 @@ class ConfigError extends Error {
     this.name = "ConfigError";
   }
 }
+function parseWorkspaces(env) {
+  const workspaces = {};
+  for (const [key, value] of Object.entries(env)) {
+    if (key.startsWith("WORKSPACE_") && value) {
+      const name = key.replace("WORKSPACE_", "").toLowerCase();
+      let paths;
+      try {
+        paths = JSON.parse(value);
+        if (!Array.isArray(paths)) {
+          throw new Error("Not an array");
+        }
+      } catch {
+        paths = value.split(",").map((p) => p.trim()).filter((p) => p.length > 0);
+      }
+      const normalizedPaths = paths.map(normalizePath);
+      const isValid = normalizedPaths.every((path) => {
+        try {
+          return existsSync(path) && statSync(path).isDirectory();
+        } catch {
+          return false;
+        }
+      });
+      workspaces[name] = {
+        paths: normalizedPaths,
+        isValid
+      };
+    }
+  }
+  return workspaces;
+}
+function getWorkspacePaths(config, workspace) {
+  const workspaceConfig = config.workspaces[workspace];
+  return workspaceConfig?.paths || [];
+}
+function isFileInWorkspace(filePath, workspacePaths) {
+  const normalizedFilePath = normalizePath(filePath);
+  return workspacePaths.some(
+    (workspacePath) => normalizedFilePath.startsWith(workspacePath + "/") || normalizedFilePath === workspacePath
+  );
+}
+function getAvailableWorkspaces(config) {
+  return Object.keys(config.workspaces);
+}
 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 workspaces = parseWorkspaces(process.env);
   const config = {
     storage: {
       sqlitePath: join(dataDir, dbFileName),
@@ -51,7 +104,8 @@ function loadConfig(options = {}) {
       ignorePatterns: [".git", "node_modules", "target", ".DS_Store"]
     },
     dataDir,
-    verbose: options.verbose ?? process.env.VERBOSE === "true"
+    verbose: options.verbose ?? process.env.VERBOSE === "true",
+    workspaces
   };
   try {
     return ConfigSchema.parse(config);
@@ -65,6 +119,9 @@ function loadConfig(options = {}) {
 }
 export {
   ConfigError,
+  getAvailableWorkspaces,
+  getWorkspacePaths,
+  isFileInWorkspace,
   loadConfig
 };
 //# sourceMappingURL=config.js.map

package/dist/config.js.map

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

@@ -114,6 +114,7 @@ async function shouldReprocessFile(filePath, existingRecord, config) {
 async function indexDirectories(paths, config) {
   let indexed = 0;
   let skipped = 0;
+  let failed = 0;
   const errors = [];
   const scanOptions = {
     ignorePatterns: config.indexing.ignorePatterns,
@@ -181,7 +182,10 @@ async function indexDirectories(paths, config) {
         } catch (error) {
           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 fullError = `Failed to process ${file.path}: ${errorMessage}${causeMessage}`;
+          errors.push(fullError);
+          failed++;
+          console.error(`❌ ${fullError}`);
         }
       }
       const directoryErrors = errors.filter((err) => err.includes(path));
@@ -193,7 +197,7 @@ async function indexDirectories(paths, config) {
       errors.push(`Failed to scan directory ${path}: ${error.message}`);
     }
   }
-  return { indexed, skipped, errors };
+  return { indexed, skipped, failed, errors };
 }
 export {
   IndexingError,

package/dist/indexing.js.map

@@ -1 +1 @@
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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  let failed = 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  // First pass: scan all directories to get total file count\n  let totalFiles = 0;\n  for (const path of paths) {\n    try {\n      if (config.verbose) {\n        console.log(`Scanning directory: ${path}`);\n      }\n      const files = await scanDirectory(path, scanOptions);\n      totalFiles += files.length;\n      if (config.verbose) {\n        console.log(`Found ${files.length} files to process in ${path}`);\n      }\n    } catch {\n      // Continue with other directories even if one fails to scan\n    }\n  }\n  \n  if (!config.verbose && totalFiles > 0) {\n    console.log(`Processing ${totalFiles} files...