mnemosyne-core 2.0.3 → 2.1.1

package/dist/mcp/index.d.mts

@@ -1,4 +1,4 @@
-export { J as JsonRpcRequest, a as JsonRpcResponse, M as McpServer, b as McpSseTransport, c as McpStdioTransport, d as McpTool, T as TOOLS } from '../index-yTOihMUk.mjs';
-import '../Store-BtdYuiUx.mjs';
+export { J as JsonRpcRequest, a as JsonRpcResponse, M as McpServer, b as McpSseTransport, c as McpStdioTransport, d as McpTool, T as TOOLS } from '../index-2AoCh09i.mjs';
+import '../Store-BJ8b6xbs.mjs';
 import 'better-sqlite3';
 import 'http';

package/dist/mcp/index.d.ts

@@ -1,4 +1,4 @@
-export { J as JsonRpcRequest, a as JsonRpcResponse, M as McpServer, b as McpSseTransport, c as McpStdioTransport, d as McpTool, T as TOOLS } from '../index-DWk78ifo.js';
-import '../Store-BtdYuiUx.js';
+export { J as JsonRpcRequest, a as JsonRpcResponse, M as McpServer, b as McpSseTransport, c as McpStdioTransport, d as McpTool, T as TOOLS } from '../index-CfqixdlW.js';
+import '../Store-BJ8b6xbs.js';
 import 'better-sqlite3';
 import 'http';

package/dist/mcp/index.js

@@ -257,7 +257,7 @@ function getVersion() {
       const pkg = JSON.parse(readFileSync(resolve(process.cwd(), "package.json"), "utf-8"));
       return pkg.version;
     } catch {
-      return "2.0.3";
+      return "2.1.0";
     }
   }
 }

package/dist/mcp/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../src/mcp/index.ts","../../src/mcp/tools.ts","../../src/mcp/server.ts","../../src/mcp/sse.ts","../../src/mcp/stdio.ts"],"sourcesContent":["export { McpServer } from \"./server.js\";\nexport { TOOLS } from \"./tools.js\";\nexport { McpSseTransport } from \"./sse.js\";\nexport { McpStdioTransport } from \"./stdio.js\";\nexport type { McpTool, JsonRpcRequest, JsonRpcResponse } from \"./types.js\";\n","/**\n * MCP Tool Definitions\n * All tools exposed to MCP clients (Claude Desktop, Cursor, etc.)\n */\n\nimport type { Store } from \"../core/Store.js\";\nimport type { McpTool } from \"./types.js\";\n\nexport const TOOLS: McpTool[] = [\n  {\n    name: \"nexus_list_projects\",\n    description: \"List all projects in the Mnemosyne knowledge base.\",\n    inputSchema: { type: \"object\", properties: {} },\n    handler: (_args, store) => {\n      return { projects: store.getProjects().map(p => ({ id: p.id, name: p.name, description: p.description, atomCount: store.getAtomsByProject(p.id).length })) };\n    },\n  },\n  {\n    name: \"nexus_search\",\n    description: \"Search atoms and blocks by keyword. Returns ranked results.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        query: { type: \"string\", description: \"Search query\" },\n        project: { type: \"string\", description: \"Project name or ID (optional)\" },\n        limit: { type: \"number\", description: \"Max results (default 10)\" },\n      },\n      required: [\"query\"],\n    },\n    handler: (args, store) => {\n      const projectId = args.project ? store.getProjectByName(args.project)?.id || args.project : \"\";\n      const results = store.search(projectId, args.query, args.limit || 10);\n      return { query: args.query, count: results.length, results };\n    },\n  },\n  {\n    name: \"nexus_read_atom\",\n    description: \"Read an atom by ID or title. Returns atom details, blocks, children, and bonds.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        id: { type: \"string\", description: \"Atom UUID\" },\n        title: { type: \"string\", description: \"Atom title (alternative to id)\" },\n        project: { type: \"string\", description: \"Project name (required if searching by title)\" },\n      },\n      required: [],\n    },\n    handler: (args, store) => {\n      let atom = args.id ? store.getAtom(args.id) : undefined;\n      if (!atom && args.title && args.project) {\n        const projectId = store.getProjectByName(args.project)?.id || args.project;\n        atom = store.getAtomsByProject(projectId).find(a => a.title === args.title);\n      }\n      if (!atom) throw new Error(\"Atom not found\");\n      const children = store.getAtomChildren(atom.id).map(a => ({ id: a.id, title: a.title, type: a.metadata?.type || \"text\" }));\n      const blocks = store.getBlocksByAtom(atom.id);\n      const bonds = store.getBondsByAtom(atom.id);\n      return { atom, children, blocks, bonds };\n    },\n  },\n  {\n    name: \"nexus_create_atom\",\n    description: \"Create a new atom in a project.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        project: { type: \"string\", description: \"Project name or ID\" },\n        title: { type: \"string\", description: \"Atom title/path\" },\n        type: { type: \"string\", description: \"Atom type (text, memory, stream, thought, task)\" },\n        parent_id: { type: \"string\", description: \"Parent atom ID (optional)\" },\n        tags: { type: \"array\", items: { type: \"string\" }, description: \"Tags (optional)\" },\n        assistant_id: { type: \"string\", description: \"Creator assistant ID\" },\n      },\n      required: [\"project\", \"title\"],\n    },\n    handler: (args, store) => {\n      const project = store.getProjectByName(args.project) || store.getProject(args.project);\n      if (!project) throw new Error(\"Project not found\");\n      const assistantId = args.assistant_id || \"mcp-assistant\";\n      const atom = store.createAtom(project.id, args.title, args.type || \"text\", assistantId, {\n        parentId: args.parent_id,\n        tags: args.tags,\n      });\n      return { success: true, atom };\n    },\n  },\n  {\n    name: \"nexus_update_atom\",\n    description: \"Update an atom's title or parent.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        id: { type: \"string\", description: \"Atom UUID\" },\n        title: { type: \"string\", description: \"New title\" },\n        parent_id: { type: [\"string\", \"null\"], description: \"New parent ID or null for root\" },\n        assistant_id: { type: \"string\", description: \"Updater assistant ID\" },\n      },\n      required: [\"id\"],\n    },\n    handler: (args, store) => {\n      const assistantId = args.assistant_id || \"mcp-assistant\";\n      if (args.parent_id !== undefined) {\n        const updated = store.updateAtomParent(args.id, args.parent_id, assistantId);\n        if (!updated) throw new Error(\"Invalid parent or atom not found\");\n      }\n      const updated = store.updateAtom(args.id, { title: args.title }, assistantId);\n      return { success: true, atom: updated || store.getAtom(args.id) };\n    },\n  },\n  {\n    name: \"nexus_create_bond\",\n    description: \"Create a bond (graph connection) between two atoms.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        source_id: { type: \"string\", description: \"Source atom ID\" },\n        target_id: { type: \"string\", description: \"Target atom ID\" },\n        label: { type: \"string\", description: \"Bond label (default: connects)\" },\n        color: { type: \"string\", description: \"Hex color (optional)\" },\n      },\n      required: [\"source_id\", \"target_id\"],\n    },\n    handler: (args, store) => {\n      const bond = store.createBond(args.source_id, args.target_id, args.label || \"connects\", args.color);\n      return { success: true, bond };\n    },\n  },\n  {\n    name: \"nexus_request_checkout\",\n    description: \"Request an exclusive checkout (lock) on an atom.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        atom_id: { type: \"string\", description: \"Atom UUID\" },\n        assistant_id: { type: \"string\", description: \"Assistant requesting checkout\" },\n        reason: { type: \"string\", description: \"Reason for checkout\" },\n      },\n      required: [\"atom_id\", \"assistant_id\"],\n    },\n    handler: (args, store) => {\n      const result = store.checkout(args.atom_id, args.assistant_id, \"exclusive\", args.reason || \"\");\n      return result;\n    },\n  },\n  {\n    name: \"nexus_release_checkout\",\n    description: \"Release a checkout (unlock) on an atom.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        atom_id: { type: \"string\", description: \"Atom UUID\" },\n        assistant_id: { type: \"string\", description: \"Assistant releasing checkout\" },\n      },\n      required: [\"atom_id\", \"assistant_id\"],\n    },\n    handler: (args, store) => {\n      const success = store.releaseCheckout(args.atom_id, args.assistant_id);\n      return { success };\n    },\n  },\n  {\n    name: \"nexus_subscribe_to_atom\",\n    description: \"Subscribe to real-time updates for an atom via WebSocket.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        atom_id: { type: \"string\", description: \"Atom UUID to subscribe to\" },\n      },\n      required: [\"atom_id\"],\n    },\n    handler: (args, _store) => {\n      return { success: true, wsEndpoint: \"ws://localhost:7321/ws\", atom_id: args.atom_id, message: \"Connect via WebSocket and send { type: 'subscribe', atomId: '<id>' }\" };\n    },\n  },\n  {\n    name: \"nexus_batch\",\n    description: \"Execute multiple MCP tools in a single request. Reduces round-trip token waste.