@fractary/codex-mcp 0.1.0 → 0.2.1

package/README.md

@@ -86,7 +86,7 @@ storage:
 
 The MCP server exposes the following tools:
 
-### codex_fetch
+### codex_document_fetch
 
 Fetch a document from the Codex knowledge base by URI.
 
@@ -112,7 +112,7 @@ Search for documents in the knowledge base.
 }
 ```
 
-### codex_list
+### codex_cache_list
 
 List cached documents.
 
@@ -124,9 +124,9 @@ List cached documents.
 }
 ```
 
-### codex_invalidate
+### codex_cache_clear
 
-Invalidate cached documents by pattern.
+Clear cached documents by pattern.
 
 ```json
 {
@@ -270,6 +270,14 @@ MIT
 - [@fractary/codex](https://www.npmjs.com/package/@fractary/codex) - Core SDK
 - [@fractary/codex-cli](https://www.npmjs.com/package/@fractary/codex-cli) - CLI tool
 
+## Documentation
+
+- [Command Reference](../../docs/guides/command-reference.md) - Complete command reference for all interfaces
+- [API Reference](../../docs/guides/api-reference.md) - Complete API documentation
+- [Naming Conventions](../../docs/guides/naming-conventions.md) - Naming standards across all interfaces
+- [MCP Migration Guide](../../docs/guides/mcp-migration-guide.md) - Migrating from old MCP tool names
+- [Troubleshooting](../../docs/guides/troubleshooting.md) - Common issues and solutions
+
 ## Links
 
 - [GitHub Repository](https://github.com/fractary/codex)

package/dist/cli.js

@@ -13,7 +13,7 @@ import { resolveReference as resolveReference2 } from "@fractary/codex";
 import { resolveReference } from "@fractary/codex";
 var CODEX_TOOLS = [
   {
-    name: "codex_fetch",
+    name: "codex_document_fetch",
     description: "Fetch a document from the Codex knowledge base by URI. Returns the document content.",
     inputSchema: {
       type: "object",
@@ -65,7 +65,7 @@ var CODEX_TOOLS = [
     }
   },
   {
-    name: "codex_list",
+    name: "codex_cache_list",
     description: "List documents in the Codex cache.",
     inputSchema: {
       type: "object",
@@ -86,8 +86,8 @@ var CODEX_TOOLS = [
     }
   },
   {
-    name: "codex_invalidate",
-    description: "Invalidate cached documents matching a pattern.",
+    name: "codex_cache_clear",
+    description: "Clear cached documents matching a pattern.",
     inputSchema: {
       type: "object",
       properties: {
@@ -160,14 +160,14 @@ async function handleSearch(args, ctx) {
   }
   const stats = await ctx.cache.getStats();
   if (stats.entryCount === 0) {
-    return textResult("No documents in cache. Use codex_fetch to load documents first.");
+    return textResult("No documents in cache. Use codex_document_fetch to load documents first.");
   }
   const message = `Search functionality requires a search index.
 Query: "${query}"
 Filters: org=${org || "any"}, project=${project || "any"}
 Limit: ${limit}
 
-To fetch documents, use codex_fetch with a specific URI like:
+To fetch documents, use codex_document_fetch with a specific URI like:
 codex://org/project/docs/file.md`;
   return textResult(message);
 }
@@ -224,7 +224,7 @@ function validateRegexPattern(pattern) {
     return { valid: false, error: message };
   }
 }
-async function handleInvalidate(args, ctx) {
+async function handleCacheClear(args, ctx) {
   const { pattern } = args;
   if (!pattern || typeof pattern !== "string") {
     return textResult("Pattern is required and must be a string", true);
@@ -236,22 +236,22 @@ async function handleInvalidate(args, ctx) {
   try {
     const regex = new RegExp(pattern);
     const count = await ctx.cache.invalidatePattern(regex);
-    return textResult(`Invalidated ${count} cache entries matching pattern: ${pattern}`);
+    return textResult(`Cleared ${count} cache entries matching pattern: ${pattern}`);
   } catch (error) {
     const message = error instanceof Error ? error.message : String(error);
-    return textResult(`Failed to invalidate cache: ${message}`, true);
+    return textResult(`Failed to clear cache: ${message}`, true);
   }
 }
 async function handleToolCall(name, args, ctx) {
   switch (name) {
-    case "codex_fetch":
+    case "codex_document_fetch":
       return handleFetch(args, ctx);
     case "codex_search":
       return handleSearch(args, ctx);
-    case "codex_list":
+    case "codex_cache_list":
       return handleList(args, ctx);
-    case "codex_invalidate":
-      return handleInvalidate(args, ctx);
+    case "codex_cache_clear":
+      return handleCacheClear(args, ctx);
     default:
       return textResult(`Unknown tool: ${name}`, true);
   }

package/dist/cli.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../src/cli.ts","../src/server.ts","../src/tools.ts"],"sourcesContent":["#!/usr/bin/env node\n/**\n * CLI entry point for @fractary/codex-mcp-server\n *\n * Provides MCP server with stdio transport.\n */\n\nimport { Command } from 'commander'\nimport { createCacheManager, createStorageManager } from '@fractary/codex'\nimport { readFileSync } from 'fs'\nimport * as yaml from 'js-yaml'\nimport { McpServer } from './server.js'\n\nconst program = new Command()\n\nprogram\n  .name('fractary-codex-mcp')\n  .description('MCP server for Fractary Codex knowledge management')\n  .version('0.1.0')\n  .option('--config <path>', 'Path to config file', '.fractary/codex.yaml')\n  .action(async (options) => {\n    // Load configuration\n    let config: Record<string, unknown> = {}\n    try {\n      const configFile = readFileSync(options.config, 'utf-8')\n      config = yaml.load(configFile) as Record<string, unknown>\n    } catch (error) {\n      // Config file is optional - continue with defaults\n      if (options.config !== '.fractary/codex.yaml') {\n        console.error(`Warning: Could not load config file: ${options.config}`)\n      }\n    }\n\n    // Initialize storage and cache managers\n    const storage = createStorageManager(config.storage as Record<string, unknown> | undefined)\n    const cache = createCacheManager({\n      cacheDir: (config.cache as Record<string, unknown>)?.cacheDir as string || '.fractary/cache',\n      ...(config.cache as Record<string, unknown>),\n    })\n\n    // Create MCP server\n    const server = new McpServer({\n      name: 'fractary-codex',\n      version: '0.1.0',\n      cache,\n      storage,\n    })\n\n    // Stdio mode\n    process.stdin.setEncoding('utf-8')\n\n    let buffer = ''\n    process.stdin.on('data', async (chunk) => {\n      buffer += chunk\n      const lines = buffer.split('\\n')\n      buffer = lines.pop() || ''\n\n      for (const line of lines) {\n        if (line.trim()) {\n          try {\n            const message = JSON.parse(line)\n            const response = await handleMessage(server, message)\n            process.stdout.write(JSON.stringify(response) + '\\n')\n          } catch (error) {\n            const errorResponse = {\n              jsonrpc: '2.0',\n              error: {\n                code: -32700,\n                message: 'Parse error',\n                data: error instanceof Error ? error.message : 'Unknown error',\n              },\n              id: null,\n            }\n            process.stdout.write(JSON.stringify(errorResponse) + '\\n')\n          }\n        }\n      }\n    })\n\n    process.stdin.on('end', () => {\n      process.exit(0)\n    })\n\n    console.error('MCP server running in stdio mode')\n  })\n\n/**\n * Handle a JSON-RPC message\n */\nasync function handleMessage(\n  server: McpServer,\n  message: Record<string, unknown>\n): Promise<Record<string, unknown>> {\n  const method = message.method as string\n  const params = (message.params as Record<string, unknown>) || {}\n  const id = message.id\n\n  try {\n    let result: unknown\n\n    switch (method) {\n      case 'initialize':\n        result = server.getServerInfo()\n        break\n\n      case 'tools/list':\n        result = { tools: server.listTools() }\n        break\n\n      case 'tools/call': {\n        const toolName = params.name as string\n        const toolArgs = params.arguments as Record<string, unknown>\n        result = await server.callTool(toolName, toolArgs)\n        break\n      }\n\n      case 'resources/list':\n        result = { resources: [] }\n        break\n\n      default:\n        return {\n          jsonrpc: '2.0',\n          error: {\n            code: -32601,\n            message: `Method not found: ${method}`,\n          },\n          id,\n        }\n    }\n\n    return {\n      jsonrpc: '2.0',\n      result,\n      id,\n    }\n  } catch (error) {\n    return {\n      jsonrpc: '2.0',\n      error: {\n        code: -32603,\n        message: 'Internal error',\n        data: error instanceof Error ? error.message : 'Unknown error',\n      },\n      id,\n    }\n  }\n}\n\n// Run the program\nprogram.parse(process.argv)\n","/**\n * MCP Server implementation\n *\n * Implements a Model Context Protocol server for the Codex SDK.