`);\n  }\n  \n  for (const path of paths) {\n    try {\n      // Mark directory as indexing\n      const normalizedPath = normalizePath(path);\n      await sqlite.upsertDirectory(normalizedPath, '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          if (config.verbose) {\n            console.log(`  Indexed: ${file.path} (${chunks.length} chunks)`);\n          }\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          const fullError = `Failed to process ${file.path}: ${errorMessage}${causeMessage}`;\n          errors.push(fullError);\n          failed++;\n          \n          // Print error immediately during processing (not just in verbose mode)\n          console.error(`❌ ${fullError}`);\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/search.js

@@ -10,24 +10,31 @@ class SearchError extends Error {
   }
 }
 async function searchContent(query, options = {}) {
-  const { limit = 10, threshold = 0 } = options;
+  const { limit = 10, threshold = 0, workspace } = options;
   try {
     const config = (await import("./config.js")).loadConfig();
-    const { qdrant } = await initializeStorage(config);
+    const { getWorkspacePaths, isFileInWorkspace } = await import("./config.js");
+    const { sqlite, qdrant } = await initializeStorage(config);
     const queryEmbedding = await generateEmbedding(query, config);
-    const points = await qdrant.searchPoints(queryEmbedding, limit * 5);
+    const workspacePaths = workspace ? getWorkspacePaths(config, workspace) : [];
+    const searchLimit = workspace ? limit * 10 : limit * 5;
+    const points = await qdrant.searchPoints(queryEmbedding, searchLimit);
     const fileGroups = /* @__PURE__ */ new Map();
     for (const point of points) {
       const score = point.score ?? 0;
       if (score < threshold) continue;
       const filePath = point.payload.filePath;
+      if (workspace && workspacePaths.length > 0) {
+        if (!isFileInWorkspace(filePath, workspacePaths)) {
+          continue;
+        }
+      }
       if (!fileGroups.has(filePath)) {
         fileGroups.set(filePath, []);
       }
       fileGroups.get(filePath).push({
         score,
-        chunkId: point.payload.chunkId,
-        parentDirectories: point.payload.parentDirectories
+        chunkId: point.payload.chunkId
       });
     }
     const results = [];
@@ -38,11 +45,13 @@ async function searchContent(query, options = {}) {
         chunkId: chunk.chunkId,
         score: chunk.score
       }));
+      const fileRecord = await sqlite.getFile(filePath);
+      const fileSizeBytes = fileRecord?.size ?? 0;
       results.push({
         filePath,
         score: avgScore,
+        fileSizeBytes,
         matchingChunks: chunks.length,
-        parentDirectories: sortedChunks[0].parentDirectories,
         chunks: chunkMatches
       });
     }
@@ -51,31 +60,63 @@ async function searchContent(query, options = {}) {
     throw new SearchError(`Failed to search content`, error);
   }
 }
-async function findSimilarFiles(filePath, limit = 5) {
+async function findSimilarFiles(filePath, limit = 5, workspace) {
   try {
     if (!await fileExists(filePath)) {
       throw new Error(`File not found: ${filePath}`);
     }
     const config = (await import("./config.js")).loadConfig();
+    const { getWorkspacePaths, isFileInWorkspace } = await import("./config.js");
     const { sqlite, qdrant } = await initializeStorage(config);
+    const workspacePaths = workspace ? getWorkspacePaths(config, workspace) : [];
     const fileRecord = await sqlite.getFile(filePath);
     if (!fileRecord || fileRecord.chunks.length === 0) {
       const content = await promises.readFile(filePath, "utf-8");
       const embedding = await generateEmbedding(content, config);
-      const points2 = await qdrant.searchPoints(embedding, limit + 1);
