mnemosyne-core 2.0.2 → 2.0.3

package/dist/server/api.mjs.map

@@ -1 +1 @@
-{"version":3,"sources":["../../src/config.ts","../../src/server/embedder.ts","../../src/mcp/tools.ts","../../src/mcp/server.ts","../../src/mcp/sse.ts","../../src/api/middleware.ts","../../src/api/utils.ts","../../src/api/routes/assistants.ts","../../src/api/routes/projects.ts","../../src/api/routes/atoms.ts","../../src/api/routes/bonds.ts","../../src/api/routes/blocks.ts","../../src/api/routes/search.ts","../../src/server/files.ts","../../src/api/routes/files.ts","../../src/server/export-format.ts","../../src/api/routes/export-import.ts","../../src/api/routes/events.ts","../../src/api/routes/health.ts","../../src/core/types.ts","../../src/api/routes/tree.ts","../../src/api/router.ts"],"sourcesContent":["/**\n * Mnemosyne Configuration Loader\n * Reads config.yaml with a minimal parser. No external YAML dependency.\n */\n\nimport { readFileSync, existsSync } from \"fs\";\nimport { resolve } from \"path\";\n\nfunction parseValue(v: string): any {\n  const trimmed = v.trim();\n  if (trimmed === \"true\") return true;\n  if (trimmed === \"false\") return false;\n  if (trimmed === \"null\" || trimmed === \"~\") return null;\n  if (/^-?\\d+$/.test(trimmed)) return parseInt(trimmed, 10);\n  if (/^-?\\d+\\.\\d+$/.test(trimmed)) return parseFloat(trimmed);\n  if ((trimmed.startsWith('\"') && trimmed.endsWith('\"')) || (trimmed.startsWith(\"'\") && trimmed.endsWith(\"'\"))) {\n    return trimmed.slice(1, -1);\n  }\n  return trimmed;\n}\n\nfunction parseYaml(text: string): any {\n  const lines = text.split(\"\\n\");\n  const root: any = {};\n  const stack: { obj: any; indent: number; isArray: boolean }[] = [{ obj: root, indent: -1, isArray: false }];\n\n  for (const rawLine of lines) {\n    const commentIdx = rawLine.indexOf(\"#\");\n    const line = commentIdx >= 0 ? rawLine.slice(0, commentIdx) : rawLine;\n    if (!line.trim()) continue;\n\n    const indent = line.length - line.trimStart().length;\n    const trimmed = line.trim();\n\n    while (stack.length > 1 && stack[stack.length - 1].indent >= indent) {\n      stack.pop();\n    }\n\n    const parent = stack[stack.length - 1];\n\n    if (trimmed.startsWith(\"- \")) {\n      const valueStr = trimmed.slice(2).trim();\n      if (!parent.isArray) {\n        // Convert parent object to array if needed (not expected in our config)\n      }\n      let target: any[] = parent.obj;\n      if (!Array.isArray(target)) {\n        // Should not happen with well-formed config\n        target = [];\n      }\n      if (valueStr.includes(\":\")) {\n        const item: any = {};\n        const colonIdx = valueStr.indexOf(\":\");\n        const k = valueStr.slice(0, colonIdx).trim();\n        const v = valueStr.slice(colonIdx + 1).trim();\n        item[k] = parseValue(v);\n        target.push(item);\n      } else {\n        target.push(parseValue(valueStr));\n      }\n      continue;\n    }\n\n    const colonIdx = trimmed.indexOf(\":\");\n    if (colonIdx === -1) continue;\n\n    const key = trimmed.slice(0, colonIdx).trim();\n    const valueStr = trimmed.slice(colonIdx + 1).trim();\n\n    if (!valueStr) {\n      const newObj: any = {};\n      parent.obj[key] = newObj;\n      stack.push({ obj: newObj, indent, isArray: false });\n    } else {\n      parent.obj[key] = parseValue(valueStr);\n    }\n  }\n\n  return root;\n}\n\nfunction loadConfig(): Config {\n  const configPath = resolve(process.cwd(), \"config.yaml\");\n  if (!existsSync(configPath)) {\n    console.warn(\"[Config] config.yaml not found, using defaults\");\n    return defaultConfig();\n  }\n  try {\n    const raw = readFileSync(configPath, \"utf-8\");\n    const parsed = parseYaml(raw);\n    return mergeDeep(defaultConfig(), parsed) as Config;\n  } catch (err: any) {\n    console.error(\"[Config] Failed to parse config.yaml:\", err.message);\n    return defaultConfig();\n  }\n}\n\nfunction getVersion(): string {\n  try {\n    const pkg = JSON.parse(readFileSync(resolve(__dirname, \"../package.json\"), \"utf-8\"));\n    return pkg.version;\n  } catch {\n    try {\n      const pkg = JSON.parse(readFileSync(resolve(process.cwd(), \"package.json\"), \"utf-8\"));\n      return pkg.version;\n    } catch {\n      return \"2.0.1\";\n    }\n  }\n}\n\nfunction defaultConfig(): Config {\n  return {\n    server: { port: 7321, host: \"localhost\", version: getVersion() },\n    database: { path: \"data/nexus.db\", wal_mode: true, vec_extension_path: \"data/vec0\" },\n    storage: { files_dir: \"data/files\", max_file_size_mb: 50, backups_dir: \"data/backups\", backup_interval_hours: 24, max_backups: 7 },\n    limits: { max_atoms_per_project: 10000, rate_limit_requests: 100, rate_limit_window_ms: 60000 },\n    embeddings: { model: \"Xenova/all-MiniLM-L6-v2\", dimension: 384, max_text_length: 10000 },\n    features: { mcp_enabled: true, auto_index_enabled: true, file_processing_enabled: true },\n    index: { debounce_ms: 30000 },\n    search: { semantic_weight: 0.6, fts_weight: 0.4 },\n    bonds: { default_type: \"relates\" },\n  };\n}\n\nfunction mergeDeep(target: any, source: any): any {\n  if (!source || typeof source !