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        operations: {\n          type: \"array\",\n          items: {\n            type: \"object\",\n            properties: {\n              tool: { type: \"string\", description: \"Tool name to call\" },\n              params: { type: \"object\", description: \"Parameters for the tool\" },\n            },\n            required: [\"tool\"],\n          },\n          description: \"Ordered list of tool calls\",\n        },\n        stop_on_error: { type: \"boolean\", description: \"If true, stop at first error. Default: false\", default: false },\n      },\n      required: [\"operations\"],\n    },\n    handler: (args, store) => {\n      const operations = args.operations || [];\n      const stopOnError = args.stop_on_error ?? false;\n      const results: any[] = [];\n      const toolMap = new Map<string, McpTool>();\n      for (const t of TOOLS) toolMap.set(t.name, t);\n\n      for (let i = 0; i < operations.length; i++) {\n        const op = operations[i];\n        const tool = toolMap.get(op.tool);\n        if (!tool) {\n          results.push({ index: i, tool: op.tool, error: `Tool not found: ${op.tool}` });\n          if (stopOnError) break;\n          continue;\n        }\n        try {\n          const result = tool.handler(op.params || {}, store);\n          results.push({ index: i, tool: op.tool, success: true, result });\n        } catch (err: any) {\n          results.push({ index: i, tool: op.tool, error: err.message });\n          if (stopOnError) break;\n        }\n      }\n      return { count: operations.length, completed: results.length, results };\n    },\n  },\n];\n","/**\n * MCP Server\n * JSON-RPC handler for Model Context Protocol.\n */\n\nimport type { Store } from \"../core/Store.js\";\nimport { TOOLS } from \"./tools.js\";\nimport type { JsonRpcRequest, JsonRpcResponse, McpTool } from \"./types.js\";\n\nfunction getVersion(): string {\n  try {\n    const { readFileSync } = require(\"fs\");\n    const { resolve } = require(\"path\");\n    const pkg = JSON.parse(readFileSync(resolve(__dirname, \"../../package.json\"), \"utf-8\"));\n    return pkg.version;\n  } catch {\n    try {\n      const { readFileSync } = require(\"fs\");\n      const { resolve } = require(\"path\");\n      const pkg = JSON.parse(readFileSync(resolve(process.cwd(), \"package.json\"), \"utf-8\"));\n      return pkg.version;\n    } catch {\n      return \"2.0.3\";\n    }\n  }\n}\n\nexport class McpServer {\n  private store: Store;\n  private toolMap = new Map<string, McpTool>();\n\n  constructor(store: Store) {\n    this.store = store;\n    for (const t of TOOLS) this.toolMap.set(t.name, t);\n  }\n\n  /**\n   * Returns `null` for notifications (no response needed).\n   */\n  handleRequest(req: JsonRpcRequest): JsonRpcResponse | null {\n    // Notifications have no id — do not send a response\n    if (req.id === null || req.id === undefined) {\n      return null;\n    }\n\n    try {\n      switch (req.method) {\n        case \"initialize\":\n          return this.ok(req.id, {\n            protocolVersion: \"2024-11-05\",\n            capabilities: { tools: {}, resources: {}, prompts: {} },\n            serverInfo: { name: \"mnemosyne-mcp\", version: getVersion() },\n          });\n\n        case \"tools/list\":\n          return this.ok(req.id, {\n            tools: TOOLS.map(t => ({ name: t.name, description: t.description, inputSchema: t.inputSchema })),\n          });\n\n        case \"tools/call\": {\n          const { name, arguments: args } = req.params || {};\n          const tool = this.toolMap.get(name);\n          if (!tool) return this.err(req.id, -32601, `Tool not found: ${name}`);\n          const result = tool.handler(args || {}, this.store);\n          return this.ok(req.id, { content: [{ type: \"text\", text: JSON.stringify(result, null, 2) }] });\n        }\n\n        case \"resources/list\":\n          return this.ok(req.id, { resources: [] });\n\n        case \"prompts/list\":\n          return this.ok(req.id, { prompts: [] });\n\n        default:\n          return this.err(req.id, -32601, `Method not found: ${req.method}`);\n      }\n    } catch (e: any) {\n      return this.err(req.id, -32603, e.message);\n    }\n  }\n\n  getManifest() {\n    return {\n      name: \"Mnemosyne\",\n      version: getVersion(),\n      description: \"Knowledge base MCP server for projects, atoms, blocks, and bonds.\",\n      protocol: \"mcp\",\n      transport: [\"stdio\", \"sse\"],\n      endpoints: {\n        sse: \"/mcp/sse\",\n        messages: \"/mcp/messages\",\n      },\n      tools: TOOLS.map(t => ({ name: t.name, description: t.description })),\n    };\n  }\n\n  private ok(id: string | number | null, result: any): JsonRpcResponse {\n    return { jsonrpc: \"2.0\", id, result };\n  }\n  private err(id: string | number | null, code: number, message: string): JsonRpcResponse {\n    return { jsonrpc: \"2.0\", id, error: { code, message } };\n  }\n}\n","/**\n * MCP SSE Transport\n * Server-Sent Events transport for MCP over HTTP.\n */\n\nimport type { McpServer } from \"./server.js\";\nimport type { JsonRpcRequest } from \"./types.js\";\n\ninterface SseSession {\n  id: string;\n  res: import(\"http\").ServerResponse;\n}\n\nexport class McpSseTransport {\n  private server: McpServer;\n  private sessions = new Map<string, SseSession>();\n  private sessionCounter = 0;\n\n  constructor(server: McpServer) {\n    this.server = server;\n  }\n\n  handleSse(req: import(\"http\").IncomingMessage, res: import(\"http\").ServerResponse): void {\n    const id = `sess_${++this.sessionCounter}_${Date.now()}`;\n    res.writeHead(200, {\n      \"Content-Type\": \"text/event-stream\",\n      \"Cache-Control\": \"no-cache\",\n      \"Connection\": \"keep-alive\",\n    });\n    this.sessions.set(id, { id, res });\n\n    // Send endpoint event\n    this.sendSse(id, \"endpoint\", \"/mcp/messages?session_id=\" + id);\n\n    req.on(\"close\", () => this.sessions.delete(id));\n  }\n\n  handleMessage(req: import(\"http\").IncomingMessage, res: import(\"http\").ServerResponse, body: any): void {\n    const url = new URL(req.url || \"/\", `http://${req.headers.host}`);\n    const sessionId = url.searchParams.get(\"session_id\") || \"\";\n\n    const request = body as JsonRpcRequest;\n    if (!request || request.jsonrpc !== \"2.0\") {\n      res.writeHead(400, { \"Content-Type\": \"application/json\" });\n      res.end(JSON.stringify({ error: \"invalid_jsonrpc\" }));\n      return;\n    }\n\n    const response = this.server.handleRequest(request);\n    // Notifications return null — send empty 200\n    if (!response) {\n      res.writeHead(200, { \"Content-Type\": \"application/json\" });\n      res.end(\"{}\");\n      return;\n    }\n\n    res.writeHead(200, { \"Content-Type\": \"application/json\" });\n    res.end(JSON.stringify(response));\n\n    // Also broadcast via SSE if the session is active\n    if (sessionId) this.sendSse(sessionId, \"message\", JSON.stringify(response));\n  }\n\n  private sendSse(sessionId: string, event: string, data: string): void {\n    const session = this.sessions.get(sessionId);\n    if (!session) return;\n    session.res.write(`event: ${event}\\ndata: ${data}\\n\\n`);\n  }\n}\n","/**\n * MCP Stdio Transport\n * Line-delimited JSON-RPC over stdin/stdout.\n * This is what Claude Desktop uses to communicate with MCP servers.\n */\n\nimport type { McpServer } from \"./server.js\";\nimport type { JsonRpcRequest, JsonRpcResponse } from \"./types.js\";\n\nexport class McpStdioTransport {\n  private server: McpServer;\n  private buffer = \"\";\n\n  constructor(server: McpServer) {\n    this.server = server;\n  }\n\n  start(): void {\n    process.stdin.setEncoding(\"utf8\");\n    process.stdin.resume();\n\n    process.stdin.on(\"data\", (chunk: string) => {\n      this.buffer += chunk;\n      const lines = this.buffer.split(\"\\n\");\n      this.buffer = lines.pop() || \"\";\n\n      for (const line of lines) {\n        if (!line.trim()) continue;\n        try {\n          const request = JSON.parse(line) as JsonRpcRequest;\n          const response = this.server.handleRequest(request);\n          if (response) this.send(response);\n          // Notifications return null — no output\n        } catch (err: any) {\n          this.send({ jsonrpc: \"2.0\", id: null, error: { code: -32700, message: \"Parse error: \" + err.message } });\n        }\n      }\n    });\n\n    process.stdin.on(\"end\", () => {\n      process.exit(0);\n    });\n  }\n\n  send(message: JsonRpcResponse): void {\n    process.stdout.write(JSON.stringify(message) + \"\\n\");\n  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+{"version":3,"sources":["../../src/mcp/index.ts","../../src/mcp/tools.ts","../../src/mcp/server.ts","../../src/mcp/sse.ts","../../src/mcp/stdio.ts"],"sourcesContent":["export { McpServer } from \"./server.js\";\nexport { TOOLS } from \"./tools.js\";\nexport { McpSseTransport } from \"./sse.js\";\nexport { McpStdioTransport } from \"./stdio.js\";\nexport type { McpTool, JsonRpcRequest, JsonRpcResponse } from \"./types.js\";\n","/**\n * MCP Tool Definitions\n * All tools exposed to MCP clients (Claude Desktop, Cursor, etc.)\n */\n\nimport type { Store } from \"../core/Store.js\";\nimport type { McpTool } from \"./types.js\";\n\nexport const TOOLS: McpTool[] = [\n  {\n    name: \"nexus_list_projects\",\n    description: \"List all projects in the Mnemosyne knowledge base.\",\n    inputSchema: { type: \"object\", properties: {} },\n    handler: (_args, store) => {\n      return { projects: store.getProjects().map(p => ({ id: p.id, name: p.name, description: p.description, atomCount: store.getAtomsByProject(p.id).length })) };\n    },\n  },\n  {\n    name: \"nexus_search\",\n    description: \"Search atoms and blocks by keyword. Returns ranked results.