-      return points2.filter((point) => point.payload.filePath !== filePath).slice(0, limit).map((point) => ({
+      const searchLimit2 = workspace ? (limit + 1) * 5 : limit + 1;
+      const points2 = await qdrant.searchPoints(embedding, searchLimit2);
+      const filteredPoints2 = points2.filter((point) => {
+        const pointFilePath = point.payload.filePath;
+        if (pointFilePath === filePath) return false;
+        if (workspace && workspacePaths.length > 0) {
+          return isFileInWorkspace(pointFilePath, workspacePaths);
+        }
+        return true;
+      }).slice(0, limit);
+      const results2 = [];
+      for (const point of filteredPoints2) {
+        const pointFileRecord = await sqlite.getFile(point.payload.filePath);
+        const fileSizeBytes = pointFileRecord?.size ?? 0;
+        results2.push({
+          filePath: point.payload.filePath,
+          score: point.score ?? 0,
+          fileSizeBytes
+        });
+      }
+      return results2;
+    }
+    const firstChunkEmbedding = await generateEmbedding(fileRecord.chunks[0].content, config);
+    const searchLimit = workspace ? (limit + 1) * 5 : limit + 1;
+    const points = await qdrant.searchPoints(firstChunkEmbedding, searchLimit);
+    const filteredPoints = points.filter((point) => {
+      const pointFilePath = point.payload.filePath;
+      if (pointFilePath === filePath) return false;
+      if (workspace && workspacePaths.length > 0) {
+        return isFileInWorkspace(pointFilePath, workspacePaths);
+      }
+      return true;
+    }).slice(0, limit);
+    const results = [];
+    for (const point of filteredPoints) {
+      const pointFileRecord = await sqlite.getFile(point.payload.filePath);
+      const fileSizeBytes = pointFileRecord?.size ?? 0;
+      results.push({
         filePath: point.payload.filePath,
         score: point.score ?? 0,
-        parentDirectories: point.payload.parentDirectories
-      }));
+        fileSizeBytes
+      });
     }
-    const firstChunkEmbedding = await generateEmbedding(fileRecord.chunks[0].content, config);
-    const points = await qdrant.searchPoints(firstChunkEmbedding, limit + 1);
-    return points.filter((point) => point.payload.filePath !== filePath).slice(0, limit).map((point) => ({
-      filePath: point.payload.filePath,
-      score: point.score ?? 0,
-      parentDirectories: point.payload.parentDirectories
-    }));
+    return results;
   } catch (error) {
     throw new SearchError(`Failed to find similar files`, error);
   }

package/dist/search.js.map

@@ -1 +1 @@
-{"version":3,"file":"search.js","sources":["../src/search.ts"],"sourcesContent":["import { promises as fs } from 'fs';\nimport { generateEmbedding } from './embedding.js';\nimport { initializeStorage } from './storage.js';\nimport { fileExists } from './utils.js';\n\nexport interface SearchOptions {\n  limit?: number;\n  threshold?: number;\n  directoryPath?: string;\n}\n\nexport interface ChunkMatch {\n  chunkId: string;\n  score: number;\n}\n\nexport interface SearchResult {\n  filePath: string;\n  score: number;\n  matchingChunks: number;\n  parentDirectories: string[];\n  chunks: ChunkMatch[];\n}\n\nexport interface SimilarFile {\n  filePath: string;\n  score: number;\n  parentDirectories: string[];\n}\n\nexport class SearchError extends Error {\n  constructor(message: string, public override cause?: Error) {\n    super(message);\n    this.name = 'SearchError';\n  }\n}\n\nexport async function searchContent(query: string, options: SearchOptions = {}): Promise<SearchResult[]> {\n  const { limit = 10, threshold = 0.0 } = options;\n  \n  try {\n    const config = (await import('./config.js')).loadConfig();\n    const { qdrant } = await initializeStorage(config);\n    \n    const queryEmbedding = await generateEmbedding(query, config);\n    // Get more points initially since we'll group by file\n    const points = await qdrant.searchPoints(queryEmbedding, limit * 5);\n    \n    // Group points by file path\n    const fileGroups = new Map<string, Array<{ score: number; chunkId: string; parentDirectories: string[] }>>();\n    \n    for (const point of points) {\n      const score = point.score ?? 