== \"object\") return target;\n  const output = { ...target };\n  for (const key of Object.keys(source)) {\n    if (source[key] && typeof source[key] === \"object\" && !Array.isArray(source[key])) {\n      output[key] = mergeDeep(target[key] || {}, source[key]);\n    } else {\n      output[key] = source[key];\n    }\n  }\n  return output;\n}\n\n// ─── Typed Config Interface ───\nexport interface Config {\n  server: {\n    port: number;\n    host: string;\n    version: string;\n  };\n  database: {\n    path: string;\n    wal_mode: boolean;\n    vec_extension_path: string;\n  };\n  storage: {\n    files_dir: string;\n    max_file_size_mb: number;\n    backups_dir: string;\n    backup_interval_hours: number;\n    max_backups: number;\n  };\n  limits: {\n    max_atoms_per_project: number;\n    rate_limit_requests: number;\n    rate_limit_window_ms: number;\n  };\n  embeddings: {\n    model: string;\n    dimension: number;\n    max_text_length: number;\n  };\n  features: {\n    mcp_enabled: boolean;\n    auto_index_enabled: boolean;\n    file_processing_enabled: boolean;\n  };\n  index: {\n    debounce_ms: number;\n  };\n  search: {\n    semantic_weight: number;\n    fts_weight: number;\n  };\n  bonds: {\n    default_type: string;\n  };\n}\n\nexport const CONFIG: Config = loadConfig();\n","/**\n * Mnemosyne Embedder\n * Lazy-loaded semantic embedding using @xenova/transformers.\n * Model: all-MiniLM-L6-v2 (384 dimensions)\n * Downloads model on first use (~50MB).\n */\n\nimport { pipeline, type FeatureExtractionPipeline } from \"@xenova/transformers\";\nimport { CONFIG } from \"../config.js\";\n\nlet extractor: FeatureExtractionPipeline | null = null;\nlet loading = false;\nlet loadError: Error | null = null;\n\nasync function getExtractor(): Promise<FeatureExtractionPipeline | null> {\n  if (extractor) return extractor;\n  if (loadError) return null;\n  if (loading) {\n    // Wait for existing load\n    while (loading) await new Promise(r => setTimeout(r, 100));\n    return extractor;\n  }\n\n  loading = true;\n  try {\n    // Use Xenova's hosted model (no local path needed)\n    extractor = await pipeline(\"feature-extraction\", CONFIG.embeddings.model, {\n      quantized: true, // Use quantized model for faster download\n    });\n    console.log(`[Embedder] Model loaded: ${CONFIG.embeddings.model}`);\n    return extractor;\n  } catch (err: any) {\n    loadError = err;\n    console.error(\"[Embedder] Failed to load model:\", err.message);\n    return null;\n  } finally {\n    loading = false;\n  }\n}\n\n/**\n * Embed a single text string into a 384-dim float array.\n * Returns null if embedder is unavailable.\n */\nexport async function embedText(text: string): Promise<number[] | null> {\n  const ext = await getExtractor();\n  if (!ext) return null;\n\n  // Truncate very long text\n  const truncated = text.slice(0, CONFIG.embeddings.max_text_length);\n  if (!truncated.trim()) return null;\n\n  try {\n    const output = await ext(truncated, { pooling: \"mean\", normalize: true });\n    // output.data is a TypedArray of 384 floats\n    return Array.from(output.data as Float32Array);\n  } catch (err: any) {\n    console.error(\"[Embedder] Embedding failed:\", err.message);\n    return null;\n  }\n}\n\n/**\n * Batch embed multiple texts.\n */\nexport async function embedTexts(texts: string[]): Promise<(number[] | null)[]> {\n  const ext = await getExtractor();\n  if (!ext) return texts.map(() => null);\n\n  const results: (number[] | null)[] = [];\n  for (const text of texts) {\n    const truncated = text.slice(0, CONFIG.embeddings.max_text_length);\n    if (!truncated.trim()) {\n      results.push(null);\n      continue;\n    }\n    try {\n      const output = await ext(truncated, { pooling: \"mean\", normalize: true });\n      results.push(Array.from(output.data as Float32Array));\n    } catch {\n      results.push(null);\n    }\n  }\n  return results;\n}\n\nexport function isReady(): boolean {\n  return extractor !== null;\n}\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\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: \"2.0.0\" },\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: ${req.method}`);\n      }\n    } catch (e: any) {\n      return this.err(req.id, -32603, e.message);\n    }\n  }\n\n  getManifest() {\n    return {\n      name: \"Mnemosyne\",\n      version: \"2.0.0\",\n      description: \"Knowledge base MCP server for projects, atoms, blocks, and bonds.