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        query: { type: \"string\", description: \"Search query\" },\n        project: { type: \"string\", description: \"Project name or ID (optional)\" },\n        limit: { type: \"number\", description: \"Max results (default 10)\" },\n      },\n      required: [\"query\"],\n    },\n    handler: (args, store) => {\n      const projectId = args.project ? store.getProjectByName(args.project)?.id || args.project : \"\";\n      const results = store.search(projectId, args.query, args.limit || 10);\n      return { query: args.query, count: results.length, results };\n    },\n  },\n  {\n    name: \"nexus_read_atom\",\n    description: \"Read an atom by ID or title. Returns atom details, blocks, children, and bonds.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        id: { type: \"string\", description: \"Atom UUID\" },\n        title: { type: \"string\", description: \"Atom title (alternative to id)\" },\n        project: { type: \"string\", description: \"Project name (required if searching by title)\" },\n      },\n      required: [],\n    },\n    handler: (args, store) => {\n      let atom = args.id ? store.getAtom(args.id) : undefined;\n      if (!atom && args.title && args.project) {\n        const projectId = store.getProjectByName(args.project)?.id || args.project;\n        atom = store.getAtomsByProject(projectId).find(a => a.title === args.title);\n      }\n      if (!atom) throw new Error(\"Atom not found\");\n      const children = store.getAtomChildren(atom.id).map(a => ({ id: a.id, title: a.title, type: a.metadata?.type || \"text\" }));\n      const blocks = store.getBlocksByAtom(atom.id);\n      const bonds = store.getBondsByAtom(atom.id);\n      return { atom, children, blocks, bonds };\n    },\n  },\n  {\n    name: \"nexus_create_atom\",\n    description: \"Create a new atom in a project.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        project: { type: \"string\", description: \"Project name or ID\" },\n        title: { type: \"string\", description: \"Atom title/path\" },\n        type: { type: \"string\", description: \"Atom type (text, memory, stream, thought, task)\" },\n        parent_id: { type: \"string\", description: \"Parent atom ID (optional)\" },\n        tags: { type: \"array\", items: { type: \"string\" }, description: \"Tags (optional)\" },\n        assistant_id: { type: \"string\", description: \"Creator assistant ID\" },\n      },\n      required: [\"project\", \"title\"],\n    },\n    handler: (args, store) => {\n      const project = store.getProjectByName(args.project) || store.getProject(args.project);\n      if (!project) throw new Error(\"Project not found\");\n      const assistantId = args.assistant_id || \"mcp-assistant\";\n      const atom = store.createAtom(project.id, args.title, args.type || \"text\", assistantId, {\n        parentId: args.parent_id,\n        tags: args.tags,\n      });\n      return { success: true, atom };\n    },\n  },\n  {\n    name: \"nexus_update_atom\",\n    description: \"Update an atom's title or parent.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        id: { type: \"string\", description: \"Atom UUID\" },\n        title: { type: \"string\", description: \"New title\" },\n        parent_id: { type: [\"string\", \"null\"], description: \"New parent ID or null for root\" },\n        assistant_id: { type: \"string\", description: \"Updater assistant ID\" },\n      },\n      required: [\"id\"],\n    },\n    handler: (args, store) => {\n      const assistantId = args.assistant_id || \"mcp-assistant\";\n      if (args.parent_id !== undefined) {\n        const updated = store.updateAtomParent(args.id, args.parent_id, assistantId);\n        if (!updated) throw new Error(\"Invalid parent or atom not found\");\n      }\n      const updated = store.updateAtom(args.id, { title: args.title }, assistantId);\n      return { success: true, atom: updated || store.getAtom(args.id) };\n    },\n  },\n  {\n    name: \"nexus_create_bond\",\n    description: \"Create a bond (graph connection) between two atoms.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        source_id: { type: \"string\", description: \"Source atom ID\" },\n        target_id: { type: \"string\", description: \"Target atom ID\" },\n        label: { type: \"string\", description: \"Bond label (default: connects)\" },\n        color: { type: \"string\", description: \"Hex color (optional)\" },\n      },\n      required: [\"source_id\", \"target_id\"],\n    },\n    handler: (args, store) => {\n      const bond = store.createBond(args.source_id, args.target_id, args.label || \"connects\", args.color);\n      return { success: true, bond };\n    },\n  },\n  {\n    name: \"nexus_request_checkout\",\n    description: \"Request an exclusive checkout (lock) on an atom.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        atom_id: { type: \"string\", description: \"Atom UUID\" },\n        assistant_id: { type: \"string\", description: \"Assistant requesting checkout\" },\n        reason: { type: \"string\", description: \"Reason for checkout\" },\n      },\n      required: [\"atom_id\", \"assistant_id\"],\n    },\n    handler: (args, store) => {\n      const result = store.checkout(args.atom_id, args.assistant_id, \"exclusive\", args.reason || \"\");\n      return result;\n    },\n  },\n  {\n    name: \"nexus_release_checkout\",\n    description: \"Release a checkout (unlock) on an atom.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        atom_id: { type: \"string\", description: \"Atom UUID\" },\n        assistant_id: { type: \"string\", description: \"Assistant releasing checkout\" },\n      },\n      required: [\"atom_id\", \"assistant_id\"],\n    },\n    handler: (args, store) => {\n      const success = store.releaseCheckout(args.atom_id, args.assistant_id);\n      return { success };\n    },\n  },\n  {\n    name: \"nexus_subscribe_to_atom\",\n    description: \"Subscribe to real-time updates for an atom via WebSocket.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        atom_id: { type: \"string\", description: \"Atom UUID to subscribe to\" },\n      },\n      required: [\"atom_id\"],\n    },\n    handler: (args, _store) => {\n      return { success: true, wsEndpoint: \"ws://localhost:7321/ws\", atom_id: args.atom_id, message: \"Connect via WebSocket and send { type: 'subscribe', atomId: '<id>' }\" };\n    },\n  },\n  {\n    name: \"nexus_batch\",\n    description: \"Execute multiple MCP tools in a single request. Reduces round-trip token waste.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        operations: {\n          type: \"array\",\n          items: {\n            type: \"object\",\n            properties: {\n              tool: { type: \"string\", description: \"Tool name to call\" },\n              params: { type: \"object\", description: \"Parameters for the tool\" },\n            },\n            required: [\"tool\"],\n          },\n          description: \"Ordered list of tool calls\",\n        },\n        stop_on_error: { type: \"boolean\", description: \"If true, stop at first error. Default: false\", default: false },\n      },\n      required: [\"operations\"],\n    },\n    handler: (args, store) => {\n      const operations = args.operations || [];\n      const stopOnError = args.stop_on_error ?? false;\n      const results: any[] = [];\n      const toolMap = new Map<string, McpTool>();\n      for (const t of TOOLS) toolMap.set(t.name, t);\n\n      for (let i = 0; i < operations.length; i++) {\n        const op = operations[i];\n        const tool = toolMap.get(op.tool);\n        if (!tool) {\n          results.push({ index: i, tool: op.tool, error: `Tool not found: ${op.tool}` });\n          if (stopOnError) break;\n          continue;\n        }\n        try {\n          const result = tool.handler(op.params || {}, store);\n          results.push({ index: i, tool: op.tool, success: true, result });\n        } catch (err: any) {\n          results.push({ index: i, tool: op.tool, error: err.message });\n          if (stopOnError) break;\n        }\n      }\n      return { count: operations.length, completed: results.length, results };\n    },\n  },\n];\n","/**\n * MCP Server\n * JSON-RPC handler for Model Context Protocol.\n */\n\nimport type { Store } from \"../core/Store.js\";\nimport { TOOLS } from \"./tools.js\";\nimport type { JsonRpcRequest, JsonRpcResponse, McpTool } from \"./types.js\";\n\nfunction getVersion(): string {\n  try {\n    const { readFileSync } = require(\"fs\");\n    const { resolve } = require(\"path\");\n    const pkg = JSON.parse(readFileSync(resolve(__dirname, \"../../package.json\"), \"utf-8\"));\n    return pkg.version;\n  } catch {\n    try {\n      const { readFileSync } = require(\"fs\");\n      const { resolve } = require(\"path\");\n      const pkg = JSON.parse(readFileSync(resolve(process.cwd(), \"package.json\"), \"utf-8\"));\n      return pkg.version;\n    } catch {\n      return \"2.1.0\";\n    }\n  }\n}\n\nexport class McpServer {\n  private store: Store;\n  private toolMap = new Map<string, McpTool>();\n\n  constructor(store: Store) {\n    this.store = store;\n    for (const t of TOOLS) this.toolMap.set(t.name, t);\n  }\n\n  /**\n   * Returns `null` for notifications (no response needed).