0;\n      if (score < threshold) continue;\n      \n      const filePath = point.payload.filePath;\n      if (!fileGroups.has(filePath)) {\n        fileGroups.set(filePath, []);\n      }\n      \n      fileGroups.get(filePath)!.push({\n        score,\n        chunkId: point.payload.chunkId,\n        parentDirectories: point.payload.parentDirectories\n      });\n    }\n    \n    // Calculate average score per file and sort\n    const results: SearchResult[] = [];\n    for (const [filePath, chunks] of fileGroups.entries()) {\n      const avgScore = chunks.reduce((sum, chunk) => sum + chunk.score, 0) / chunks.length;\n      \n      // Sort chunks by score (best first) and create chunk matches\n      const sortedChunks = chunks.sort((a, b) => b.score - a.score);\n      const chunkMatches: ChunkMatch[] = sortedChunks.map(chunk => ({\n        chunkId: chunk.chunkId,\n        score: chunk.score\n      }));\n      \n      results.push({\n        filePath,\n        score: avgScore,\n        matchingChunks: chunks.length,\n        parentDirectories: sortedChunks[0].parentDirectories,\n        chunks: chunkMatches\n      });\n    }\n    \n    // Sort by average score and return top results\n    return results\n      .sort((a, b) => b.score - a.score)\n      .slice(0, limit);\n  } catch (error) {\n    throw new SearchError(`Failed to search content`, error as Error);\n  }\n}\n\nexport async function findSimilarFiles(filePath: string, limit: number = 5): Promise<SimilarFile[]> {\n  try {\n    if (!await fileExists(filePath)) {\n      throw new Error(`File not found: ${filePath}`);\n    }\n    \n    const config = (await import('./config.js')).loadConfig();\n    const { sqlite, qdrant } = await initializeStorage(config);\n    \n    const fileRecord = await sqlite.getFile(filePath);\n    if (!fileRecord || fileRecord.chunks.length === 0) {\n      const content = await fs.readFile(filePath, 'utf-8');\n      const embedding = await generateEmbedding(content, config);\n      const points = await qdrant.searchPoints(embedding, limit + 1);\n      \n      return points\n        .filter(point => point.payload.filePath !== filePath)\n        .slice(0, limit)\n        .map(point => ({\n          filePath: point.payload.filePath,\n          score: point.score ?? 0,\n          parentDirectories: point.payload.parentDirectories\n        }));\n    }\n    \n    const firstChunkEmbedding = await generateEmbedding(fileRecord.chunks[0].content, config);\n    const points = await qdrant.searchPoints(firstChunkEmbedding, limit + 1);\n    \n    return points\n      .filter(point => point.payload.filePath !== filePath)\n      .slice(0, limit)\n      .map(point => ({\n        filePath: point.payload.filePath,\n        score: point.score ?? 0,\n        parentDirectories: point.payload.parentDirectories\n      }));\n  } catch (error) {\n    throw new SearchError(`Failed to find similar files`, error as Error);\n  }\n}\n\nexport async function getChunkContent(filePath: string, chunkId: string): Promise<string> {\n  try {\n    if (!await fileExists(filePath)) {\n      throw new Error(`File not found: ${filePath}`);\n    }\n    \n    const config = (await import('./config.js')).loadConfig();\n    const { sqlite } = await initializeStorage(config);\n    \n    const fileRecord = await sqlite.getFile(filePath);\n    if (!fileRecord || fileRecord.chunks.length === 0) {\n      throw new Error(`File not indexed: ${filePath}`);\n    }\n    \n    const chunk = fileRecord.chunks.find(c => c.id === chunkId);\n    if (!chunk) {\n      throw new Error(`Chunk ${chunkId} not found in file: ${filePath}`);\n    }\n    \n    return chunk.content;\n  } catch (error) {\n    throw new SearchError(`Failed to get chunk content`, error