\n * This server can be used standalone or embedded in other applications.\n */\n\nimport type { CacheManager } from '@fractary/codex'\nimport type { StorageManager } from '@fractary/codex'\nimport { resolveReference } from '@fractary/codex'\nimport type {\n  McpServerInfo,\n  McpCapabilities,\n  McpTool,\n  McpResource,\n  McpResourceTemplate,\n  ResourceContent,\n  ToolResult,\n} from './types.js'\nimport { CODEX_TOOLS, handleToolCall, type ToolHandlerContext } from './tools.js'\n\n/**\n * MCP Server configuration\n */\nexport interface McpServerConfig {\n  /** Server name */\n  name?: string\n  /** Server version */\n  version?: string\n  /** Cache manager instance */\n  cache: CacheManager\n  /** Storage manager instance */\n  storage: StorageManager\n}\n\n/**\n * MCP Server for Codex\n *\n * Provides a Model Context Protocol server implementation that exposes\n * Codex functionality as MCP tools and resources.\n */\nexport class McpServer {\n  private config: Required<Omit<McpServerConfig, 'cache' | 'storage'>> & Pick<McpServerConfig, 'cache' | 'storage'>\n  private toolContext: ToolHandlerContext\n\n  constructor(config: McpServerConfig) {\n    this.config = {\n      name: config.name ?? 'codex',\n      version: config.version ?? '1.0.0',\n      cache: config.cache,\n      storage: config.storage,\n    }\n\n    this.toolContext = {\n      cache: config.cache,\n      storage: config.storage,\n    }\n  }\n\n  /**\n   * Get server info\n   */\n  getServerInfo(): McpServerInfo {\n    return {\n      name: this.config.name,\n      version: this.config.version,\n      capabilities: this.getCapabilities(),\n    }\n  }\n\n  /**\n   * Get server capabilities\n   */\n  getCapabilities(): McpCapabilities {\n    return {\n      tools: {\n        listChanged: false,\n      },\n      resources: {\n        subscribe: false,\n        listChanged: false,\n      },\n    }\n  }\n\n  /**\n   * List available tools\n   */\n  listTools(): McpTool[] {\n    return CODEX_TOOLS\n  }\n\n  /**\n   * Call a tool\n   */\n  async callTool(name: string, args: Record<string, unknown>): Promise<ToolResult> {\n    return handleToolCall(name, args, this.toolContext)\n  }\n\n  /**\n   * List available resources\n   */\n  async listResources(): Promise<McpResource[]> {\n    // List cached documents as resources\n    const resources: McpResource[] = []\n\n    // Get cache stats for info\n    const stats = await this.config.cache.getStats()\n\n    // Add a summary resource\n    resources.push({\n      uri: 'codex://cache/summary',\n      name: 'Cache Summary',\n      description: `${stats.entryCount} cached documents`,\n      mimeType: 'text/plain',\n    })\n\n    return resources\n  }\n\n  /**\n   * List resource templates\n   */\n  listResourceTemplates(): McpResourceTemplate[] {\n    return [\n      {\n        uriTemplate: 'codex://{org}/{project}/{path}',\n        name: 'Codex Document',\n        description: 'Fetch a document from the Codex knowledge base',\n        mimeType: 'text/markdown',\n      },\n    ]\n  }\n\n  /**\n   * Read a resource\n   */\n  async readResource(uri: string): Promise<ResourceContent[]> {\n    // Handle special URIs\n    if (uri === 'codex://cache/summary') {\n      const stats = await this.config.cache.getStats()\n      return [\n        {\n          uri,\n          mimeType: 'text/plain',\n          text: `Cache Statistics:\n- Total entries: ${stats.entryCount}\n- Memory entries: ${stats.memoryEntries}\n- Fresh: ${stats.freshCount}\n- Stale: ${stats.staleCount}\n- Expired: ${stats.expiredCount}`,\n        },\n      ]\n    }\n\n    // Resolve and fetch the reference\n    const ref = resolveReference(uri)\n    if (!ref) {\n      throw new Error(`Invalid codex URI: ${uri}`)\n    }\n\n    const result = await this.config.cache.get(ref)\n    return [\n      {\n        uri,\n        mimeType: result.contentType,\n        text: result.content.toString('utf-8'),\n      },\n    ]\n  }\n\n  /**\n   * Handle JSON-RPC request\n   *\n   * This method handles the low-level MCP protocol messages.\n   */\n  async handleRequest(method: string, params?: Record<string, unknown>): Promise<unknown> {\n    switch (method) {\n      case 'initialize':\n        return {\n          protocolVersion: '2024-11-05',\n          serverInfo: this.getServerInfo(),\n          capabilities: this.getCapabilities(),\n        }\n\n      case 'tools/list':\n        return { tools: this.listTools() }\n\n      case 'tools/call': {\n        const { name, arguments: args } = params as { name: string; arguments: Record<string, unknown> }\n        return await this.callTool(name, args)\n      }\n\n      case 'resources/list':\n        return { resources: await this.listResources() }\n\n      case 'resources/templates/list':\n        return { resourceTemplates: this.listResourceTemplates() }\n\n      case 'resources/read': {\n        const { uri } = params as { uri: string }\n        return { contents: await this.readResource(uri) }\n      }\n\n      case 'prompts/list':\n        return { prompts: [] }\n\n      default:\n        throw new Error(`Unknown method: ${method}`)\n    }\n  }\n\n  /**\n   * Process a JSON-RPC message\n   */\n  async processMessage(message: string): Promise<string> {\n    let id: unknown = null\n\n    try {\n      const request = JSON.parse(message)\n      id = request.id\n      const { method, params } = request\n\n      const result = await this.handleRequest(method, params)\n\n      return JSON.stringify({\n        jsonrpc: '2.0',\n        id,\n        result,\n      })\n    } catch (error) {\n      const errorMessage = error instanceof Error ? error.message : String(error)\n\n      return JSON.stringify({\n        jsonrpc: '2.0',\n        id,\n        error: {\n          code: -32603,\n          message: errorMessage,\n        },\n      })\n    }\n  }\n}\n\n/**\n * Create an MCP server\n */\nexport function createMcpServer(config: McpServerConfig): McpServer {\n  return new McpServer(config)\n}\n","/**\n * MCP Tool definitions and handlers\n *\n * Implements the tools exposed by the Codex MCP server.