\n   */\n  handleRequest(req: JsonRpcRequest): JsonRpcResponse | null {\n    // Notifications have no id — do not send a response\n    if (req.id === null || req.id === undefined) {\n      return null;\n    }\n\n    try {\n      switch (req.method) {\n        case \"initialize\":\n          return this.ok(req.id, {\n            protocolVersion: \"2024-11-05\",\n            capabilities: { tools: {}, resources: {}, prompts: {} },\n            serverInfo: { name: \"mnemosyne-mcp\", version: getVersion() },\n          });\n\n        case \"tools/list\":\n          return this.ok(req.id, {\n            tools: TOOLS.map(t => ({ name: t.name, description: t.description, inputSchema: t.inputSchema })),\n          });\n\n        case \"tools/call\": {\n          const { name, arguments: args } = req.params || {};\n          const tool = this.toolMap.get(name);\n          if (!tool) return this.err(req.id, -32601, `Tool not found: ${name}`);\n          const result = tool.handler(args || {}, this.store);\n          return this.ok(req.id, { content: [{ type: \"text\", text: JSON.stringify(result, null, 2) }] });\n        }\n\n        case \"resources/list\":\n          return this.ok(req.id, { resources: [] });\n\n        case \"prompts/list\":\n          return this.ok(req.id, { prompts: [] });\n\n        default:\n          return this.err(req.id, -32601, `Method not found: ${req.method}`);\n      }\n    } catch (e: any) {\n      return this.err(req.id, -32603, e.message);\n    }\n  }\n\n  getManifest() {\n    return {\n      name: \"Mnemosyne\",\n      version: getVersion(),\n      description: \"Knowledge base MCP server for projects, atoms, blocks, and bonds.\",\n      protocol: \"mcp\",\n      transport: [\"stdio\", \"sse\"],\n      endpoints: {\n        sse: \"/mcp/sse\",\n        messages: \"/mcp/messages\",\n      },\n      tools: TOOLS.map(t => ({ name: t.name, description: t.description })),\n    };\n  }\n\n  private ok(id: string | number | null, result: any): JsonRpcResponse {\n    return { jsonrpc: \"2.0\", id, result };\n  }\n  private err(id: string | number | null, code: number, message: string): JsonRpcResponse {\n    return { jsonrpc: \"2.0\", id, error: { code, message } };\n  }\n}\n","/**\n * MCP SSE Transport\n * Server-Sent Events transport for MCP over HTTP.\n */\n\nimport type { McpServer } from \"./server.js\";\nimport type { JsonRpcRequest } from \"./types.js\";\n\ninterface SseSession {\n  id: string;\n  res: import(\"http\").ServerResponse;\n}\n\nexport class McpSseTransport {\n  private server: McpServer;\n  private sessions = new Map<string, SseSession>();\n  private sessionCounter = 0;\n\n  constructor(server: McpServer) {\n    this.server = server;\n  }\n\n  handleSse(req: import(\"http\").IncomingMessage, res: import(\"http\").ServerResponse): void {\n    const id = `sess_${++this.sessionCounter}_${Date.now()}`;\n    res.writeHead(200, {\n      \"Content-Type\": \"text/event-stream\",\n      \"Cache-Control\": \"no-cache\",\n      \"Connection\": \"keep-alive\",\n    });\n    this.sessions.set(id, { id, res });\n\n    // Send endpoint event\n    this.sendSse(id, \"endpoint\", \"/mcp/messages?session_id=\" + id);\n\n    req.on(\"close\", () => this.sessions.delete(id));\n  }\n\n  handleMessage(req: import(\"http\").IncomingMessage, res: import(\"http\").ServerResponse, body: any): void {\n    const url = new URL(req.url || \"/\", `http://${req.headers.host}`);\n    const sessionId = url.searchParams.get(\"session_id\") || \"\";\n\n    const request = body as JsonRpcRequest;\n    if (!request || request.jsonrpc !== \"2.0\") {\n      res.writeHead(400, { \"Content-Type\": \"application/json\" });\n      res.end(JSON.stringify({ error: \"invalid_jsonrpc\" }));\n      return;\n    }\n\n    const response = this.server.handleRequest(request);\n    // Notifications return null — send empty 200\n    if (!response) {\n      res.writeHead(200, { \"Content-Type\": \"application/json\" });\n      res.end(\"{}\");\n      return;\n    }\n\n    res.writeHead(200, { \"Content-Type\": \"application/json\" });\n    res.end(JSON.stringify(response));\n\n    // Also broadcast via SSE if the session is active\n    if (sessionId) this.sendSse(sessionId, \"message\", JSON.stringify(response));\n  }\n\n  private sendSse(sessionId: string, event: string, data: string): void {\n    const session = this.sessions.get(sessionId);\n    if (!session) return;\n    session.res.write(`event: ${event}\\ndata: ${data}\\n\\n`);\n  }\n}\n","/**\n * MCP Stdio Transport\n * Line-delimited JSON-RPC over stdin/stdout.\n * This is what Claude Desktop uses to communicate with MCP servers.\n */\n\nimport type { McpServer } from \"./server.js\";\nimport type { JsonRpcRequest, JsonRpcResponse } from \"./types.js\";\n\nexport class McpStdioTransport {\n  private server: McpServer;\n  private buffer = \"\";\n\n  constructor(server: McpServer) {\n    this.server = server;\n  }\n\n  start(): void {\n    process.stdin.setEncoding(\"utf8\");\n    process.stdin.resume();\n\n    process.stdin.on(\"data\", (chunk: string) => {\n      this.buffer += chunk;\n      const lines = this.buffer.split(\"\\n\");\n      this.buffer = lines.pop() || \"\";\n\n      for (const line of lines) {\n        if (!line.trim()) continue;\n        try {\n          const request = JSON.parse(line) as JsonRpcRequest;\n          const response = this.server.handleRequest(request);\n          if (response) this.send(response);\n          // Notifications return null — no output\n        } catch (err: any) {\n          this.send({ jsonrpc: \"2.0\", id: null, error: { code: -32700, message: \"Parse error: \" + err.message } });\n        }\n      }\n    });\n\n    process.stdin.on(\"end\", () => {\n      process.exit(0);\n    });\n  }\n\n  send(message: JsonRpcResponse): void {\n    process.stdout.write(JSON.stringify(message) + \"\\n\");\n  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package/dist/mcp/index.mjs

@@ -235,7 +235,7 @@ function getVersion() {
       const pkg = JSON.parse(readFileSync(resolve(process.cwd(), "package.json"), "utf-8"));
       return pkg.version;
     } catch {
-      return "2.0.3";
+      return "2.1.0";
     }
   }
 }

package/dist/mcp/index.mjs.map

@@ -1 +1 @@
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Returns ranked results.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        query: { type: \"string\", description: \"Search query\" },\n        project: { type: \"string\", description: \"Project name or ID (optional)\" },\n        limit: { type: \"number\", description: \"Max results (default 10)\" },\n      },\n      required: [\"query\"],\n    },\n    handler: (args, store) => {\n      const projectId = args.project ? store.getProjectByName(args.project)?.id || args.project : \"\";\n      const results = store.search(projectId, args.query, args.limit || 10);\n      return { query: args.query, count: results.length, results };\n    },\n  },\n  {\n    name: \"nexus_read_atom\",\n    description: \"Read an atom by ID or title. Returns atom details, blocks, children, and bonds.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        id: { type: \"string\", description: \"Atom UUID\" },\n        title: { type: \"string\", description: \"Atom title (alternative to id)\" },\n        project: { type: \"string\", description: \"Project name (required if searching by title)\" },\n      },\n      required: [],\n    },\n    handler: (args, store) => {\n      let atom = args.id ? store.getAtom(args.id) : undefined;\n      if (!atom && args.title && args.project) {\n        const projectId = store.getProjectByName(args.project)?.id || args.project;\n        atom = store.getAtomsByProject(projectId).find(a => a.title === args.title);\n      }\n      if (!atom) throw new Error(\"Atom not found\");\n      const children = store.getAtomChildren(atom.id).map(a => ({ id: a.id, title: a.title, type: a.metadata?.type || \"text\" }));\n      const blocks = store.getBlocksByAtom(atom.id);\n      const bonds = store.getBondsByAtom(atom.id);\n      return { atom, children, blocks, bonds };\n    },\n  },\n  {\n    name: \"nexus_create_atom\",\n    description: \"Create a new atom in a project.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        project: { type: \"string\", description: \"Project name or ID\" },\n        title: { type: \"string\", description: \"Atom title/path\" },\n        type: { type: \"string\", description: \"Atom type (text, memory, stream, thought, task)\" },\n        parent_id: { type: \"string\", description: \"Parent atom ID (optional)\" },\n        tags: { type: \"array\", items: { type: \"string\" }, description: \"Tags (optional)\" },\n        assistant_id: { type: \"string\", description: \"Creator assistant ID\" },\n      },\n      required: [\"project\", \"title\"],\n    },\n    handler: (args, store) => {\n      const project = store.getProjectByName(args.project) || store.getProject(args.project);\n      if (!project) throw new Error(\"Project not found\");\n      const assistantId = args.assistant_id || \"mcp-assistant\";\n      const atom = store.createAtom(project.id, args.title, args.type || \"text\", assistantId, {\n        parentId: args.parent_id,\n        tags: args.tags,\n      });\n      return { success: true, atom };\n    },\n  },\n  {\n    name: \"nexus_update_atom\",\n    description: \"Update an atom's title or parent.