as Error);\n  }\n}\n\nexport async function getFileContent(filePath: string, chunks?: string): Promise<string> {\n  try {\n    if (!await fileExists(filePath)) {\n      throw new Error(`File not found: ${filePath}`);\n    }\n    \n    const config = (await import('./config.js')).loadConfig();\n    const { sqlite } = await initializeStorage(config);\n    \n    const fileRecord = await sqlite.getFile(filePath);\n    \n    if (!chunks) {\n      return await fs.readFile(filePath, 'utf-8');\n    }\n    \n    if (!fileRecord || fileRecord.chunks.length === 0) {\n      return await fs.readFile(filePath, 'utf-8');\n    }\n    \n    const chunkRange = parseChunkRange(chunks);\n    const selectedChunks = fileRecord.chunks.filter(chunk => {\n      const chunkNum = parseInt(chunk.id);\n      return chunkNum >= chunkRange.start && chunkNum <= chunkRange.end;\n    });\n    \n    return selectedChunks.map(chunk => chunk.content).join('');\n  } catch (error) {\n    throw new SearchError(`Failed to get file content`, error as Error);\n  }\n}\n\nfunction parseChunkRange(chunks: string): { start: number; 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+{"version":3,"file":"search.js","sources":["../src/search.ts"],"sourcesContent":["import { promises as fs } from 'fs';\nimport { generateEmbedding } from './embedding.js';\nimport { initializeStorage } from './storage.js';\nimport { fileExists } from './utils.js';\n\nexport interface SearchOptions {\n  limit?: number;\n  threshold?: number;\n  directoryPath?: string;\n  workspace?: string;\n}\n\nexport interface ChunkMatch {\n  chunkId: string;\n  score: number;\n}\n\nexport interface SearchResult {\n  filePath: string;\n  score: number;\n  fileSizeBytes: number;\n  matchingChunks: number;\n  chunks: ChunkMatch[];\n}\n\nexport interface SimilarFile {\n  filePath: string;\n  score: number;\n  fileSizeBytes: number;\n}\n\nexport class SearchError extends Error {\n  constructor(message: string, public override cause?: Error) {\n    super(message);\n    this.name = 'SearchError';\n  }\n}\n\nexport async function searchContent(query: string, options: SearchOptions = {}): Promise<SearchResult[]> {\n  const { limit = 10, threshold = 0.0, workspace } = options;\n  \n  try {\n    const config = (await import('./config.js')).loadConfig();\n    const { getWorkspacePaths, isFileInWorkspace } = await import('./config.js');\n    const { sqlite, qdrant } = await initializeStorage(config);\n    \n    const queryEmbedding = await generateEmbedding(query, config);\n    \n    // Get workspace paths if workspace is specified\n    const workspacePaths = workspace ? getWorkspacePaths(config, workspace) : [];\n    \n    // Get more points initially since we'll group by file and potentially filter by workspace\n    const searchLimit = workspace ? limit * 10 : limit * 5;\n    const points = await qdrant.searchPoints(queryEmbedding, searchLimit);\n    \n    // Group points by file path, filtering by workspace if specified\n    const fileGroups = new Map<string, Array<{ score: number; chunkId: string }>>();\n    \n    for (const point of points) {\n      const score = point.score ?? 0;\n      if (score < threshold) continue;\n      \n      const filePath = point.payload.filePath;\n      \n      // Filter by workspace if specified\n      if (workspace && workspacePaths.length > 0) {\n        if (!isFileInWorkspace(filePath, workspacePaths)) {\n          continue;\n        }\n      }\n      \n      if (!fileGroups.has(filePath)) {\n        fileGroups.set(filePath, []);\n      }\n      \n      fileGroups.get(filePath)!.push({\n        score,\n        chunkId: point.payload.chunkId\n      });\n    }\n    \n    // Calculate average score per file and sort\n    const results: SearchResult[] = [];\n    for (const [filePath, chunks] of fileGroups.entries()) {\n      const avgScore = chunks.reduce((sum, chunk) => sum + chunk.score, 0) / chunks.length;\n      \n      // Sort chunks by score (best first) and create chunk matches\n      const sortedChunks = chunks.sort((a, b) => b.score - a.score);\n      const chunkMatches: ChunkMatch[] = sortedChunks.map(chunk => ({\n        chunkId: chunk.chunkId,\n        score: chunk.score\n      }));\n      \n      // Get file size from SQLite database\n      const fileRecord = await sqlite.getFile(filePath);\n      const fileSizeBytes = fileRecord?.size ?? 