\n */\n\nimport type { CacheManager } from '@fractary/codex'\nimport type { StorageManager } from '@fractary/codex'\nimport { resolveReference } from '@fractary/codex'\nimport type {\n  McpTool,\n  ToolResult,\n  FetchToolArgs,\n  SearchToolArgs,\n  ListToolArgs,\n  InvalidateToolArgs,\n} from './types.js'\n\n/**\n * Tool definitions for the MCP server\n */\nexport const CODEX_TOOLS: McpTool[] = [\n  {\n    name: 'codex_fetch',\n    description: 'Fetch a document from the Codex knowledge base by URI. Returns the document content.',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        uri: {\n          type: 'string',\n          description: 'Codex URI in format: codex://org/project/path/to/file.md',\n        },\n        branch: {\n          type: 'string',\n          description: 'Git branch to fetch from (default: main)',\n        },\n        noCache: {\n          type: 'boolean',\n          description: 'Bypass cache and fetch fresh content',\n        },\n      },\n      required: ['uri'],\n    },\n  },\n  {\n    name: 'codex_search',\n    description: 'Search for documents in the Codex knowledge base.',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        query: {\n          type: 'string',\n          description: 'Search query string',\n        },\n        org: {\n          type: 'string',\n          description: 'Filter by organization',\n        },\n        project: {\n          type: 'string',\n          description: 'Filter by project',\n        },\n        limit: {\n          type: 'number',\n          description: 'Maximum number of results (default: 10)',\n        },\n        type: {\n          type: 'string',\n          description: 'Filter by artifact type (e.g., docs, specs, logs)',\n        },\n      },\n      required: ['query'],\n    },\n  },\n  {\n    name: 'codex_list',\n    description: 'List documents in the Codex cache.',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        org: {\n          type: 'string',\n          description: 'Filter by organization',\n        },\n        project: {\n          type: 'string',\n          description: 'Filter by project',\n        },\n        includeExpired: {\n          type: 'boolean',\n          description: 'Include expired cache entries',\n        },\n      },\n    },\n  },\n  {\n    name: 'codex_invalidate',\n    description: 'Invalidate cached documents matching a pattern.',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        pattern: {\n          type: 'string',\n          description: 'URI pattern to invalidate (supports regex)',\n        },\n      },\n      required: ['pattern'],\n    },\n  },\n]\n\n/**\n * Tool handler context\n */\nexport interface ToolHandlerContext {\n  cache: CacheManager\n  storage: StorageManager\n}\n\n/**\n * Create a text result\n */\nfunction textResult(text: string, isError = false): ToolResult {\n  return {\n    content: [{ type: 'text', text }],\n    isError,\n  }\n}\n\n/**\n * Create a resource result\n */\nfunction resourceResult(uri: string, content: string, mimeType?: string): ToolResult {\n  return {\n    content: [\n      {\n        type: 'resource',\n        resource: {\n          uri,\n          mimeType,\n          text: content,\n        },\n      },\n    ],\n  }\n}\n\n/**\n * Handle codex_fetch tool\n */\nexport async function handleFetch(args: FetchToolArgs, ctx: ToolHandlerContext): Promise<ToolResult> {\n  const { uri, branch, noCache } = args\n\n  // Validate input\n  if (!uri || typeof uri !== 'string') {\n    return textResult('URI is required and must be a string', true)\n  }\n\n  if (branch && typeof branch !== 'string') {\n    return textResult('Branch must be a string', true)\n  }\n\n  // Resolve the reference\n  const ref = resolveReference(uri)\n  if (!ref) {\n    return textResult(`Invalid codex URI: ${uri}`, true)\n  }\n\n  try {\n    let result\n\n    if (noCache) {\n      // Bypass cache, fetch directly\n      result = await ctx.storage.fetch(ref, { branch })\n      // Still cache the result for next time\n      await ctx.cache.set(uri, result)\n    } else {\n      // Use cache\n      result = await ctx.cache.get(ref, { branch })\n    }\n\n    const content = result.content.toString('utf-8')\n    return resourceResult(uri, content, result.contentType)\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error)\n    return textResult(`Failed to fetch ${uri}: ${message}`, true)\n  }\n}\n\n/**\n * Handle codex_search tool\n *\n * Note: This is a basic implementation that searches cached entries.\n * A more sophisticated implementation might use a search index.\n */\nexport async function handleSearch(args: SearchToolArgs, ctx: ToolHandlerContext): Promise<ToolResult> {\n  const { query, org, project, limit = 10 } = args\n\n  // Validate input\n  if (!query || typeof query !== 'string') {\n    return textResult('Query is required and must be a string', true)\n  }\n\n  if (query.length > 500) {\n    return textResult('Query too long (max 500 characters)', true)\n  }\n\n  if (typeof limit !== 'number' || limit < 1 || limit > 100) {\n    return textResult('Limit must be a number between 1 and 100', true)\n  }\n\n  // Get all cached entries\n  const stats = await ctx.cache.getStats()\n  if (stats.entryCount === 0) {\n    return textResult('No documents in cache. Use codex_fetch to load documents first.')\n  }\n\n  // This is a simplified search - in a real implementation,\n  // we would use a proper search index\n  // For now, we search through the cached URIs and content\n\n  // Note: This is a placeholder. The actual search implementation\n  // would depend on having access to the cache persistence layer's\n  // list of URIs and their content.\n\n  const message = `Search functionality requires a search index.\nQuery: \"${query}\"\nFilters: org=${org || 'any'}, project=${project || 'any'}\nLimit: ${limit}\n\nTo fetch documents, use codex_fetch with a specific URI like:\ncodex://org/project/docs/file.md`\n\n  return textResult(message)\n}\n\n/**\n * Handle codex_list tool\n */\nexport async function handleList(args: ListToolArgs, ctx: ToolHandlerContext): Promise<ToolResult> {\n  const { org, project, includeExpired } = args\n\n  // Get cache stats and any available info\n  const stats = await ctx.cache.getStats()\n\n  let message = `Cache Statistics:\n- Total entries: ${stats.entryCount}\n- Memory entries: ${stats.memoryEntries}\n- Memory size: ${formatBytes(stats.memorySize)}\n- Total size: ${formatBytes(stats.totalSize)}\n- Fresh: ${stats.freshCount}\n- Stale: ${stats.staleCount}\n- Expired: ${stats.expiredCount}`\n\n  if (org) {\n    message += `\\n\\nFiltered by org: ${org}`\n  }\n  if (project) {\n    message += `\\nFiltered by project: ${project}`\n  }\n  if (includeExpired) {\n    message += `\\nIncluding expired entries`\n  }\n\n  return textResult(message)\n}\n\n/**\n * Validate and sanitize regex pattern to prevent ReDoS attacks\n */\nfunction validateRegexPattern(pattern: string): { valid: boolean; error?: string } {\n  // Check pattern length (prevent extremely long patterns)\n  if (pattern.length > 1000) {\n    return { valid: false, error: 'Pattern too long (max 1000 characters)' }\n  }\n\n  // Check for common ReDoS patterns\n  const redosPatterns = [\n    /(\\.\\*){3,}/,           // Multiple consecutive .*\n    /(\\+\\+|\\*\\*|\\?\\?)/,     // Nested quantifiers\n    /(\\([^)]*){10,}/,       // Too many groups\n    /(\\[[^\\]]{100,})/,      // Very long character classes\n  ]\n\n  for (const redos of redosPatterns) {\n    if (redos.test(pattern)) {\n      return { valid: false, error: 'Pattern contains potentially dangerous constructs' }\n    }\n  }\n\n  // Try to compile the regex to check for syntax errors\n  try {\n    new RegExp(pattern)\n    return { valid: true }\n  } catch (error) {\n    const message = error instanceof Error ? error.message : 'Invalid regex'\n    return { valid: false, error: message }\n  }\n}\n\n/**\n * Handle codex_invalidate tool\n */\nexport async function handleInvalidate(args: InvalidateToolArgs, ctx: ToolHandlerContext): Promise<ToolResult> {\n  const { pattern } = args\n\n  if (!pattern || typeof pattern !== 'string') {\n    return textResult('Pattern is required and must be a string', true)\n  }\n\n  // Validate pattern to prevent ReDoS\n  const validation = validateRegexPattern(pattern)\n  if (!validation.valid) {\n    return textResult(`Invalid pattern: ${validation.error}`, true)\n  }\n\n  try {\n    const regex = new RegExp(pattern)\n    const count = await ctx.cache.invalidatePattern(regex)\n\n    return textResult(`Invalidated ${count} cache entries matching pattern: ${pattern}`)\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error)\n    return textResult(`Failed to invalidate cache: ${message}`, true)\n  }\n}\n\n/**\n * Route a tool call to its handler\n */\nexport async function handleToolCall(\n  name: string,\n  args: Record<string, unknown>,\n  ctx: ToolHandlerContext\n): Promise<ToolResult> {\n  switch (name) {\n    case 'codex_fetch':\n      return handleFetch(args as unknown as FetchToolArgs, ctx)\n    case 'codex_search':\n      return handleSearch(args as unknown as SearchToolArgs, ctx)\n    case 'codex_list':\n      return handleList(args as unknown as ListToolArgs, ctx)\n    case 'codex_invalidate':\n      return handleInvalidate(args as unknown as InvalidateToolArgs, ctx)\n    default:\n      return textResult(`Unknown tool: ${name}`, true)\n  }\n}\n\n/**\n * Format bytes to human readable string\n */\nfunction formatBytes(bytes: number): string {\n  if (bytes === 0) return '0 B'\n  const k = 1024\n  const sizes = ['B', 'KB', 'MB', 'GB']\n  const i = Math.floor(Math.log(bytes) / Math.log(k))\n  return `${parseFloat((bytes / Math.pow(k, i)).toFixed(2))} 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+{"version":3,"sources":["../src/cli.ts","../src/server.ts","../src/tools.ts"],"sourcesContent":["#!