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        id: { type: \"string\", description: \"Atom UUID\" },\n        title: { type: \"string\", description: \"New title\" },\n        parent_id: { type: [\"string\", \"null\"], description: \"New parent ID or null for root\" },\n        assistant_id: { type: \"string\", description: \"Updater assistant ID\" },\n      },\n      required: [\"id\"],\n    },\n    handler: (args, store) => {\n      const assistantId = args.assistant_id || \"mcp-assistant\";\n      if (args.parent_id !== undefined) {\n        const updated = store.updateAtomParent(args.id, args.parent_id, assistantId);\n        if (!updated) throw new Error(\"Invalid parent or atom not found\");\n      }\n      const updated = store.updateAtom(args.id, { title: args.title }, assistantId);\n      return { success: true, atom: updated || store.getAtom(args.id) };\n    },\n  },\n  {\n    name: \"nexus_create_bond\",\n    description: \"Create a bond (graph connection) between two atoms.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        source_id: { type: \"string\", description: \"Source atom ID\" },\n        target_id: { type: \"string\", description: \"Target atom ID\" },\n        label: { type: \"string\", description: \"Bond label (default: connects)\" },\n        color: { type: \"string\", description: \"Hex color (optional)\" },\n      },\n      required: [\"source_id\", \"target_id\"],\n    },\n    handler: (args, store) => {\n      const bond = store.createBond(args.source_id, args.target_id, args.label || \"connects\", args.color);\n      return { success: true, bond };\n    },\n  },\n  {\n    name: \"nexus_request_checkout\",\n    description: \"Request an exclusive checkout (lock) on an atom.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        atom_id: { type: \"string\", description: \"Atom UUID\" },\n        assistant_id: { type: \"string\", description: \"Assistant requesting checkout\" },\n        reason: { type: \"string\", description: \"Reason for checkout\" },\n      },\n      required: [\"atom_id\", \"assistant_id\"],\n    },\n    handler: (args, store) => {\n      const result = store.checkout(args.atom_id, args.assistant_id, \"exclusive\", args.reason || \"\");\n      return result;\n    },\n  },\n  {\n    name: \"nexus_release_checkout\",\n    description: \"Release a checkout (unlock) on an atom.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        atom_id: { type: \"string\", description: \"Atom UUID\" },\n        assistant_id: { type: \"string\", description: \"Assistant releasing checkout\" },\n      },\n      required: [\"atom_id\", \"assistant_id\"],\n    },\n    handler: (args, store) => {\n      const success = store.releaseCheckout(args.atom_id, args.assistant_id);\n      return { success };\n    },\n  },\n  {\n    name: \"nexus_subscribe_to_atom\",\n    description: \"Subscribe to real-time updates for an atom via WebSocket.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        atom_id: { type: \"string\", description: \"Atom UUID to subscribe to\" },\n      },\n      required: [\"atom_id\"],\n    },\n    handler: (args, _store) => {\n      return { success: true, wsEndpoint: \"ws://localhost:7321/ws\", atom_id: args.atom_id, message: \"Connect via WebSocket and send { type: 'subscribe', atomId: '<id>' }\" };\n    },\n  },\n  {\n    name: \"nexus_batch\",\n    description: \"Execute multiple MCP tools in a single request. Reduces round-trip token waste.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        operations: {\n          type: \"array\",\n          items: {\n            type: \"object\",\n            properties: {\n              tool: { type: \"string\", description: \"Tool name to call\" },\n              params: { type: \"object\", description: \"Parameters for the tool\" },\n            },\n            required: [\"tool\"],\n          },\n          description: \"Ordered list of tool calls\",\n        },\n        stop_on_error: { type: \"boolean\", description: \"If true, stop at first error. Default: false\", default: false },\n      },\n      required: [\"operations\"],\n    },\n    handler: (args, store) => {\n      const operations = args.operations || [];\n      const stopOnError = args.stop_on_error ?? false;\n      const results: any[] = [];\n      const toolMap = new Map<string, McpTool>();\n      for (const t of TOOLS) toolMap.set(t.name, t);\n\n      for (let i = 0; i < operations.length; i++) {\n        const op = operations[i];\n        const tool = toolMap.get(op.tool);\n        if (!tool) {\n          results.push({ index: i, tool: op.tool, error: `Tool not found: ${op.tool}` });\n          if (stopOnError) break;\n          continue;\n        }\n        try {\n          const result = tool.handler(op.params || {}, store);\n          results.push({ index: i, tool: op.tool, success: true, result });\n        } catch (err: any) {\n          results.push({ index: i, tool: op.tool, error: err.message });\n          if (stopOnError) break;\n        }\n      }\n      return { count: operations.length, completed: results.length, results };\n    },\n  },\n];\n","/**\n * MCP Server\n * JSON-RPC handler for Model Context Protocol.\n */\n\nimport type { Store } from \"../core/Store.js\";\nimport { TOOLS } from \"./tools.js\";\nimport type { JsonRpcRequest, JsonRpcResponse, McpTool } from \"./types.js\";\n\nfunction getVersion(): string {\n  try {\n    const { readFileSync } = require(\"fs\");\n    const { resolve } = require(\"path\");\n    const pkg = JSON.parse(readFileSync(resolve(__dirname, \"../../package.json\"), \"utf-8\"));\n    return pkg.version;\n  } catch {\n    try {\n      const { readFileSync } = require(\"fs\");\n      const { resolve } = require(\"path\");\n      const pkg = JSON.parse(readFileSync(resolve(process.cwd(), \"package.json\"), \"utf-8\"));\n      return pkg.version;\n    } catch {\n      return \"2.0.3\";\n    }\n  }\n}\n\nexport class McpServer {\n  private store: Store;\n  private toolMap = new Map<string, McpTool>();\n\n  constructor(store: Store) {\n    this.store = store;\n    for (const t of TOOLS) this.toolMap.set(t.name, t);\n  }\n\n  /**\n   * Returns `null` for notifications (no response needed).\n   */\n  handleRequest(req: JsonRpcRequest): JsonRpcResponse | null {\n    // Notifications have no id — do not send a response\n    if (req.id === null || req.id === undefined) {\n      return null;\n    }\n\n    try {\n      switch (req.method) {\n        case \"initialize\":\n          return this.ok(req.id, {\n            protocolVersion: \"2024-11-05\",\n            capabilities: { tools: {}, resources: {}, prompts: {} },\n            serverInfo: { name: \"mnemosyne-mcp\", version: getVersion() },\n          });\n\n        case \"tools/list\":\n          return this.ok(req.id, {\n            tools: TOOLS.map(t => ({ name: t.name, description: t.description, inputSchema: t.inputSchema })),\n          });\n\n        case \"tools/call\": {\n          const { name, arguments: args } = req.params || {};\n          const tool = this.toolMap.get(name);\n          if (!tool) return this.err(req.id, -32601, `Tool not found: ${name}`);\n          const result = tool.handler(args || {}, this.store);\n          return this.ok(req.id, { content: [{ type: \"text\", text: JSON.stringify(result, null, 2) }] });\n        }\n\n        case \"resources/list\":\n          return this.ok(req.id, { resources: [] });\n\n        case \"prompts/list\":\n          return this.ok(req.id, { prompts: [] });\n\n        default:\n          return this.err(req.id, -32601, `Method not found: ${req.method}`);\n      }\n    } catch (e: any) {\n      return this.err(req.id, -32603, e.message);\n    }\n  }\n\n  getManifest() {\n    return {\n      name: \"Mnemosyne\",\n      version: getVersion(),\n      description: \"Knowledge base MCP server for projects, atoms, blocks, and bonds.\",\n      protocol: \"mcp\",\n      transport: [\"stdio\", \"sse\"],\n      endpoints: {\n        sse: \"/mcp/sse\",\n        messages: \"/mcp/messages\",\n      },\n      tools: TOOLS.map(t => ({ name: t.name, description: t.description })),\n    };\n  }\n\n  private ok(id: string | number | null, result: any): JsonRpcResponse {\n    return { jsonrpc: \"2.0\", id, result };\n  }\n  private err(id: string | number | null, code: number, message: string): JsonRpcResponse {\n    return { jsonrpc: \"2.0\", id, error: { code, message } };\n  }\n}\n","/**\n * MCP SSE Transport\n * Server-Sent Events transport for MCP over HTTP.\n */\n\nimport type { McpServer } from \"./server.js\";\nimport type { JsonRpcRequest } from \"./types.js\";\n\ninterface SseSession {\n  id: string;\n  res: import(\"http\").ServerResponse;\n}\n\nexport class McpSseTransport {\n  private server: McpServer;\n  private sessions = new Map<string, SseSession>();\n  private sessionCounter = 0;\n\n  constructor(server: McpServer) {\n    this.server = server;\n  }\n\n  handleSse(req: import(\"http\").IncomingMessage, res: import(\"http\").ServerResponse): void {\n    const id = `sess_${++this.sessionCounter}_${Date.now()}`;\n    res.writeHead(200, {\n      \"Content-Type\": \"text/event-stream\",\n      \"Cache-Control\": \"no-cache\",\n      \"Connection\": \"keep-alive\",\n    });\n    this.sessions.set(id, { id, res });\n\n    // Send endpoint event\n    this.sendSse(id, \"endpoint\", \"/mcp/messages?session_id=\" + id);\n\n    req.on(\"close\", () => this.sessions.delete(id));\n  }\n\n  handleMessage(req: import(\"http\").IncomingMessage, res: import(\"http\").ServerResponse, body: any): void {\n    const url = new URL(req.url || \"/\", `http://${req.headers.host}`);\n    const sessionId = url.searchParams.get(\"session_id\") || \"\";\n\n    const request = body as JsonRpcRequest;\n    if (!request || request.jsonrpc !