\",\n      protocol: \"mcp\",\n      transport: [\"stdio\", \"sse\"],\n      endpoints: {\n        sse: \"/mcp/sse\",\n        messages: \"/mcp/messages\",\n      },\n      tools: TOOLS.map(t => ({ name: t.name, description: t.description })),\n    };\n  }\n\n  private ok(id: string | number | null, result: any): JsonRpcResponse {\n    return { jsonrpc: \"2.0\", id, result };\n  }\n  private err(id: string | number | null, code: number, message: string): JsonRpcResponse {\n    return { jsonrpc: \"2.0\", id, error: { code, message } };\n  }\n}\n","/**\n * MCP SSE Transport\n * Server-Sent Events transport for MCP over HTTP.\n */\n\nimport type { McpServer } from \"./server.js\";\nimport type { JsonRpcRequest } from \"./types.js\";\n\ninterface SseSession {\n  id: string;\n  res: import(\"http\").ServerResponse;\n}\n\nexport class McpSseTransport {\n  private server: McpServer;\n  private sessions = new Map<string, SseSession>();\n  private sessionCounter = 0;\n\n  constructor(server: McpServer) {\n    this.server = server;\n  }\n\n  handleSse(req: import(\"http\").IncomingMessage, res: import(\"http\").ServerResponse): void {\n    const id = `sess_${++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 * API Middleware\n * Rate limiting, CORS, auth helpers.\n */\n\nimport type { Store } from \"../core/Store.js\";\nimport type { Assistant } from \"../core/types.js\";\n\ninterface RateWindow {\n  count: number;\n  resetAt: number;\n}\n\nexport class RateLimiter {\n  private rates = new Map<string, RateWindow>();\n  private limit: number;\n  private windowMs: number;\n\n  constructor(limit: number, windowMs: number) {\n    this.limit = limit;\n    this.windowMs = windowMs;\n    setInterval(() => this.cleanup(), 60000);\n  }\n\n  check(token: string): boolean {\n    const now = Date.now();\n    let window = this.rates.get(token);\n    if (!window || window.resetAt < now) {\n      window = { count: 0, resetAt: now + this.windowMs };\n      this.rates.set(token, window);\n    }\n    if (window.count >= this.limit) return false;\n    window.count++;\n    return true;\n  }\n\n  private cleanup(): void {\n    const now = Date.now();\n    for (const [key, window] of this.rates.entries()) {\n      if (window.resetAt < now) this.rates.delete(key);\n    }\n  }\n}\n\nexport function setCorsHeaders(res: import(\"http\").ServerResponse): void {\n  res.setHeader(\"Access-Control-Allow-Origin\", \"*\");\n  res.setHeader(\"Access-Control-Allow-Methods\", \"GET, POST, PATCH, DELETE, OPTIONS\");\n  res.setHeader(\"Access-Control-Allow-Headers\", \"Content-Type, Authorization\");\n  res.setHeader(\"Cache-Control\", \"no-store, no-cache, must-revalidate, proxy-revalidate\");\n  res.setHeader(\"Pragma\", \"no-cache\");\n  res.setHeader(\"Expires\", \"0\");\n}\n\nexport function authenticate(store: Store, req: import(\"http\").IncomingMessage): Assistant | undefined {\n  const token = req.headers.authorization?.replace(\"Bearer \", \"\");\n  return token ? store.getAssistant(token) : undefined;\n}\n","/**\n * API Utilities\n * Shared helpers for route handlers.\n */\n\nimport type { Store } from \"../core/Store.js\";\n\nexport function json(res: import(\"http\").ServerResponse, status: number, data: any): void {\n  res.writeHead(status, { \"Content-Type\": \"application/json\" });\n  res.end(JSON.stringify(data));\n}\n\nexport function readBody(req: import(\"http\").IncomingMessage): Promise<any> {\n  return new Promise((resolve) => {\n    let body = \"\";\n    req.on(\"data\", chunk => body += chunk);\n    req.on(\"end\", () => { try { resolve(JSON.parse(body)); } catch { resolve({}); } });\n  });\n}\n\nexport function resolveProjectId(store: Store, idOrName: string): string {\n  if (!idOrName) return \"\";\n  if (/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(idOrName)) return idOrName;\n  const p = store.getProjectByName(idOrName);\n  return p?.id || idOrName;\n}\n\nexport function serializeAtom(store: Store, atom: any, compact = false): any {\n  if (compact) {\n    return {\n      id: atom.id,\n      title: atom.title,\n      type: atom.metadata?.type || \"memory\",\n      status: atom.status,\n    };\n  }\n  const blockCount = atom.block_count ?? store.getBlocksByAtom(atom.id).length;\n  return {\n    id: atom.id,\n    project_id: atom.project_id,\n    parent_id: atom.parent_id,\n    title: atom.title,\n    summary: atom.summary,\n    type: atom.metadata?.type || \"memory\",\n    icon: atom.icon,\n    color: atom.color,\n    metadata: atom.metadata,\n    auto_path: atom.auto_path,\n    path_overridden: atom.path_overridden,\n    status: atom.status,\n    status_updated_at: atom.status_updated_at,\n    block_count: atom.block_count,\n    bond_count: atom.bond_count,\n    template_id: atom.template_id,\n    embedding_status: atom.embedding_status,\n    state: {\n      lock: atom.locked_by ? { assistantId: atom.locked_by, reason: atom.locked_reason } : null,\n      queue: [],\n      blockCount: blockCount,\n      lastActivity: atom.updated_at,\n    },\n  };\n}\n\nexport function pickFields(obj: any, fields: string[]): any {\n  const result: any = {};\n  for (const f of fields) {\n    if (f.includes(\".