/usr/bin/env node\n/**\n * CLI entry point for @fractary/codex-mcp-server\n *\n * Provides MCP server with stdio transport.\n */\n\nimport { Command } from 'commander'\nimport { createCacheManager, createStorageManager } from '@fractary/codex'\nimport { readFileSync } from 'fs'\nimport * as yaml from 'js-yaml'\nimport { McpServer } from './server.js'\n\nconst program = new Command()\n\nprogram\n  .name('fractary-codex-mcp')\n  .description('MCP server for Fractary Codex knowledge management')\n  .version('0.1.0')\n  .option('--config <path>', 'Path to config file', '.fractary/codex.yaml')\n  .action(async (options) => {\n    // Load configuration\n    let config: Record<string, unknown> = {}\n    try {\n      const configFile = readFileSync(options.config, 'utf-8')\n      config = yaml.load(configFile) as Record<string, unknown>\n    } catch (error) {\n      // Config file is optional - continue with defaults\n      if (options.config !== '.fractary/codex.yaml') {\n        console.error(`Warning: Could not load config file: ${options.config}`)\n      }\n    }\n\n    // Initialize storage and cache managers\n    const storage = createStorageManager(config.storage as Record<string, unknown> | undefined)\n    const cache = createCacheManager({\n      cacheDir: (config.cache as Record<string, unknown>)?.cacheDir as string || '.fractary/cache',\n      ...(config.cache as Record<string, unknown>),\n    })\n\n    // Create MCP server\n    const server = new McpServer({\n      name: 'fractary-codex',\n      version: '0.1.0',\n      cache,\n      storage,\n    })\n\n    // Stdio mode\n    process.stdin.setEncoding('utf-8')\n\n    let buffer = ''\n    process.stdin.on('data', async (chunk) => {\n      buffer += chunk\n      const lines = buffer.split('\\n')\n      buffer = lines.pop() || ''\n\n      for (const line of lines) {\n        if (line.trim()) {\n          try {\n            const message = JSON.parse(line)\n            const response = await handleMessage(server, message)\n            process.stdout.write(JSON.stringify(response) + '\\n')\n          } catch (error) {\n            const errorResponse = {\n              jsonrpc: '2.0',\n              error: {\n                code: -32700,\n                message: 'Parse error',\n                data: error instanceof Error ? error.message : 'Unknown error',\n              },\n              id: null,\n            }\n            process.stdout.write(JSON.stringify(errorResponse) + '\\n')\n          }\n        }\n      }\n    })\n\n    process.stdin.on('end', () => {\n      process.exit(0)\n    })\n\n    console.error('MCP server running in stdio mode')\n  })\n\n/**\n * Handle a JSON-RPC message\n */\nasync function handleMessage(\n  server: McpServer,\n  message: Record<string, unknown>\n): Promise<Record<string, unknown>> {\n  const method = message.method as string\n  const params = (message.params as Record<string, unknown>) || {}\n  const id = message.id\n\n  try {\n    let result: unknown\n\n    switch (method) {\n      case 'initialize':\n        result = server.getServerInfo()\n        break\n\n      case 'tools/list':\n        result = { tools: server.listTools() }\n        break\n\n      case 'tools/call': {\n        const toolName = params.name as string\n        const toolArgs = params.arguments as Record<string, unknown>\n        result = await server.callTool(toolName, toolArgs)\n        break\n      }\n\n      case 'resources/list':\n        result = { resources: [] }\n        break\n\n      default:\n        return {\n          jsonrpc: '2.0',\n          error: {\n            code: -32601,\n            message: `Method not found: ${method}`,\n          },\n          id,\n        }\n    }\n\n    return {\n      jsonrpc: '2.0',\n      result,\n      id,\n    }\n  } catch (error) {\n    return {\n      jsonrpc: '2.0',\n      error: {\n        code: -32603,\n        message: 'Internal error',\n        data: error instanceof Error ? error.message : 'Unknown error',\n      },\n      id,\n    }\n  }\n}\n\n// Run the program\nprogram.parse(process.argv)\n","/**\n * MCP Server implementation\n *\n * Implements a Model Context Protocol server for the Codex SDK.\n * This server can be used standalone or embedded in other applications.\n */\n\nimport type { CacheManager } from '@fractary/codex'\nimport type { StorageManager } from '@fractary/codex'\nimport { resolveReference } from '@fractary/codex'\nimport type {\n  McpServerInfo,\n  McpCapabilities,\n  McpTool,\n  McpResource,\n  McpResourceTemplate,\n  ResourceContent,\n  ToolResult,\n} from './types.js'\nimport { CODEX_TOOLS, handleToolCall, type ToolHandlerContext } from './tools.js'\n\n/**\n * MCP Server configuration\n */\nexport interface McpServerConfig {\n  /** Server name */\n  name?: string\n  /** Server version */\n  version?: string\n  /** Cache manager instance */\n  cache: CacheManager\n  /** Storage manager instance */\n  storage: StorageManager\n}\n\n/**\n * MCP Server for Codex\n *\n * Provides a Model Context Protocol server implementation that exposes\n * Codex functionality as MCP tools and resources.\n */\nexport class McpServer {\n  private config: Required<Omit<McpServerConfig, 'cache' | 'storage'>> & Pick<McpServerConfig, 'cache' | 'storage'>\n  private toolContext: ToolHandlerContext\n\n  constructor(config: McpServerConfig) {\n    this.config = {\n      name: config.name ?? 'codex',\n      version: config.version ?? '1.0.0',\n      cache: config.cache,\n      storage: config.storage,\n    }\n\n    this.toolContext = {\n      cache: config.cache,\n      storage: config.storage,\n    }\n  }\n\n  /**\n   * Get server info\n   */\n  getServerInfo(): McpServerInfo {\n    return {\n      name: this.config.name,\n      version: this.config.version,\n      capabilities: this.getCapabilities(),\n    }\n  }\n\n  /**\n   * Get server capabilities\n   */\n  getCapabilities(): McpCapabilities {\n    return {\n      tools: {\n        listChanged: false,\n      },\n      resources: {\n        subscribe: false,\n        listChanged: false,\n      },\n    }\n  }\n\n  /**\n   * List available tools\n   */\n  listTools(): McpTool[] {\n    return CODEX_TOOLS\n  }\n\n  /**\n   * Call a tool\n   */\n  async callTool(name: string, args: Record<string, unknown>): Promise<ToolResult> {\n    return handleToolCall(name, args, this.toolContext)\n  }\n\n  /**\n   * List available resources\n   */\n  async listResources(): Promise<McpResource[]> {\n    // List cached documents as resources\n    const resources: McpResource[] = []\n\n    // Get cache stats for info\n    const stats = await this.config.cache.getStats()\n\n    // Add a summary resource\n    resources.push({\n      uri: 'codex://cache/summary',\n      name: 'Cache Summary',\n      description: `${stats.entryCount} cached documents`,\n      mimeType: 'text/plain',\n    })\n\n    return resources\n  }\n\n  /**\n   * List resource templates\n   */\n  listResourceTemplates(): McpResourceTemplate[] {\n    return [\n      {\n        uriTemplate: 'codex://{org}/{project}/{path}',\n        name: 'Codex Document',\n        description: 'Fetch a document from the Codex knowledge base',\n        mimeType: 'text/markdown',\n      },\n    ]\n  }\n\n  /**\n   * Read a resource\n   */\n  async readResource(uri: string): Promise<ResourceContent[]> {\n    // Handle special URIs\n    if (uri === 'codex://cache/summary') {\n      const stats = await this.config.cache.getStats()\n      return [\n        {\n          uri,\n          mimeType: 'text/plain',\n          text: `Cache Statistics:\n- Total entries: ${stats.entryCount}\n- Memory entries: ${stats.memoryEntries}\n- Fresh: ${stats.freshCount}\n- Stale: ${stats.staleCount}\n- Expired: ${stats.expiredCount}`,\n        },\n      ]\n    }\n\n    // Resolve and fetch the reference\n    const ref = resolveReference(uri)\n    if (!ref) {\n      throw new Error(`Invalid codex URI: ${uri}`)\n    }\n\n    const result = await this.config.cache.get(ref)\n    return [\n      {\n        uri,\n        mimeType: result.contentType,\n        text: result.content.toString('utf-8'),\n      },\n    ]\n  }\n\n  /**\n   * Handle JSON-RPC request\n   *\n   * This method handles the low-level MCP protocol messages.