== \"2.0\") {\n      res.writeHead(400, { \"Content-Type\": \"application/json\" });\n      res.end(JSON.stringify({ error: \"invalid_jsonrpc\" }));\n      return;\n    }\n\n    const response = this.server.handleRequest(request);\n    // Notifications return null — send empty 200\n    if (!response) {\n      res.writeHead(200, { \"Content-Type\": \"application/json\" });\n      res.end(\"{}\");\n      return;\n    }\n\n    res.writeHead(200, { \"Content-Type\": \"application/json\" });\n    res.end(JSON.stringify(response));\n\n    // Also broadcast via SSE if the session is active\n    if (sessionId) this.sendSse(sessionId, \"message\", JSON.stringify(response));\n  }\n\n  private sendSse(sessionId: string, event: string, data: string): void {\n    const session = this.sessions.get(sessionId);\n    if (!session) return;\n    session.res.write(`event: ${event}\\ndata: ${data}\\n\\n`);\n  }\n}\n","/**\n * MCP Stdio Transport\n * Line-delimited JSON-RPC over stdin/stdout.\n * This is what Claude Desktop uses to communicate with MCP servers.\n */\n\nimport type { McpServer } from \"./server.js\";\nimport type { JsonRpcRequest, JsonRpcResponse } from \"./types.js\";\n\nexport class McpStdioTransport {\n  private server: McpServer;\n  private buffer = \"\";\n\n  constructor(server: McpServer) {\n    this.server = server;\n  }\n\n  start(): void {\n    process.stdin.setEncoding(\"utf8\");\n    process.stdin.resume();\n\n    process.stdin.on(\"data\", (chunk: string) => {\n      this.buffer += chunk;\n      const lines = this.buffer.split(\"\\n\");\n      this.buffer = lines.pop() || \"\";\n\n      for (const line of lines) {\n        if (!line.trim()) continue;\n        try {\n          const request = JSON.parse(line) as JsonRpcRequest;\n          const response = this.server.handleRequest(request);\n          if (response) this.send(response);\n          // Notifications return null — no output\n        } catch (err: any) {\n          this.send({ jsonrpc: \"2.0\", id: null, error: { code: -32700, message: \"Parse error: \" + err.message } });\n        }\n      }\n    });\n\n    process.stdin.on(\"end\", () => {\n      process.exit(0);\n    });\n  }\n\n  send(message: JsonRpcResponse): void {\n    process.stdout.write(JSON.stringify(message) + \"\\n\");\n  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+{"version":3,"sources":["../../src/mcp/tools.ts","../../src/mcp/server.ts","../../src/mcp/sse.ts","../../src/mcp/stdio.ts"],"sourcesContent":["/**\n * MCP Tool Definitions\n * All tools exposed to MCP clients (Claude Desktop, Cursor, etc.)\n */\n\nimport type { Store } from \"../core/Store.js\";\nimport type { McpTool } from \"./types.js\";\n\nexport const TOOLS: McpTool[] = [\n  {\n    name: \"nexus_list_projects\",\n    description: \"List all projects in the Mnemosyne knowledge base.\",\n    inputSchema: { type: \"object\", properties: {} },\n    handler: (_args, store) => {\n      return { projects: store.getProjects().map(p => ({ id: p.id, name: p.name, description: p.description, atomCount: store.getAtomsByProject(p.id).length })) };\n    },\n  },\n  {\n    name: \"nexus_search\",\n    description: \"Search atoms and blocks by keyword. Returns ranked results.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        query: { type: \"string\", description: \"Search query\" },\n        project: { type: \"string\", description: \"Project name or ID (optional)\" },\n        limit: { type: \"number\", description: \"Max results (default 10)\" },\n      },\n      required: [\"query\"],\n    },\n    handler: (args, store) => {\n      const projectId = args.project ? store.getProjectByName(args.project)?.id || args.project : \"\";\n      const results = store.search(projectId, args.query, args.limit || 10);\n      return { query: args.query, count: results.length, results };\n    },\n  },\n  {\n    name: \"nexus_read_atom\",\n    description: \"Read an atom by ID or title. Returns atom details, blocks, children, and bonds.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        id: { type: \"string\", description: \"Atom UUID\" },\n        title: { type: \"string\", description: \"Atom title (alternative to id)\" },\n        project: { type: \"string\", description: \"Project name (required if searching by title)\" },\n      },\n      required: [],\n    },\n    handler: (args, store) => {\n      let atom = args.id ? store.getAtom(args.id) : undefined;\n      if (!atom && args.title && args.project) {\n        const projectId = store.getProjectByName(args.project)?.id || args.project;\n        atom = store.getAtomsByProject(projectId).find(a => a.title === args.title);\n      }\n      if (!atom) throw new Error(\"Atom not found\");\n      const children = store.getAtomChildren(atom.id).map(a => ({ id: a.id, title: a.title, type: a.metadata?.type || \"text\" }));\n      const blocks = store.getBlocksByAtom(atom.id);\n      const bonds = store.getBondsByAtom(atom.id);\n      return { atom, children, blocks, bonds };\n    },\n  },\n  {\n    name: \"nexus_create_atom\",\n    description: \"Create a new atom in a project.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        project: { type: \"string\", description: \"Project name or ID\" },\n        title: { type: \"string\", description: \"Atom title/path\" },\n        type: { type: \"string\", description: \"Atom type (text, memory, stream, thought, task)\" },\n        parent_id: { type: \"string\", description: \"Parent atom ID (optional)\" },\n        tags: { type: \"array\", items: { type: \"string\" }, description: \"Tags (optional)\" },\n        assistant_id: { type: \"string\", description: \"Creator assistant ID\" },\n      },\n      required: [\"project\", \"title\"],\n    },\n    handler: (args, store) => {\n      const project = store.getProjectByName(args.project) || store.getProject(args.project);\n      if (!project) throw new Error(\"Project not found\");\n      const assistantId = args.assistant_id || \"mcp-assistant\";\n      const atom = store.createAtom(project.id, args.title, args.type || \"text\", assistantId, {\n        parentId: args.parent_id,\n        tags: args.tags,\n      });\n      return { success: true, atom };\n    },\n  },\n  {\n    name: \"nexus_update_atom\",\n    description: \"Update an atom's title or parent.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        id: { type: \"string\", description: \"Atom UUID\" },\n        title: { type: \"string\", description: \"New title\" },\n        parent_id: { type: [\"string\", \"null\"], description: \"New parent ID or null for root\" },\n        assistant_id: { type: \"string\", description: \"Updater assistant ID\" },\n      },\n      required: [\"id\"],\n    },\n    handler: (args, store) => {\n      const assistantId = args.assistant_id || \"mcp-assistant\";\n      if (args.parent_id !== undefined) {\n        const updated = store.updateAtomParent(args.id, args.parent_id, assistantId);\n        if (!updated) throw new Error(\"Invalid parent or atom not found\");\n      }\n      const updated = store.updateAtom(args.id, { title: args.title }, assistantId);\n      return { success: true, atom: updated || store.getAtom(args.id) };\n    },\n  },\n  {\n    name: \"nexus_create_bond\",\n    description: \"Create a bond (graph connection) between two atoms.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        source_id: { type: \"string\", description: \"Source atom ID\" },\n        target_id: { type: \"string\", description: \"Target atom ID\" },\n        label: { type: \"string\", description: \"Bond label (default: connects)\" },\n        color: { type: \"string\", description: \"Hex color (optional)\" },\n      },\n      required: [\"source_id\", \"target_id\"],\n    },\n    handler: (args, store) => {\n      const bond = store.createBond(args.source_id, args.target_id, args.label || \"connects\", args.color);\n      return { success: true, bond };\n    },\n  },\n  {\n    name: \"nexus_request_checkout\",\n    description: \"Request an exclusive checkout (lock) on an atom.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        atom_id: { type: \"string\", description: \"Atom UUID\" },\n        assistant_id: { type: \"string\", description: \"Assistant requesting checkout\" },\n        reason: { type: \"string\", description: \"Reason for checkout\" },\n      },\n      required: [\"atom_id\", \"assistant_id\"],\n    },\n    handler: (args, store) => {\n      const result = store.checkout(args.atom_id, args.assistant_id, \"exclusive\", args.reason || \"\");\n      return result;\n    },\n  },\n  {\n    name: \"nexus_release_checkout\",\n    description: \"Release a checkout (unlock) on an atom.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        atom_id: { type: \"string\", description: \"Atom UUID\" },\n        assistant_id: { type: \"string\", description: \"Assistant releasing checkout\" },\n      },\n      required: [\"atom_id\", \"assistant_id\"],\n    },\n    handler: (args, store) => {\n      const success = store.releaseCheckout(args.atom_id, args.assistant_id);\n      return { success };\n    },\n  },\n  {\n    name: \"nexus_subscribe_to_atom\",\n    description: \"Subscribe to real-time updates for an atom via WebSocket.