\")) {\n      const [head, ...tail] = f.split(\".\");\n      if (obj[head] != null) {\n        result[head] = result[head] || (Array.isArray(obj[head]) ? [] : {});\n        if (Array.isArray(obj[head])) {\n          result[head] = obj[head].map((item: any) => pickFields(item, [tail.join(\".\")]));\n        } else {\n          const nested = pickFields(obj[head], [tail.join(\".\")]);\n          Object.assign(result[head], nested);\n        }\n      }\n    } else if (obj[f] !== undefined) {\n      result[f] = obj[f];\n    }\n  }\n  return result;\n}\n\nexport function exportAtomMarkdown(store: Store, atom: any): string {\n  const blocks = store.getBlocksByAtom(atom.id).sort((a: any, b: any) => (a.order_index || 0) - (b.order_index || 0));\n  const bonds = store.getBondsByAtom(atom.id);\n  const parent = atom.parent_id ? store.getAtom(atom.parent_id) : null;\n\n  let md = `---\\n`;\n  md += `title: \"${atom.title}\"\\n`;\n  md += `type: ${atom.type || \"memory\"}\\n`;\n  md += `status: ${atom.status || \"draft\"}\\n`;\n  md += `path: ${atom.auto_path || \"/\"}\\n`;\n  if (atom.summary) md += `summary: \"${atom.summary}\"\\n`;\n  if (atom.metadata?.tags?.length) md += `tags: [${atom.metadata.tags.map((t: string) => `\"${t}\"`).join(\", \")}]\\n`;\n  if (parent) md += `parent: \"${parent.title}\"\\n`;\n  md += `exported_at: ${new Date().toISOString()}\\n`;\n  md += `---\\n\\n`;\n\n  md += `# ${atom.title}\\n\\n`;\n  if (atom.summary) md += `${atom.summary}\\n\\n`;\n\n  for (const b of blocks) {\n    const content = b.content || \"\";\n    if (b.type === \"text\") {\n      try { const p = JSON.parse(content); md += `${p.text || content}\\n\\n`; } catch { md += `${content}\\n\\n`; }\n    } else if (b.type === \"code\") {\n      const lines = content.split(\"\\n\");\n      const first = lines[0]?.trim() || \"\";\n      let lang = \"\";\n      let code = content;\n      if (first.startsWith(\"```\")) { lang = first.replace(/```/g, \"\").trim(); code = lines.slice(1).join(\"\\n\").replace(/```$/, \"\").trim(); }\n      md += `\\`\\`\\`${lang}\\n${code}\\n\\`\\`\\`\\n\\n`;\n    } else if (b.type === \"checklist\") {\n      try {\n        const items = JSON.parse(content);\n        if (Array.isArray(items)) {\n          for (const item of items) md += `- [${item.checked ? \"x\" : \" \"}] ${item.text}\\n`;\n          md += \"\\n\";\n        }\n      } catch { md += `${content}\\n\\n`; }\n    } else if (b.type === \"table\") {\n      try {\n        const rows = JSON.parse(content);\n        if (Array.isArray(rows) && rows.length) {\n          const headers = Object.keys(rows[0]);\n          md += `| ${headers.join(\" | \")} |\\n`;\n          md += `| ${headers.map(() => \"---\").join(\" | \")} |\\n`;\n          for (const row of rows) md += `| ${headers.map(h => String(row[h] ?? \"\")).join(\" | \")} |\\n`;\n          md += \"\\n\";\n        }\n      } catch { md += `${content}\\n\\n`; }\n    } else if (b.type === \"image\" || b.type === \"file\") {\n      try {\n        const meta = JSON.parse(content);\n        if (b.type === \"image\") md += `![${meta.file_name || \"image\"}](${meta.hash})\\n\\n`;\n        else md += `[${meta.file_name || \"file\"}](${meta.hash})\\n\\n`;\n      } catch { md += `${content}\\n\\n`; }\n    } else if (b.type === \"link\") {\n      const url = content.trim().startsWith(\"http\") ? content.trim() : \"https://\" + content.trim();\n      md += `[${content.trim()}](${url})\\n\\n`;\n    } else {\n      md += `${content}\\n\\n`;\n    }\n  }\n\n  const allBonds = [...(bonds.outgoing || []), ...(bonds.incoming || [])];\n  if (allBonds.length) {\n    md += `---\\n\\n## Connections\\n\\n`;\n    for (const b of allBonds) {\n      const otherId = b.source_id === atom.id ? b.target_id : b.source_id;\n      const other = store.getAtom(otherId);\n      const dir = b.source_id === atom.id ? \"→\" : \"←\";\n      md += `- ${dir} [[${other ? other.title : otherId}]] (${b.label})\\n`;\n    }\n    md += \"\\n\";\n  }\n\n  return md;\n}\n\nexport function exportMarkdown(store: Store, projectId: string): string {\n  const project = projectId ? store.getProject(projectId) : undefined;\n  const atoms = projectId ? store.getAtomsByProject(projectId) : [];\n  const bonds = projectId ? store.getGraph(projectId).bonds : [];\n  const blockMap = new Map<string, any>();\n  for (const atom of atoms) {\n    for (const b of store.getBlocksByAtom(atom.id)) {\n      blockMap.set(b.id, b);\n    }\n  }\n\n  let md = `# ${project ? project.name : \"Mnemosyne Export\"}\\n\\n`;\n  md += `*Exported on ${new Date().toISOString()}*\\n\\n`;\n\n  const atomMap = new Map(atoms.map(a => [a.id, a]));\n  const rootAtoms = atoms.filter(a => !a.parent_id);\n\n  function renderAtom(atom: any, depth: number) {\n    const indent = \"  \".repeat(depth);\n    md += `${indent}## ${atom.title}\\n\\n`;\n    if (atom.summary) md += `${indent}${atom.summary}\\n\\n`;\n    if (atom.metadata?.tags?.length) md += `${indent}*Tags: ${atom.metadata.tags.join(\", \")}*\\n\\n`;\n\n    const atomBlocks = Array.from(blockMap.values()).filter(b => b.atom_id === atom.id).sort((a, b) => a.order_index - b.order_index);\n    for (const b of atomBlocks) {\n      try {\n        const parsed = JSON.parse(b.content || \"{}\");\n        if (parsed.text) md += `${indent}${parsed.text}\\n\\n`;\n        else md += `${indent}\\`\\`\\`json\\n${indent}${JSON.stringify(parsed, null, 2).split(\"\\n\").join(\"\\n\" + indent)}\\n${indent}\\`\\`\\`\\n\\n`;\n      } catch {\n        md += `${indent}${b.content || \"\"}\\n\\n`;\n      }\n    }\n\n    const children = atoms.filter(a => a.parent_id === atom.id);\n    for (const child of children) renderAtom(child, depth + 1);\n  }\n\n  for (const root of rootAtoms) renderAtom(root, 0);\n\n  if (bonds.length) {\n    md += `---\\n\\n## Bonds\\n\\n`;\n    for (const b of bonds) {\n      const src = atomMap.get(b.source_id);\n      const tgt = atomMap.get(b.target_id);\n      md += `- [[${src ? src.title : b.source_id}]] —${b.label}→ [[${tgt ? tgt.title : b.target_id}]]\\n`;\n    }\n    md += \"\\n\";\n  }\n\n  return md;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport type { AssistantRole } from \"../../core/types.js\";\nimport { json } from \"../utils.js\";\n\nexport function handleAssistants(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  body: any\n): boolean {\n  if (pathname === \"/api/v1/assistants/register\" && method === \"POST\") {\n    const a = body as { id?: string; name: string; role: AssistantRole; capabilities?: string[]; description?: string; provider?: string; instructions?: string; config?: Record<string, any> };\n    const id = a.id || a.name || crypto.randomUUID();\n    const existing = store.getAssistant(id);\n    if (existing) {\n      json(res, 200, { success: true, token: existing.id, assistant: existing });\n      return true;\n    }\n    const newAssistant = store.registerAssistant({ id, name: a.name || id, role: a.role || \"developer\", capabilities: a.capabilities || [], description: a.description, provider: a.provider, instructions: a.instructions, config: a.config });\n    json(res, 200, { success: true, token: newAssistant.id, assistant: newAssistant });\n    return true;\n  }\n\n  if (pathname.startsWith(\"/api/v1/assistants/\") && pathname.endsWith(\"/heartbeat\") && method === \"POST\") {\n    const id = pathname.split(\"/\")[4];\n    store.heartbeat(id);\n    json(res, 200, { success: true });\n    return true;\n  }\n\n  if (pathname === \"/api/v1/assistants\" && method === \"GET\") {\n    const compact = new URL(pathname, \"http://localhost\").searchParams.get(\"compact\") === \"true\";\n    const assistants = store.getAllAssistants().map(a => compact\n      ? { id: a.id, name: a.name, role: a.role, status: a.status }\n      : a\n    );\n    json(res, 200, { assistants });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/assistants\\/[^\\/]+$/) && method === \"PATCH\") {\n    const id = pathname.replace(\"/api/v1/assistants/\", \"\");\n    const a = body as { name?: string; role?: AssistantRole; description?: string; provider?: string; instructions?: string; config?: Record<string, any>; capabilities?: string[]; status?: string };\n    const updated = store.updateAssistant(id, a);\n    if (!updated) { json(res, 404, { error: \"assistant_not_found\" }); return true; }\n    json(res, 200, { assistant: updated });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/assistants\\/[^\\/]+$/) && method === \"DELETE\") {\n    const id = pathname.replace(\"/api/v1/assistants/\", \"\");\n    const ok = store.deleteAssistant(id);\n    json(res, ok ? 