\n   */\n  async handleRequest(method: string, params?: Record<string, unknown>): Promise<unknown> {\n    switch (method) {\n      case 'initialize':\n        return {\n          protocolVersion: '2024-11-05',\n          serverInfo: this.getServerInfo(),\n          capabilities: this.getCapabilities(),\n        }\n\n      case 'tools/list':\n        return { tools: this.listTools() }\n\n      case 'tools/call': {\n        const { name, arguments: args } = params as { name: string; arguments: Record<string, unknown> }\n        return await this.callTool(name, args)\n      }\n\n      case 'resources/list':\n        return { resources: await this.listResources() }\n\n      case 'resources/templates/list':\n        return { resourceTemplates: this.listResourceTemplates() }\n\n      case 'resources/read': {\n        const { uri } = params as { uri: string }\n        return { contents: await this.readResource(uri) }\n      }\n\n      case 'prompts/list':\n        return { prompts: [] }\n\n      default:\n        throw new Error(`Unknown method: ${method}`)\n    }\n  }\n\n  /**\n   * Process a JSON-RPC message\n   */\n  async processMessage(message: string): Promise<string> {\n    let id: unknown = null\n\n    try {\n      const request = JSON.parse(message)\n      id = request.id\n      const { method, params } = request\n\n      const result = await this.handleRequest(method, params)\n\n      return JSON.stringify({\n        jsonrpc: '2.0',\n        id,\n        result,\n      })\n    } catch (error) {\n      const errorMessage = error instanceof Error ? error.message : String(error)\n\n      return JSON.stringify({\n        jsonrpc: '2.0',\n        id,\n        error: {\n          code: -32603,\n          message: errorMessage,\n        },\n      })\n    }\n  }\n}\n\n/**\n * Create an MCP server\n */\nexport function createMcpServer(config: McpServerConfig): McpServer {\n  return new McpServer(config)\n}\n","/**\n * MCP Tool definitions and handlers\n *\n * Implements the tools exposed by the Codex MCP server.\n */\n\nimport type { CacheManager } from '@fractary/codex'\nimport type { StorageManager } from '@fractary/codex'\nimport { resolveReference } from '@fractary/codex'\nimport type {\n  McpTool,\n  ToolResult,\n  FetchToolArgs,\n  SearchToolArgs,\n  ListToolArgs,\n  CacheClearToolArgs,\n} from './types.js'\n\n/**\n * Tool definitions for the MCP server\n */\nexport const CODEX_TOOLS: McpTool[] = [\n  {\n    name: 'codex_document_fetch',\n    description: 'Fetch a document from the Codex knowledge base by URI. Returns the document content.',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        uri: {\n          type: 'string',\n          description: 'Codex URI in format: codex://org/project/path/to/file.md',\n        },\n        branch: {\n          type: 'string',\n          description: 'Git branch to fetch from (default: main)',\n        },\n        noCache: {\n          type: 'boolean',\n          description: 'Bypass cache and fetch fresh content',\n        },\n      },\n      required: ['uri'],\n    },\n  },\n  {\n    name: 'codex_search',\n    description: 'Search for documents in the Codex knowledge base.',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        query: {\n          type: 'string',\n          description: 'Search query string',\n        },\n        org: {\n          type: 'string',\n          description: 'Filter by organization',\n        },\n        project: {\n          type: 'string',\n          description: 'Filter by project',\n        },\n        limit: {\n          type: 'number',\n          description: 'Maximum number of results (default: 10)',\n        },\n        type: {\n          type: 'string',\n          description: 'Filter by artifact type (e.g., docs, specs, logs)',\n        },\n      },\n      required: ['query'],\n    },\n  },\n  {\n    name: 'codex_cache_list',\n    description: 'List documents in the Codex cache.',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        org: {\n          type: 'string',\n          description: 'Filter by organization',\n        },\n        project: {\n          type: 'string',\n          description: 'Filter by project',\n        },\n        includeExpired: {\n          type: 'boolean',\n          description: 'Include expired cache entries',\n        },\n      },\n    },\n  },\n  {\n    name: 'codex_cache_clear',\n    description: 'Clear cached documents matching a pattern.',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        pattern: {\n          type: 'string',\n          description: 'URI pattern to invalidate (supports regex)',\n        },\n      },\n      required: ['pattern'],\n    },\n  },\n]\n\n/**\n * Tool handler context\n */\nexport interface ToolHandlerContext {\n  cache: CacheManager\n  storage: StorageManager\n}\n\n/**\n * Create a text result\n */\nfunction textResult(text: string, isError = false): ToolResult {\n  return {\n    content: [{ type: 'text', text }],\n    isError,\n  }\n}\n\n/**\n * Create a resource result\n */\nfunction resourceResult(uri: string, content: string, mimeType?: string): ToolResult {\n  return {\n    content: [\n      {\n        type: 'resource',\n        resource: {\n          uri,\n          mimeType,\n          text: content,\n        },\n      },\n    ],\n  }\n}\n\n/**\n * Handle codex_document_fetch tool\n */\nexport async function handleFetch(args: FetchToolArgs, ctx: ToolHandlerContext): Promise<ToolResult> {\n  const { uri, branch, noCache } = args\n\n  // Validate input\n  if (!uri || typeof uri !== 'string') {\n    return textResult('URI is required and must be a string', true)\n  }\n\n  if (branch && typeof branch !== 'string') {\n    return textResult('Branch must be a string', true)\n  }\n\n  // Resolve the reference\n  const ref = resolveReference(uri)\n  if (!ref) {\n    return textResult(`Invalid codex URI: ${uri}`, true)\n  }\n\n  try {\n    let result\n\n    if (noCache) {\n      // Bypass cache, fetch directly\n      result = await ctx.storage.fetch(ref, { branch })\n      // Still cache the result for next time\n      await ctx.cache.set(uri, result)\n    } else {\n      // Use cache\n      result = await ctx.cache.get(ref, { branch })\n    }\n\n    const content = result.content.toString('utf-8')\n    return resourceResult(uri, content, result.contentType)\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error)\n    return textResult(`Failed to fetch ${uri}: ${message}`, true)\n  }\n}\n\n/**\n * Handle codex_search tool\n *\n * Note: This is a basic implementation that searches cached entries.\n * A more sophisticated implementation might use a search index.\n */\nexport async function handleSearch(args: SearchToolArgs, ctx: ToolHandlerContext): Promise<ToolResult> {\n  const { query, org, project, limit = 10 } = args\n\n  // Validate input\n  if (!query || typeof query !== 'string') {\n    return textResult('Query is required and must be a string', true)\n  }\n\n  if (query.length > 500) {\n    return textResult('Query too long (max 500 characters)', true)\n  }\n\n  if (typeof limit !