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        atom_id: { type: \"string\", description: \"Atom UUID to subscribe to\" },\n      },\n      required: [\"atom_id\"],\n    },\n    handler: (args, _store) => {\n      return { success: true, wsEndpoint: \"ws://localhost:7321/ws\", atom_id: args.atom_id, message: \"Connect via WebSocket and send { type: 'subscribe', atomId: '<id>' }\" };\n    },\n  },\n  {\n    name: \"nexus_batch\",\n    description: \"Execute multiple MCP tools in a single request. Reduces round-trip token waste.\",\n    inputSchema: {\n      type: \"object\",\n      properties: {\n        operations: {\n          type: \"array\",\n          items: {\n            type: \"object\",\n            properties: {\n              tool: { type: \"string\", description: \"Tool name to call\" },\n              params: { type: \"object\", description: \"Parameters for the tool\" },\n            },\n            required: [\"tool\"],\n          },\n          description: \"Ordered list of tool calls\",\n        },\n        stop_on_error: { type: \"boolean\", description: \"If true, stop at first error. Default: false\", default: false },\n      },\n      required: [\"operations\"],\n    },\n    handler: (args, store) => {\n      const operations = args.operations || [];\n      const stopOnError = args.stop_on_error ?? false;\n      const results: any[] = [];\n      const toolMap = new Map<string, McpTool>();\n      for (const t of TOOLS) toolMap.set(t.name, t);\n\n      for (let i = 0; i < operations.length; i++) {\n        const op = operations[i];\n        const tool = toolMap.get(op.tool);\n        if (!tool) {\n          results.push({ index: i, tool: op.tool, error: `Tool not found: ${op.tool}` });\n          if (stopOnError) break;\n          continue;\n        }\n        try {\n          const result = tool.handler(op.params || {}, store);\n          results.push({ index: i, tool: op.tool, success: true, result });\n        } catch (err: any) {\n          results.push({ index: i, tool: op.tool, error: err.message });\n          if (stopOnError) break;\n        }\n      }\n      return { count: operations.length, completed: results.length, results };\n    },\n  },\n];\n","/**\n * MCP Server\n * JSON-RPC handler for Model Context Protocol.\n */\n\nimport type { Store } from \"../core/Store.js\";\nimport { TOOLS } from \"./tools.js\";\nimport type { JsonRpcRequest, JsonRpcResponse, McpTool } from \"./types.js\";\n\nfunction getVersion(): string {\n  try {\n    const { readFileSync } = require(\"fs\");\n    const { resolve } = require(\"path\");\n    const pkg = JSON.parse(readFileSync(resolve(__dirname, \"../../package.json\"), \"utf-8\"));\n    return pkg.version;\n  } catch {\n    try {\n      const { readFileSync } = require(\"fs\");\n      const { resolve } = require(\"path\");\n      const pkg = JSON.parse(readFileSync(resolve(process.cwd(), \"package.json\"), \"utf-8\"));\n      return pkg.version;\n    } catch {\n      return \"2.1.0\";\n    }\n  }\n}\n\nexport class McpServer {\n  private store: Store;\n  private toolMap = new Map<string, McpTool>();\n\n  constructor(store: Store) {\n    this.store = store;\n    for (const t of TOOLS) this.toolMap.set(t.name, t);\n  }\n\n  /**\n   * Returns `null` for notifications (no response needed).\n   */\n  handleRequest(req: JsonRpcRequest): JsonRpcResponse | null {\n    // Notifications have no id — do not send a response\n    if (req.id === null || req.id === undefined) {\n      return null;\n    }\n\n    try {\n      switch (req.method) {\n        case \"initialize\":\n          return this.ok(req.id, {\n            protocolVersion: \"2024-11-05\",\n            capabilities: { tools: {}, resources: {}, prompts: {} },\n            serverInfo: { name: \"mnemosyne-mcp\", version: getVersion() },\n          });\n\n        case \"tools/list\":\n          return this.ok(req.id, {\n            tools: TOOLS.map(t => ({ name: t.name, description: t.description, inputSchema: t.inputSchema })),\n          });\n\n        case \"tools/call\": {\n          const { name, arguments: args } = req.params || {};\n          const tool = this.toolMap.get(name);\n          if (!tool) return this.err(req.id, -32601, `Tool not found: ${name}`);\n          const result = tool.handler(args || {}, this.store);\n          return this.ok(req.id, { content: [{ type: \"text\", text: JSON.stringify(result, null, 2) }] });\n        }\n\n        case \"resources/list\":\n          return this.ok(req.id, { resources: [] });\n\n        case \"prompts/list\":\n          return this.ok(req.id, { prompts: [] });\n\n        default:\n          return this.err(req.id, -32601, `Method not found: ${req.method}`);\n      }\n    } catch (e: any) {\n      return this.err(req.id, -32603, e.message);\n    }\n  }\n\n  getManifest() {\n    return {\n      name: \"Mnemosyne\",\n      version: getVersion(),\n      description: \"Knowledge base MCP server for projects, atoms, blocks, and bonds.\",\n      protocol: \"mcp\",\n      transport: [\"stdio\", \"sse\"],\n      endpoints: {\n        sse: \"/mcp/sse\",\n        messages: \"/mcp/messages\",\n      },\n      tools: TOOLS.map(t => ({ name: t.name, description: t.description })),\n    };\n  }\n\n  private ok(id: string | number | null, result: any): JsonRpcResponse {\n    return { jsonrpc: \"2.0\", id, result };\n  }\n  private err(id: string | number | null, code: number, message: string): JsonRpcResponse {\n    return { jsonrpc: \"2.0\", id, error: { code, message } };\n  }\n}\n","/**\n * MCP SSE Transport\n * Server-Sent Events transport for MCP over HTTP.\n */\n\nimport type { McpServer } from \"./server.js\";\nimport type { JsonRpcRequest } from \"./types.js\";\n\ninterface SseSession {\n  id: string;\n  res: import(\"http\").ServerResponse;\n}\n\nexport class McpSseTransport {\n  private server: McpServer;\n  private sessions = new Map<string, SseSession>();\n  private sessionCounter = 0;\n\n  constructor(server: McpServer) {\n    this.server = server;\n  }\n\n  handleSse(req: import(\"http\").IncomingMessage, res: import(\"http\").ServerResponse): void {\n    const id = `sess_${++this.sessionCounter}_${Date.now()}`;\n    res.writeHead(200, {\n      \"Content-Type\": \"text/event-stream\",\n      \"Cache-Control\": \"no-cache\",\n      \"Connection\": \"keep-alive\",\n    });\n    this.sessions.set(id, { id, res });\n\n    // Send endpoint event\n    this.sendSse(id, \"endpoint\", \"/mcp/messages?session_id=\" + id);\n\n    req.on(\"close\", () => this.sessions.delete(id));\n  }\n\n  handleMessage(req: import(\"http\").IncomingMessage, res: import(\"http\").ServerResponse, body: any): void {\n    const url = new URL(req.url || \"/\", `http://${req.headers.host}`);\n    const sessionId = url.searchParams.get(\"session_id\") || \"\";\n\n    const request = body as JsonRpcRequest;\n    if (!request || request.jsonrpc !== \"2.0\") {\n      res.writeHead(400, { \"Content-Type\": \"application/json\" });\n      res.end(JSON.stringify({ error: \"invalid_jsonrpc\" }));\n      return;\n    }\n\n    const response = this.server.handleRequest(request);\n    // Notifications return null — send empty 200\n    if (!response) {\n      res.writeHead(200, { \"Content-Type\": \"application/json\" });\n      res.end(\"{}\");\n      return;\n    }\n\n    res.writeHead(200, { \"Content-Type\": \"application/json\" });\n    res.end(JSON.stringify(response));\n\n    // Also broadcast via SSE if the session is active\n    if (sessionId) this.sendSse(sessionId, \"message\", JSON.stringify(response));\n  }\n\n  private sendSse(sessionId: string, event: string, data: string): void {\n    const session = this.sessions.get(sessionId);\n    if (!session) return;\n    session.res.write(`event: ${event}\\ndata: ${data}\\n\\n`);\n  }\n}\n","/**\n * MCP Stdio Transport\n * Line-delimited JSON-RPC over stdin/stdout.\n * This is what Claude Desktop uses to communicate with MCP servers.\n */\n\nimport type { McpServer } from \"./server.js\";\nimport type { JsonRpcRequest, JsonRpcResponse } from \"./types.js\";\n\nexport class McpStdioTransport {\n  private server: McpServer;\n  private buffer = \"\";\n\n  constructor(server: McpServer) {\n    this.server = server;\n  }\n\n  start(): void {\n    process.stdin.setEncoding(\"utf8\");\n    process.stdin.resume();\n\n    process.stdin.on(\"data\", (chunk: string) => {\n      this.buffer += chunk;\n      const lines = this.buffer.split(\"\\n\");\n      this.buffer = lines.pop() || \"\";\n\n      for (const line of lines) {\n        if (!line.trim()) continue;\n        try {\n          const request = JSON.parse(line) as JsonRpcRequest;\n          const response = this.server.handleRequest(request);\n          if (response) this.send(response);\n          // Notifications return null — no output\n        } catch (err: any) {\n          this.send({ jsonrpc: \"2.0\", id: null, error: { code: -32700, message: \"Parse error: \" + err.message } });\n        }\n      }\n    });\n\n    process.stdin.on(\"end\", () => {\n      process.exit(0);\n    });\n  }\n\n  send(message: JsonRpcResponse): void {\n    process.stdout.write(JSON.stringify(message) + \"\\n\");\n  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package/dist/sdk/index.d.mts

@@ -1,63 +1,104 @@
 /**
- * SDK shared types — mirror of core types with runtime-safe defaults.