200 : 404, { success: ok });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport { json, resolveProjectId } from \"../utils.js\";\n\nexport function handleProjects(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  body: any,\n  searchParams: URLSearchParams\n): boolean {\n  if (pathname === \"/api/v1/projects\" && method === \"GET\") {\n    const compact = searchParams.get(\"compact\") === \"true\";\n    const projects = store.getProjects().map(p => compact\n      ? { id: p.id, name: p.name, description: p.description }\n      : p\n    );\n    json(res, 200, { projects });\n    return true;\n  }\n\n  if (pathname === \"/api/v1/projects\" && method === \"POST\") {\n    const { name, description } = body as { name: string; description?: string };\n    if (!name) { json(res, 400, { error: \"name_required\" }); return true; }\n    const project = store.createProject(name, description);\n    json(res, 200, { success: true, project });\n    return true;\n  }\n\n  // Project Index (__INDEX__ atom)\n  const projectIndexMatch = pathname.match(/^\\/api\\/v1\\/projects\\/([^/]+)\\/index$/);\n  if (projectIndexMatch && method === \"GET\") {\n    const projectId = resolveProjectId(store, projectIndexMatch[1]);\n    const indexAtom = store.getProjectIndexAtom(projectId);\n    if (!indexAtom) {\n      json(res, 404, { error: \"index_not_found\" });\n      return true;\n    }\n    const blocks = store.getBlocksByAtom(indexAtom.id);\n    const manifestBlock = blocks.find(b => b.type === \"text\");\n    let manifest: any = {};\n    try {\n      if (manifestBlock) manifest = JSON.parse(manifestBlock.content || \"{}\");\n    } catch {}\n    json(res, 200, {\n      project_id: projectId,\n      atom_id: indexAtom.id,\n      generated_at: indexAtom.updated_at,\n      manifest,\n    });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport type { Assistant } from \"../../core/types.js\";\nimport { json, resolveProjectId, serializeAtom, pickFields, exportAtomMarkdown } from \"../utils.js\";\n\nexport function handleAtoms(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  body: any,\n  searchParams: URLSearchParams,\n  assistant?: Assistant\n): boolean {\n  if (pathname === \"/api/v1/atoms\" && method === \"POST\") {\n    const { project_id, title, type, parent_id, tags, template, status, auto_path, path_overridden } = body as { project_id: string; title: string; type: string; parent_id?: string; tags?: string[]; template?: string; status?: string; auto_path?: string; path_overridden?: boolean };\n    if (!project_id || !title) { json(res, 400, { error: \"project_id_and_title_required\" }); return true; }\n    const resolvedProjectId = resolveProjectId(store, project_id);\n    if (!resolvedProjectId) { json(res, 400, { error: \"project_not_found\" }); return true; }\n    if (!assistant || !store.can(assistant.role, \"create\", undefined, assistant.id)) {\n      json(res, 403, { error: \"permission_denied\" }); return true; }\n    const atom = store.createAtom(resolvedProjectId, title, type || \"text\", assistant.id, { parentId: parent_id, tags, template, status, auto_path, path_overridden });\n    json(res, 200, { atom: serializeAtom(store, atom) });\n    return true;\n  }\n\n  if (pathname === \"/api/v1/atoms\" && method === \"GET\") {\n    const projectId = resolveProjectId(store, searchParams.get(\"project_id\") || \"\");\n    const compact = searchParams.get(\"compact\") === \"true\";\n    const atoms = projectId\n      ? store.getAtomsByProject(projectId).map(d => serializeAtom(store, d, compact))\n      : [];\n    json(res, 200, { atoms });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+$/) && method === \"GET\" && !pathname.includes(\"/blocks\") && !pathname.includes(\"/bonds\") && !pathname.includes(\"/checkout\") && !pathname.includes(\"/queue\")) {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\");\n    const atom = store.getAtom(atomId);\n    if (!atom) { json(res, 404, { error: \"atom_not_found\" }); return true; }\n    const fieldsParam = searchParams.get(\"fields\");\n    const children = store.getAtomChildren(atomId).map(a => ({ id: a.id, title: a.title, type: a.metadata?.type || \"memory\", blockCount: store.getBlocksByAtom(a.id).length }));\n    const full = {\n      atom: serializeAtom(store, atom),\n      children,\n      blocks: store.getBlocksByAtom(atomId),\n      bonds: store.getBondsByAtom(atomId),\n    };\n    const response = fieldsParam ? pickFields(full, fieldsParam.split(\",\")) : full;\n    json(res, 200, response);\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+$/) && (method === \"PATCH\" || method === \"POST\") && !pathname.includes(\"/blocks\") && !pathname.includes(\"/bonds\")) {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\");\n    const { parent_id, title, summary, tags, status, auto_path, path_overridden } = body as { parent_id?: string | null; title?: string; summary?: string; tags?: string[]; status?: string; auto_path?: string; path_overridden?: boolean };\n    if (!assistant || !store.can(assistant.role, \"update\", atomId, assistant.id)) {\n      json(res, 403, { error: \"permission_denied\" }); return true; }\n    if (parent_id !