== 'number' || limit < 1 || limit > 100) {\n    return textResult('Limit must be a number between 1 and 100', true)\n  }\n\n  // Get all cached entries\n  const stats = await ctx.cache.getStats()\n  if (stats.entryCount === 0) {\n    return textResult('No documents in cache. Use codex_document_fetch to load documents first.')\n  }\n\n  // This is a simplified search - in a real implementation,\n  // we would use a proper search index\n  // For now, we search through the cached URIs and content\n\n  // Note: This is a placeholder. The actual search implementation\n  // would depend on having access to the cache persistence layer's\n  // list of URIs and their content.\n\n  const message = `Search functionality requires a search index.\nQuery: \"${query}\"\nFilters: org=${org || 'any'}, project=${project || 'any'}\nLimit: ${limit}\n\nTo fetch documents, use codex_document_fetch with a specific URI like:\ncodex://org/project/docs/file.md`\n\n  return textResult(message)\n}\n\n/**\n * Handle codex_cache_list tool\n */\nexport async function handleList(args: ListToolArgs, ctx: ToolHandlerContext): Promise<ToolResult> {\n  const { org, project, includeExpired } = args\n\n  // Get cache stats and any available info\n  const stats = await ctx.cache.getStats()\n\n  let message = `Cache Statistics:\n- Total entries: ${stats.entryCount}\n- Memory entries: ${stats.memoryEntries}\n- Memory size: ${formatBytes(stats.memorySize)}\n- Total size: ${formatBytes(stats.totalSize)}\n- Fresh: ${stats.freshCount}\n- Stale: ${stats.staleCount}\n- Expired: ${stats.expiredCount}`\n\n  if (org) {\n    message += `\\n\\nFiltered by org: ${org}`\n  }\n  if (project) {\n    message += `\\nFiltered by project: ${project}`\n  }\n  if (includeExpired) {\n    message += `\\nIncluding expired entries`\n  }\n\n  return textResult(message)\n}\n\n/**\n * Validate and sanitize regex pattern to prevent ReDoS attacks\n */\nfunction validateRegexPattern(pattern: string): { valid: boolean; error?: string } {\n  // Check pattern length (prevent extremely long patterns)\n  if (pattern.length > 1000) {\n    return { valid: false, error: 'Pattern too long (max 1000 characters)' }\n  }\n\n  // Check for common ReDoS patterns\n  const redosPatterns = [\n    /(\\.\\*){3,}/,           // Multiple consecutive .*\n    /(\\+\\+|\\*\\*|\\?\\?)/,     // Nested quantifiers\n    /(\\([^)]*){10,}/,       // Too many groups\n    /(\\[[^\\]]{100,})/,      // Very long character classes\n  ]\n\n  for (const redos of redosPatterns) {\n    if (redos.test(pattern)) {\n      return { valid: false, error: 'Pattern contains potentially dangerous constructs' }\n    }\n  }\n\n  // Try to compile the regex to check for syntax errors\n  try {\n    new RegExp(pattern)\n    return { valid: true }\n  } catch (error) {\n    const message = error instanceof Error ? error.message : 'Invalid regex'\n    return { valid: false, error: message }\n  }\n}\n\n/**\n * Handle codex_cache_clear tool\n */\nexport async function handleCacheClear(args: CacheClearToolArgs, ctx: ToolHandlerContext): Promise<ToolResult> {\n  const { pattern } = args\n\n  if (!pattern || typeof pattern !== 'string') {\n    return textResult('Pattern is required and must be a string', true)\n  }\n\n  // Validate pattern to prevent ReDoS\n  const validation = validateRegexPattern(pattern)\n  if (!validation.valid) {\n    return textResult(`Invalid pattern: ${validation.error}`, true)\n  }\n\n  try {\n    const regex = new RegExp(pattern)\n    const count = await ctx.cache.invalidatePattern(regex)\n\n    return textResult(`Cleared ${count} cache entries matching pattern: ${pattern}`)\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error)\n    return textResult(`Failed to clear cache: ${message}`, true)\n  }\n}\n\n/**\n * Route a tool call to its handler\n */\nexport async function handleToolCall(\n  name: string,\n  args: Record<string, unknown>,\n  ctx: ToolHandlerContext\n): Promise<ToolResult> {\n  switch (name) {\n    case 'codex_document_fetch':\n      return handleFetch(args as unknown as FetchToolArgs, ctx)\n    case 'codex_search':\n      return handleSearch(args as unknown as SearchToolArgs, ctx)\n    case 'codex_cache_list':\n      return handleList(args as unknown as ListToolArgs, ctx)\n    case 'codex_cache_clear':\n      return handleCacheClear(args as unknown as CacheClearToolArgs, ctx)\n    default:\n      return textResult(`Unknown tool: ${name}`, true)\n  }\n}\n\n/**\n * Format bytes to human readable string\n */\nfunction formatBytes(bytes: number): string {\n  if (bytes === 0) return '0 B'\n  const k = 1024\n  const sizes = ['B', 'KB', 'MB', 'GB']\n  const i = Math.floor(Math.log(bytes) / Math.log(k))\n  return `${parseFloat((bytes / Math.pow(k, i)).toFixed(2))} 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package/dist/index.d.ts

@@ -38,7 +38,7 @@ interface ListToolArgs {
     project?: string;
     includeExpired?: boolean;
 }
-interface InvalidateToolArgs {
+interface CacheClearToolArgs {
     pattern: string;
 }
 interface ToolResult {
@@ -115,7 +115,7 @@ interface ToolHandlerContext {
 declare function handleFetch(args: FetchToolArgs, ctx: ToolHandlerContext): Promise<ToolResult>;
 declare function handleSearch(args: SearchToolArgs, ctx: ToolHandlerContext): Promise<ToolResult>;
 declare function handleList(args: ListToolArgs, ctx: ToolHandlerContext): Promise<ToolResult>;
-declare function handleInvalidate(args: InvalidateToolArgs, ctx: ToolHandlerContext): Promise<ToolResult>;
+declare function handleCacheClear(args: CacheClearToolArgs, ctx: ToolHandlerContext): Promise<ToolResult>;
 declare function handleToolCall(name: string, args: Record<string, unknown>, ctx: ToolHandlerContext): Promise<ToolResult>;
 
-export { CODEX_TOOLS, type FetchToolArgs, type InvalidateToolArgs, type ListToolArgs, type McpCapabilities, type McpResource, type McpResourceTemplate, McpServer, type McpServerConfig, type McpServerInfo, type McpTool, type ResourceContent, type SearchResult, type SearchToolArgs, type ToolHandlerContext, type ToolResult, createMcpServer, handleFetch, handleInvalidate, handleList, handleSearch, handleToolCall };
+export { CODEX_TOOLS, type CacheClearToolArgs, type FetchToolArgs, type ListToolArgs, type McpCapabilities, type McpResource, type McpResourceTemplate, McpServer, type McpServerConfig, type McpServerInfo, type McpTool, type ResourceContent, type SearchResult, type SearchToolArgs, type ToolHandlerContext, type ToolResult, createMcpServer, handleCacheClear, handleFetch, handleList, handleSearch, handleToolCall };

package/dist/index.js

@@ -5,7 +5,7 @@ import { resolveReference as resolveReference2 } from "@fractary/codex";
 import { resolveReference } from "@fractary/codex";
 var CODEX_TOOLS = [
   {
-    name: "codex_fetch",
+    name: "codex_document_fetch",
     description: "Fetch a document from the Codex knowledge base by URI. Returns the document content.",
     inputSchema: {
       type: "object",
@@ -57,7 +57,7 @@ var CODEX_TOOLS = [
     }
   },
   {
-    name: "codex_list",
+    name: "codex_cache_list",
     description: "List documents in the Codex cache.",
     inputSchema: {
       type: "object",
@@ -78,8 +78,8 @@ var CODEX_TOOLS = [
     }
   },
   {
-    name: "codex_invalidate",
-    description: "Invalidate cached documents matching a pattern.",
+    name: "codex_cache_clear",
+    description: "Clear cached documents matching a pattern.",
     inputSchema: {
       type: "object",
       properties: {
@@ -152,14 +152,14 @@ async function handleSearch(args, ctx) {
   }
   const stats = await ctx.cache.getStats();
   if (stats.entryCount === 0) {
-    return textResult("No documents in cache. Use codex_fetch to load documents first.");
+    return textResult("No documents in cache. Use codex_document_fetch to load documents first.");
   }
   const message = `Search functionality requires a search index.