+ * SDK shared types — mirror of server responses with runtime-safe defaults.
  */
-interface Atom {
+interface Project {
     id: string;
     name: string;
-    assistant_id: string;
-    content_type: "text" | "image" | "audio" | "file";
-    content: string;
-    embedding_type?: string;
+    description: string | null;
+    icon: string;
+    color: string;
+    created_at: number;
+    updated_at: number;
+    owner: string;
+    metadata: Record<string, any>;
+}
+interface Atom {
+    id: string;
     project_id: string;
-    created_at: string;
-    updated_at: string;
+    parent_id: string | null;
+    title: string;
+    summary: string | null;
+    type: string;
+    icon: string;
+    color: string | null;
+    status: string;
+    metadata: Record<string, any>;
+    auto_path?: string;
+    path_overridden?: boolean;
+    status_updated_at?: number;
+    block_count?: number;
+    bond_count?: number;
+    template_id?: string | null;
+    embedding_status?: string | null;
+    state: {
+        lock: {
+            assistantId: string;
+            reason: string;
+        } | null;
+        queue: any[];
+        blockCount: number;
+        lastActivity: number;
+    };
 }
 interface Block {
     id: string;
     atom_id: string;
-    block_type: "content" | "file" | "export" | "import";
-    content: string;
-    file_path?: string;
-    file_original_name?: string;
-    file_type?: string;
-    source_type?: string;
-    created_at: string;
+    type: string;
+    content: string | null;
+    order_index: number;
+    created_at: number;
+    updated_at: number;
+    metadata: Record<string, any>;
 }
-interface Project {
+interface Bond {
     id: string;
-    name: string;
-    description?: string;
-    created_at: string;
+    source_id: string;
+    target_id: string;
+    label: string;
+    color: string | null;
+    created_at: number;
 }
 interface Assistant {
     id: string;
     name: string;
-    role?: string;
-    model?: string;
-    system_prompt?: string;
-    created_at: string;
-}
-interface Bond {
-    id: string;
-    source_id: string;
-    target_id: string;
-    bond_type: "related" | "child" | "parent" | "reference";
-    strength: number;
-    created_at: string;
+    role: string;
+    permissions: Record<string, any>;
+    status: string;
+    provider: string | null;
+    connected_at: number;
+    last_seen: number;
+    metadata: Record<string, any>;
 }
 interface SearchResult {
-    atoms: Array<Atom & {
+    query: string;
+    semantic: boolean;
+    count: number;
+    results: Array<Atom & {
         similarity?: number;
         score?: number;
     }>;
-    time: number;
-    total: number;
 }
 interface HealthStatus {
     status: "ok" | "degraded" | "error";
     version: string;
     database: string;
     uptime: number;
+    counts: Record<string, number>;
+}
+interface CheckoutResult {
+    success: boolean;
+    queuePosition?: number;
+}
+interface QueueStatus {
+    atomId: string;
+    queue: Array<{
+        id: string;
+        assistant_id: string;
+        requested_at: number;
+        priority: number;
+        status: string;
+        reason: string | null;
+    }>;
 }
 
 interface ClientOptions {
@@ -74,17 +115,52 @@ declare class MnemosyneClient {
     health(): Promise<HealthStatus>;
     listProjects(): Promise<Project[]>;
     getProject(id: string): Promise<Project>;
-    createProject(data: Omit<Project, "id" | "created_at">): Promise<Project>;
+    createProject(data: {
+        name: string;
+        description?: string;
+    }): Promise<Project>;
     deleteProject(id: string): Promise<void>;
     listAtoms(projectId?: string): Promise<Atom[]>;
     getAtom(id: string): Promise<Atom>;
-    createAtom(data: Omit<Atom, "id" | "created_at" | "updated_at">): Promise<Atom>;
-    updateAtom(id: string, data: Partial<Omit<Atom, "id" | "created_at">>): Promise<Atom>;
+    createAtom(data: {
+        project_id: string;
+        title: string;
+        type?: string;
+        parent_id?: string | null;
+        tags?: string[];
+        template?: string;
+        status?: string;
+        auto_path?: string;
+        path_overridden?: boolean;
+    }): Promise<Atom>;
+    updateAtom(id: string, data: {
+        title?: string;
+        summary?: string;
+        tags?: string[];
+        status?: string;
+        auto_path?: string;
+        path_overridden?: boolean;
+        parent_id?: string | null;
+    }): Promise<Atom>;
     deleteAtom(id: string): Promise<void>;
     getBlocks(atomId: string): Promise<Block[]>;
-    createBlock(atomId: string, data: Omit<Block, "id" | "atom_id" | "created_at">): Promise<Block>;
-    listBonds(): Promise<Bond[]>;
-    createBond(data: Omit<Bond, "id" | "created_at">): Promise<Bond>;
+    createBlock(atomId: string, data: {
+        type: string;
+        content: string;
+        tags?: string[];
+    }): Promise<Block>;
+    updateBlock(id: string, data: {
+        content?: string;
+        type?: string;
+        metadata?: Record<string, any>;
+    }): Promise<Block>;
+    deleteBlock(id: string): Promise<void>;
+    listBonds(atomId?: string): Promise<Bond[]>;
+    createBond(atomId: string, data: {
+        target_id: string;
+        label?: string;
+        color?: string;
+    }): Promise<Bond>;
     deleteBond(id: string): Promise<void>;
     searchSemantic(query: string, options?: {
         projectId?: string;
@@ -94,9 +170,36 @@ declare class MnemosyneClient {
         projectId?: string;
         limit?: number;
     }): Promise<SearchResult>;
+    searchKeyword(query: string, options?: {
+        projectId?: string;
+        limit?: number;
+    }): Promise<SearchResult>;
     listAssistants(): Promise<Assistant[]>;
     getAssistant(id: string): Promise<Assistant>;
-    createAssistant(data: Omit<Assistant, "id" | "created_at">): Promise<Assistant>;
+    createAssistant(data: {
+        id?: string;
+        name: string;
+        role: string;
+        capabilities?: string[];
+        description?: string;
+        provider?: string;
+        instructions?: string;
+        config?: Record<string, any>;
+    }): Promise<Assistant>;
+    updateAssistant(id: string, data: {
+        name?: string;
+        role?: string;
+        description?: string;
+        provider?: string;
+        instructions?: string;
+        config?: Record<string, any>;
+        capabilities?: string[];
+        status?: string;
+    }): Promise<Assistant>;
+    deleteAssistant(id: string): Promise<void>;
+    checkoutAtom(atomId: string, mode?: "exclusive" | "shared", reason?: string): Promise<CheckoutResult>;
+    releaseCheckout(atomId: string): Promise<boolean>;
+    getQueueStatus(atomId: string): Promise<QueueStatus>;
 }
 
 export { type Assistant, type Atom, type Block, type Bond, type HealthStatus, MnemosyneClient, type Project, type SearchResult };