== undefined) {\n      const updated = store.updateAtomParent(atomId, parent_id ?? null, assistant.id);\n      if (!updated) { json(res, 400, { error: \"invalid_parent\" }); return true; }\n      json(res, 200, { atom: serializeAtom(store, updated) });\n      return true;\n    }\n    try {\n      const updated = store.updateAtom(atomId, { title, summary, tags, status, auto_path, path_overridden }, assistant.id);\n      if (!updated) { json(res, 404, { error: \"atom_not_found\" }); return true; }\n      json(res, 200, { atom: serializeAtom(store, updated) });\n    } catch (err: any) {\n      json(res, 400, { error: err.message });\n    }\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+$/) && method === \"DELETE\" && !pathname.includes(\"/blocks\") && !pathname.includes(\"/bonds\") && !pathname.includes(\"/checkout\")) {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\");\n    if (!assistant || !store.can(assistant.role, \"delete\", atomId, assistant.id)) {\n      json(res, 403, { error: \"permission_denied\" }); return true; }\n    const ok = store.deleteAtom(atomId, assistant.id);\n    json(res, ok ? 200 : 404, { success: ok });\n    return true;\n  }\n\n  // Checkout\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/checkout$/) && method === \"POST\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/checkout\", \"\");\n    const { mode, reason } = body as { mode: any; reason: string };\n    if (!assistant || !store.can(assistant.role, \"lock\", atomId, assistant.id)) {\n      json(res, 403, { error: \"permission_denied\" }); return true; }\n    const result = store.checkout(atomId, assistant.id, mode || \"exclusive\", reason || \"\");\n    json(res, result.success ? 200 : 423, result);\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/checkout$/) && method === \"DELETE\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/checkout\", \"\");\n    if (!assistant) { json(res, 403, { error: \"unauthorized\" }); return true; }\n    const success = store.releaseCheckout(atomId, assistant.id);\n    json(res, success ? 200 : 400, { success });\n    return true;\n  }\n\n  // Queue\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/queue$/) && method === \"GET\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/queue\", \"\");\n    const status = store.getQueueStatus(atomId);\n    json(res, status ? 200 : 404, status || { error: \"atom_not_found\" });\n    return true;\n  }\n\n  const queueGrantMatch = pathname.match(/^\\/api\\/v1\\/atoms\\/([^\\/]+)\\/queue\\/([^\\/]+)\\/grant$/);\n  if (queueGrantMatch && method === \"POST\") {\n    const atomId = queueGrantMatch[1];\n    const queueId = queueGrantMatch[2];\n    const ok = store.grantQueueItem(atomId, queueId);\n    json(res, ok ? 200 : 400, { success: ok });\n    return true;\n  }\n\n  const queueRejectMatch = pathname.match(/^\\/api\\/v1\\/atoms\\/([^\\/]+)\\/queue\\/([^\\/]+)\\/reject$/);\n  if (queueRejectMatch && method === \"POST\") {\n    const atomId = queueRejectMatch[1];\n    const queueId = queueRejectMatch[2];\n    const ok = store.rejectQueueItem(atomId, queueId);\n    json(res, ok ? 200 : 400, { success: ok });\n    return true;\n  }\n\n  const queueBumpMatch = pathname.match(/^\\/api\\/v1\\/atoms\\/([^\\/]+)\\/queue\\/([^\\/]+)\\/bump$/);\n  if (queueBumpMatch && method === \"POST\") {\n    const atomId = queueBumpMatch[1];\n    const queueId = queueBumpMatch[2];\n    const ok = store.bumpQueueItem(atomId, queueId);\n    json(res, ok ? 200 : 400, { success: ok });\n    return true;\n  }\n\n  // Permissions\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/permissions$/) && method === \"GET\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/permissions\", \"\");\n    const perms = store.getAtomPermissions(atomId);\n    json(res, 200, { atom_id: atomId, permissions: perms });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/permissions$/) && method === \"POST\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/permissions\", \"\");\n    const { assistant_id, level } = body as { assistant_id: string; level: string };\n    if (!assistant_id || !level) { json(res, 400, { error: \"assistant_id_and_level_required\" }); return true; }\n    store.setAtomPermission(atomId, assistant_id, level as any, assistant?.id);\n    json(res, 200, { success: true });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/permissions\\/[^\\/]+$/) && method === \"DELETE\") {\n    const parts = pathname.replace(\"/api/v1/atoms/\", \"\").split(\"/\");\n    const atomId = parts[0];\n    const assistantId = parts[2];\n    const ok = store.removeAtomPermission(atomId, assistantId);\n    json(res, ok ? 