0;\n      \n      results.push({\n        filePath,\n        score: avgScore,\n        fileSizeBytes,\n        matchingChunks: chunks.length,\n        chunks: chunkMatches\n      });\n    }\n    \n    // Sort by average score and return top results\n    return results\n      .sort((a, b) => b.score - a.score)\n      .slice(0, limit);\n  } catch (error) {\n    throw new SearchError(`Failed to search content`, error as Error);\n  }\n}\n\nexport async function findSimilarFiles(filePath: string, limit: number = 5, workspace?: string): Promise<SimilarFile[]> {\n  try {\n    if (!await fileExists(filePath)) {\n      throw new Error(`File not found: ${filePath}`);\n    }\n    \n    const config = (await import('./config.js')).loadConfig();\n    const { getWorkspacePaths, isFileInWorkspace } = await import('./config.js');\n    const { sqlite, qdrant } = await initializeStorage(config);\n    \n    // Get workspace paths if workspace is specified\n    const workspacePaths = workspace ? getWorkspacePaths(config, workspace) : [];\n    \n    const fileRecord = await sqlite.getFile(filePath);\n    if (!fileRecord || fileRecord.chunks.length === 0) {\n      const content = await fs.readFile(filePath, 'utf-8');\n      const embedding = await generateEmbedding(content, config);\n      const searchLimit = workspace ? 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Promise<string> {\n  try {\n    if (!await fileExists(filePath)) {\n      throw new Error(`File not found: ${filePath}`);\n    }\n    \n    const config = (await import('./config.js')).loadConfig();\n    const { sqlite } = await initializeStorage(config);\n    \n    const fileRecord = await sqlite.getFile(filePath);\n    \n    if (!chunks) {\n      return await fs.readFile(filePath, 'utf-8');\n    }\n    \n    if (!fileRecord || fileRecord.chunks.length === 0) {\n      return await fs.readFile(filePath, 'utf-8');\n    }\n    \n    const chunkRange = parseChunkRange(chunks);\n    const selectedChunks = fileRecord.chunks.filter(chunk => {\n      const chunkNum = parseInt(chunk.id);\n      return chunkNum >= chunkRange.start && chunkNum <= chunkRange.end;\n    });\n    \n    return selectedChunks.map(chunk => chunk.content).join('');\n  } catch (error) {\n    throw new SearchError(`Failed to get file content`, error as Error);\n  }\n}\n\nfunction parseChunkRange(chunks: string): { start: 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package/dist/storage.js

@@ -268,6 +268,38 @@ async function initializeStorage(config) {
 async function initDatabase(dbPath) {
   return new Database(dbPath);
 }
+async function calculateWorkspaceStatistics(sqlite, config) {
+  const { getAvailableWorkspaces, getWorkspacePaths, isFileInWorkspace } = await import("./config.js");
+  const workspaces = [];
+  for (const workspaceName of getAvailableWorkspaces(config)) {
+    const workspacePaths = getWorkspacePaths(config, workspaceName);
+    const workspaceConfig = config.workspaces[workspaceName];
+    const filesStmt = sqlite.db.prepare("SELECT path, chunks_json FROM files");
+    const allFiles = filesStmt.all();
+    let filesCount = 0;
+    let chunksCount = 0;
+    for (const file of allFiles) {
+      if (isFileInWorkspace(file.path, workspacePaths)) {
+        filesCount++;
+        if (file.chunks_json) {
+          try {
+            const chunks = JSON.parse(file.chunks_json);
+            chunksCount += chunks.length;
+          } catch {
+          }
+        }
+      }
+    }
+    workspaces.push({
+      name: workspaceName,
+      paths: workspacePaths,