 Query: "${query}"
 Filters: org=${org || "any"}, project=${project || "any"}
 Limit: ${limit}
 
-To fetch documents, use codex_fetch with a specific URI like:
+To fetch documents, use codex_document_fetch with a specific URI like:
 codex://org/project/docs/file.md`;
   return textResult(message);
 }
@@ -216,7 +216,7 @@ function validateRegexPattern(pattern) {
     return { valid: false, error: message };
   }
 }
-async function handleInvalidate(args, ctx) {
+async function handleCacheClear(args, ctx) {
   const { pattern } = args;
   if (!pattern || typeof pattern !== "string") {
     return textResult("Pattern is required and must be a string", true);
@@ -228,22 +228,22 @@ async function handleInvalidate(args, ctx) {
   try {
     const regex = new RegExp(pattern);
     const count = await ctx.cache.invalidatePattern(regex);
-    return textResult(`Invalidated ${count} cache entries matching pattern: ${pattern}`);
+    return textResult(`Cleared ${count} cache entries matching pattern: ${pattern}`);
   } catch (error) {
     const message = error instanceof Error ? error.message : String(error);
-    return textResult(`Failed to invalidate cache: ${message}`, true);
+    return textResult(`Failed to clear cache: ${message}`, true);
   }
 }
 async function handleToolCall(name, args, ctx) {
   switch (name) {
-    case "codex_fetch":
+    case "codex_document_fetch":
       return handleFetch(args, ctx);
     case "codex_search":
       return handleSearch(args, ctx);
-    case "codex_list":
+    case "codex_cache_list":
       return handleList(args, ctx);
-    case "codex_invalidate":
-      return handleInvalidate(args, ctx);
+    case "codex_cache_clear":
+      return handleCacheClear(args, ctx);
     default:
       return textResult(`Unknown tool: ${name}`, true);
   }
@@ -435,8 +435,8 @@ export {
   CODEX_TOOLS,
   McpServer,
   createMcpServer,
+  handleCacheClear,
   handleFetch,
-  handleInvalidate,
   handleList,
   handleSearch,
   handleToolCall

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../src/server.ts","../src/tools.ts"],"sourcesContent":["/**\n * MCP Server implementation\n *\n * Implements a Model Context Protocol server for the Codex SDK.\n * This server can be used standalone or embedded in other applications.\n */\n\nimport type { CacheManager } from '@fractary/codex'\nimport type { StorageManager } from '@fractary/codex'\nimport { resolveReference } from '@fractary/codex'\nimport type {\n  McpServerInfo,\n  McpCapabilities,\n  McpTool,\n  McpResource,\n  McpResourceTemplate,\n  ResourceContent,\n  ToolResult,\n} from './types.js'\nimport { CODEX_TOOLS, handleToolCall, type ToolHandlerContext } from './tools.js'\n\n/**\n * MCP Server configuration\n */\nexport interface McpServerConfig {\n  /** Server name */\n  name?: string\n  /** Server version */\n  version?: string\n  /** Cache manager instance */\n  cache: CacheManager\n  /** Storage manager instance */\n  storage: StorageManager\n}\n\n/**\n * MCP Server for Codex\n *\n * Provides a Model Context Protocol server implementation that exposes\n * Codex functionality as MCP tools and resources.\n */\nexport class McpServer {\n  private config: Required<Omit<McpServerConfig, 'cache' | 'storage'>> & Pick<McpServerConfig, 'cache' | 'storage'>\n  private toolContext: ToolHandlerContext\n\n  constructor(config: McpServerConfig) {\n    this.config = {\n      name: config.name ?? 'codex',\n      version: config.version ?? '1.0.0',\n      cache: config.cache,\n      storage: config.storage,\n    }\n\n    this.toolContext = {\n      cache: config.cache,\n      storage: config.storage,\n    }\n  }\n\n  /**\n   * Get server info\n   */\n  getServerInfo(): McpServerInfo {\n    return {\n      name: this.config.name,\n      version: this.config.version,\n      capabilities: this.getCapabilities(),\n    }\n  }\n\n  /**\n   * Get server capabilities\n   */\n  getCapabilities(): McpCapabilities {\n    return {\n      tools: {\n        listChanged: false,\n      },\n      resources: {\n        subscribe: false,\n        listChanged: false,\n      },\n    }\n  }\n\n  /**\n   * List available tools\n   */\n  listTools(): McpTool[] {\n    return CODEX_TOOLS\n  }\n\n  /**\n   * Call a tool\n   */\n  async callTool(name: string, args: Record<string, unknown>): Promise<ToolResult> {\n    return handleToolCall(name, args, this.toolContext)\n  }\n\n  /**\n   * List available resources\n   */\n  async listResources(): Promise<McpResource[]> {\n    // List cached documents as resources\n    const resources: McpResource[] = []\n\n    // Get cache stats for info\n    const stats = await this.config.cache.getStats()\n\n    // Add a summary resource\n    resources.push({\n      uri: 'codex://cache/summary',\n      name: 'Cache Summary',\n      description: `${stats.entryCount} cached documents`,\n      mimeType: 'text/plain',\n    })\n\n    return resources\n  }\n\n  /**\n   * List resource templates\n   */\n  listResourceTemplates(): McpResourceTemplate[] {\n    return [\n      {\n        uriTemplate: 'codex://{org}/{project}/{path}',\n        name: 'Codex Document',\n        description: 'Fetch a document from the Codex knowledge base',\n        mimeType: 'text/markdown',\n      },\n    ]\n  }\n\n  /**\n   * Read a resource\n   */\n  async readResource(uri: string): Promise<ResourceContent[]> {\n    // Handle special URIs\n    if (uri === 'codex://cache/summary') {\n      const stats = await this.config.cache.getStats()\n      return [\n        {\n          uri,\n          mimeType: 'text/plain',\n          text: `Cache Statistics:\n- Total entries: ${stats.entryCount}\n- Memory entries: ${stats.memoryEntries}\n- Fresh: ${stats.freshCount}\n- Stale: ${stats.staleCount}\n- Expired: ${stats.expiredCount}`,\n        },\n      ]\n    }\n\n    // Resolve and fetch the reference\n    const ref = resolveReference(uri)\n    if (!ref) {\n      throw new Error(`Invalid codex URI: ${uri}`)\n    }\n\n    const result = await this.config.cache.get(ref)\n    return [\n      {\n        uri,\n        mimeType: result.contentType,\n        text: result.content.toString('utf-8'),\n      },\n    ]\n  }\n\n  /**\n   * Handle JSON-RPC request\n   *\n   * This method handles the low-level MCP protocol messages.\n   */\n  async handleRequest(method: string, params?: Record<string, unknown>): Promise<unknown> {\n    switch (method) {\n      case 'initialize':\n        return {\n          protocolVersion: '2024-11-05',\n          serverInfo: this.getServerInfo(),\n          capabilities: this.getCapabilities(),\n        }\n\n      case 'tools/list':\n        return { tools: this.listTools() }\n\n      case 'tools/call': {\n        const { name, arguments: args } = params as { name: string; arguments: Record<string, unknown> }\n        return await this.callTool(name, args)\n      }\n\n      case 'resources/list':\n        return { resources: await this.listResources() }\n\n      case 'resources/templates/list':\n        return { resourceTemplates: this.listResourceTemplates() }\n\n      case 'resources/read': {\n        const { uri } = params as { uri: string }\n        return { contents: await this.readResource(uri) }\n      }\n\n      case 'prompts/list':\n        return { prompts: [] }\n\n      default:\n        throw new Error(`Unknown method: ${method}`)\n    }\n  }\n\n  /**\n   * Process a JSON-RPC message\n   */\n  async processMessage(message: string): Promise<string> {\n    let id: unknown = null\n\n    try {\n      const request = JSON.parse(message)\n      id = request.id\n      const { method, params } = request\n\n      const result = await this.handleRequest(method, params)\n\n      return JSON.stringify({\n        jsonrpc: '2.0',\n        id,\n        result,\n      })\n    } catch (error) {\n      const errorMessage = error instanceof Error ? error.message : String(error)\n\n      return JSON.stringify({\n        jsonrpc: '2.0',\n        id,\n        error: {\n          code: -32603,\n          message: errorMessage,\n        },\n      })\n    }\n  }\n}\n\n/**\n * Create an MCP server\n */\nexport function createMcpServer(config: McpServerConfig): McpServer {\n  return new McpServer(config)\n}\n","/**\n * MCP Tool definitions and handlers\n *\n * Implements the tools exposed by the Codex MCP server.