+      isValid: workspaceConfig.isValid,
+      filesCount,
+      chunksCount
+    });
+  }
+  return workspaces;
+}
 async function checkQdrantConsistency(sqlite, config) {
   const issues = [];
   try {
@@ -373,6 +405,7 @@ async function getIndexStatus() {
       };
     });
     const qdrantConsistency = await checkQdrantConsistency(sqlite, config);
+    const workspaces = await calculateWorkspaceStatistics(sqlite, config);
     const fs = await import("fs");
     let databaseSize = "0 KB";
     try {
@@ -396,6 +429,7 @@ async function getIndexStatus() {
       lastIndexed: lastIndexedResult.last_indexed ? new Date(lastIndexedResult.last_indexed).toISOString() : null,
       errors: allErrors,
       directories,
+      workspaces,
       qdrantConsistency
     };
   } finally {

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(`${this.config.storage.qdrantEndpoint}/healthz`);\n      return response.ok;\n    } catch {\n      return false;\n    }\n  }\n\n  async createCollection(): Promise<void> {\n    const collectionName = this.config.storage.qdrantCollection;\n    \n    try {\n      const checkResponse = await fetch(`${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  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 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 = 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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 WorkspaceStatus {\n  name: string;\n  paths: string[];\n  isValid: boolean;\n  filesCount: number;\n  chunksCount: number;\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  qdrantConsistency: {\n    isConsistent: boolean;\n    issues: string[];\n  };\n}\n\nasync function calculateWorkspaceStatistics(sqlite: SQLiteStorage, config: Config): Promise<WorkspaceStatus[]> {\n  const { getAvailableWorkspaces, getWorkspacePaths, isFileInWorkspace } = await import('./config.js');\n  const workspaces: WorkspaceStatus[] = [];\n  \n  for (const workspaceName of getAvailableWorkspaces(config)) {\n    const workspacePaths = getWorkspacePaths(config, workspaceName);\n    const workspaceConfig = config.workspaces[workspaceName];\n    \n    // Get all files and count those in this workspace\n    const filesStmt = sqlite.db.prepare('SELECT path, chunks_json FROM files');\n    const allFiles = filesStmt.all() as { path: string; chunks_json: string | null }[];\n    \n    let filesCount = 0;\n    let chunksCount = 0;\n    \n    for (const file of allFiles) {\n      if (isFileInWorkspace(file.path, workspacePaths)) {\n        filesCount++;\n        if (file.chunks_json) {\n          try {\n            const chunks = JSON.parse(file.chunks_json);\n            chunksCount += chunks.length;\n          } catch {\n            // Skip malformed JSON\n          }\n        }\n      }\n    }\n    \n    workspaces.push({\n      name: workspaceName,\n      paths: workspacePaths,\n      isValid: workspaceConfig.isValid,\n      filesCount,\n      chunksCount\n    });\n  }\n  \n  return workspaces;\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 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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "directory-indexer",
-  "version": "0.1.1",
+  "version": "0.1.3",
   "description": "AI-powered directory indexing with semantic search for MCP servers",
   "main": "dist/cli.js",
   "bin": {
@@ -11,7 +11,7 @@
     "build": "vite build",
     "dev": "vite build --watch",
     "test": "vitest run",
-    "test:unit": "vitest run tests/unit.test.ts tests/cli.unit.test.ts tests/edge-cases.unit.test.ts tests/error-handling.unit.test.ts tests/providers.unit.test.ts",
+    "test:unit": "vitest run tests/unit.test.ts tests/cli.unit.test.ts tests/edge-cases.unit.test.ts tests/error-handling.unit.test.ts tests/providers.unit.test.ts tests/mcp-handlers.test.ts",
     "test:integration": "vitest run tests/integration.test.ts",
     "test:watch": "vitest",
     "test:coverage": "vitest run --coverage",