\n */\n\nimport type { CacheManager } from '@fractary/codex'\nimport type { StorageManager } from '@fractary/codex'\nimport { resolveReference } from '@fractary/codex'\nimport type {\n  McpTool,\n  ToolResult,\n  FetchToolArgs,\n  SearchToolArgs,\n  ListToolArgs,\n  InvalidateToolArgs,\n} from './types.js'\n\n/**\n * Tool definitions for the MCP server\n */\nexport const CODEX_TOOLS: McpTool[] = [\n  {\n    name: 'codex_fetch',\n    description: 'Fetch a document from the Codex knowledge base by URI. Returns the document content.',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        uri: {\n          type: 'string',\n          description: 'Codex URI in format: codex://org/project/path/to/file.md',\n        },\n        branch: {\n          type: 'string',\n          description: 'Git branch to fetch from (default: main)',\n        },\n        noCache: {\n          type: 'boolean',\n          description: 'Bypass cache and fetch fresh content',\n        },\n      },\n      required: ['uri'],\n    },\n  },\n  {\n    name: 'codex_search',\n    description: 'Search for documents in the Codex knowledge base.',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        query: {\n          type: 'string',\n          description: 'Search query string',\n        },\n        org: {\n          type: 'string',\n          description: 'Filter by organization',\n        },\n        project: {\n          type: 'string',\n          description: 'Filter by project',\n        },\n        limit: {\n          type: 'number',\n          description: 'Maximum number of results (default: 10)',\n        },\n        type: {\n          type: 'string',\n          description: 'Filter by artifact type (e.g., docs, specs, logs)',\n        },\n      },\n      required: ['query'],\n    },\n  },\n  {\n    name: 'codex_list',\n    description: 'List documents in the Codex cache.',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        org: {\n          type: 'string',\n          description: 'Filter by organization',\n        },\n        project: {\n          type: 'string',\n          description: 'Filter by project',\n        },\n        includeExpired: {\n          type: 'boolean',\n          description: 'Include expired cache entries',\n        },\n      },\n    },\n  },\n  {\n    name: 'codex_invalidate',\n    description: 'Invalidate cached documents matching a pattern.',\n    inputSchema: {\n      type: 'object',\n      properties: {\n        pattern: {\n          type: 'string',\n          description: 'URI pattern to invalidate (supports regex)',\n        },\n      },\n      required: ['pattern'],\n    },\n  },\n]\n\n/**\n * Tool handler context\n */\nexport interface ToolHandlerContext {\n  cache: CacheManager\n  storage: StorageManager\n}\n\n/**\n * Create a text result\n */\nfunction textResult(text: string, isError = false): ToolResult {\n  return {\n    content: [{ type: 'text', text }],\n    isError,\n  }\n}\n\n/**\n * Create a resource result\n */\nfunction resourceResult(uri: string, content: string, mimeType?: string): ToolResult {\n  return {\n    content: [\n      {\n        type: 'resource',\n        resource: {\n          uri,\n          mimeType,\n          text: content,\n        },\n      },\n    ],\n  }\n}\n\n/**\n * Handle codex_fetch tool\n */\nexport async function handleFetch(args: FetchToolArgs, ctx: ToolHandlerContext): Promise<ToolResult> {\n  const { uri, branch, noCache } = args\n\n  // Validate input\n  if (!uri || typeof uri !== 'string') {\n    return textResult('URI is required and must be a string', true)\n  }\n\n  if (branch && typeof branch !== 'string') {\n    return textResult('Branch must be a string', true)\n  }\n\n  // Resolve the reference\n  const ref = resolveReference(uri)\n  if (!ref) {\n    return textResult(`Invalid codex URI: ${uri}`, true)\n  }\n\n  try {\n    let result\n\n    if (noCache) {\n      // Bypass cache, fetch directly\n      result = await ctx.storage.fetch(ref, { branch })\n      // Still cache the result for next time\n      await ctx.cache.set(uri, result)\n    } else {\n      // Use cache\n      result = await ctx.cache.get(ref, { branch })\n    }\n\n    const content = result.content.toString('utf-8')\n    return resourceResult(uri, content, result.contentType)\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error)\n    return textResult(`Failed to fetch ${uri}: ${message}`, true)\n  }\n}\n\n/**\n * Handle codex_search tool\n *\n * Note: This is a basic implementation that searches cached entries.\n * A more sophisticated implementation might use a search index.\n */\nexport async function handleSearch(args: SearchToolArgs, ctx: ToolHandlerContext): Promise<ToolResult> {\n  const { query, org, project, limit = 10 } = args\n\n  // Validate input\n  if (!query || typeof query !== 'string') {\n    return textResult('Query is required and must be a string', true)\n  }\n\n  if (query.length > 500) {\n    return textResult('Query too long (max 500 characters)', true)\n  }\n\n  if (typeof limit !== 'number' || limit < 1 || limit > 100) {\n    return textResult('Limit must be a number between 1 and 100', true)\n  }\n\n  // Get all cached entries\n  const stats = await ctx.cache.getStats()\n  if (stats.entryCount === 0) {\n    return textResult('No documents in cache. Use codex_fetch to load documents first.')\n  }\n\n  // This is a simplified search - in a real implementation,\n  // we would use a proper search index\n  // For now, we search through the cached URIs and content\n\n  // Note: This is a placeholder. The actual search implementation\n  // would depend on having access to the cache persistence layer's\n  // list of URIs and their content.\n\n  const message = `Search functionality requires a search index.\nQuery: \"${query}\"\nFilters: org=${org || 'any'}, project=${project || 'any'}\nLimit: ${limit}\n\nTo fetch documents, use codex_fetch with a specific URI like:\ncodex://org/project/docs/file.md`\n\n  return textResult(message)\n}\n\n/**\n * Handle codex_list tool\n */\nexport async function handleList(args: ListToolArgs, ctx: ToolHandlerContext): Promise<ToolResult> {\n  const { org, project, includeExpired } = args\n\n  // Get cache stats and any available info\n  const stats = await ctx.cache.getStats()\n\n  let message = `Cache Statistics:\n- Total entries: ${stats.entryCount}\n- Memory entries: ${stats.memoryEntries}\n- Memory size: ${formatBytes(stats.memorySize)}\n- Total size: ${formatBytes(stats.totalSize)}\n- Fresh: ${stats.freshCount}\n- Stale: ${stats.staleCount}\n- Expired: ${stats.expiredCount}`\n\n  if (org) {\n    message += `\\n\\nFiltered by org: ${org}`\n  }\n  if (project) {\n    message += `\\nFiltered by project: ${project}`\n  }\n  if (includeExpired) {\n    message += `\\nIncluding expired entries`\n  }\n\n  return textResult(message)\n}\n\n/**\n * Validate and sanitize regex pattern to prevent ReDoS attacks\n */\nfunction validateRegexPattern(pattern: string): { valid: boolean; error?: string } {\n  // Check pattern length (prevent extremely long patterns)\n  if (pattern.length > 1000) {\n    return { valid: false, error: 'Pattern too long (max 1000 characters)' }\n  }\n\n  // Check for common ReDoS patterns\n  const redosPatterns = [\n    /(\\.\\*){3,}/,           // Multiple consecutive .*\n    /(\\+\\+|\\*\\*|\\?\\?)/,     // Nested quantifiers\n    /(\\([^)]*){10,}/,       // Too many groups\n    /(\\[[^\\]]{100,})/,      // Very long character classes\n  ]\n\n  for (const redos of redosPatterns) {\n    if (redos.test(pattern)) {\n      return { valid: false, error: 'Pattern contains potentially dangerous constructs' }\n    }\n  }\n\n  // Try to compile the regex to check for syntax errors\n  try {\n    new RegExp(pattern)\n    return { valid: true }\n  } catch (error) {\n    const message = error instanceof Error ? error.message : 'Invalid regex'\n    return { valid: false, error: message }\n  }\n}\n\n/**\n * Handle codex_invalidate tool\n */\nexport async function handleInvalidate(args: InvalidateToolArgs, ctx: ToolHandlerContext): Promise<ToolResult> {\n  const { pattern } = args\n\n  if (!pattern || typeof pattern !== 'string') {\n    return textResult('Pattern is required and must be a string', true)\n  }\n\n  // Validate pattern to prevent ReDoS\n  const validation = validateRegexPattern(pattern)\n  if (!validation.valid) {\n    return textResult(`Invalid pattern: ${validation.error}`, true)\n  }\n\n  try {\n    const regex = new RegExp(pattern)\n    const count = await ctx.cache.invalidatePattern(regex)\n\n    return textResult(`Invalidated ${count} cache entries matching pattern: ${pattern}`)\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error)\n    return textResult(`Failed to invalidate cache: ${message}`, true)\n  }\n}\n\n/**\n * Route a tool call to its handler\n */\nexport async function handleToolCall(\n  name: string,\n  args: Record<string, unknown>,\n  ctx: ToolHandlerContext\n): Promise<ToolResult> {\n  switch (name) {\n    case 'codex_fetch':\n      return handleFetch(args as unknown as FetchToolArgs, ctx)\n    case 'codex_search':\n      return handleSearch(args as unknown as SearchToolArgs, ctx)\n    case 'codex_list':\n      return handleList(args as unknown as ListToolArgs, ctx)\n    case 'codex_invalidate':\n      return handleInvalidate(args as unknown as InvalidateToolArgs, ctx)\n    default:\n      return textResult(`Unknown tool: ${name}`, true)\n  }\n}\n\n/**\n * Format bytes to human readable string\n */\nfunction formatBytes(bytes: number): string {\n  if (bytes === 0) return '0 B'\n  const k = 1024\n  const sizes = ['B', 'KB', 'MB', 'GB']\n  const i = Math.floor(Math.log(bytes) / Math.log(k))\n  return `${parseFloat((bytes / Math.pow(k, i)).toFixed(2))} 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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@fractary/codex-mcp",
-  "version": "0.1.0",
+  "version": "0.2.1",
   "description": "MCP server for Fractary Codex knowledge management",
   "keywords": [
     "codex",