200 : 404, { success: ok });\n    return true;\n  }\n\n  // History\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/history$/) && method === \"GET\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/history\", \"\");\n    const history = store.getAtomHistory(atomId);\n    json(res, 200, { atom_id: atomId, history });\n    return true;\n  }\n\n  // Export\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/export$/) && method === \"GET\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/export\", \"\");\n    const format = searchParams.get(\"format\") || \"markdown\";\n    const atom = store.getAtom(atomId);\n    if (!atom) { json(res, 404, { error: \"atom_not_found\" }); return true; }\n    if (format === \"markdown\") {\n      const md = exportAtomMarkdown(store, atom);\n      const safeName = (atom.title || \"memory\").replace(/[^a-z0-9\\-_]/gi, \"_\").toLowerCase();\n      res.writeHead(200, { \"Content-Type\": \"text/markdown; charset=utf-8\", \"Content-Disposition\": `attachment; filename=\"${safeName}.md\"` });\n      res.end(md);\n      return true;\n    }\n    json(res, 400, { error: \"unsupported_format\" });\n    return true;\n  }\n\n  // Force Release\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/force-release$/) && method === \"POST\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/force-release\", \"\");\n    const atom = store.getAtom(atomId);\n    if (!atom) { json(res, 404, { error: \"atom_not_found\" }); return true; }\n    if (!atom.locked_by) { json(res, 200, { success: true, note: \"not_locked\" }); return true; }\n    const ok = store.forceRelease(atomId, assistant?.id || \"system\");\n    json(res, ok ? 200 : 400, { success: ok });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport { json } from \"../utils.js\";\n\nexport function handleBonds(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  body: any\n): boolean {\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/bonds$/) && method === \"GET\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/bonds\", \"\");\n    json(res, 200, store.getBondsByAtom(atomId));\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/bonds$/) && method === \"POST\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/bonds\", \"\");\n    const { target_id, label, color } = body as { target_id: string; label: string; color?: string };\n    if (!target_id) { json(res, 400, { error: \"target_id_required\" }); return true; }\n    const bond = store.createBond(atomId, target_id, label || \"connects\", color);\n    json(res, 200, { bond });\n    return true;\n  }\n\n  if (pathname === \"/api/v1/bonds\" && method === \"DELETE\") {\n    const { bond_id } = body as { bond_id: string };\n    const ok = store.deleteBond(bond_id);\n    json(res, ok ? 200 : 404, { success: ok });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/bonds\\/[^\\/]+$/) && method === \"DELETE\") {\n    const bondId = pathname.replace(\"/api/v1/bonds/\", \"\");\n    const ok = store.deleteBond(bondId);\n    json(res, ok ? 200 : 404, { success: ok });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/bonds\\/[^\\/]+$/) && method === \"PATCH\") {\n    const bondId = pathname.replace(\"/api/v1/bonds/\", \"\");\n    const { label, color } = body as { label?: string; color?: string };\n    const updated = store.updateBond(bondId, { label, color });\n    if (!updated) { json(res, 404, { error: \"bond_not_found\" }); return true; }\n    json(res, 200, { bond: updated });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport type { Assistant } from \"../../core/types.js\";\nimport { json } from \"../utils.js\";\n\nexport function handleBlocks(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  body: any,\n  assistant?: Assistant\n): boolean {\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/blocks$/) && method === \"POST\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/blocks\", \"\");\n    const { type, content, tags } = body as { type: string; content: string; tags?: string[] };\n    const isSuggestion = type === \"suggestion\";\n    const requiredAction = isSuggestion ? \"suggest\" : \"write\";\n    if (!assistant || !store.can(assistant.role, requiredAction as any, atomId, assistant.id)) {\n      json(res, 403, { error: \"permission_denied\" }); return true;\n    }\n    const block = store.createBlock(atomId, type || \"text\", content || \"\", assistant.id, { tags });\n    if (type === \"file\" || type === \"image\") {\n      store.processFileBlock(atomId, content || \"\").catch(() => {});\n    }\n    json(res, 200, { block });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/blocks\\/[^\\/]+$/) && method === \"GET\") {\n    const blockId = pathname.replace(\"/api/v1/blocks/\", \"\");\n    const block = store.getBlock(blockId);\n    if (!block) { json(res, 404, { error: \"block_not_found\" }); return true; }\n    json(res, 200, { block });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/blocks\\/[^\\/]+$/) && method === \"PATCH\") {\n    const blockId = pathname.replace(\"/api/v1/blocks/\", \"\");\n    const { content, type, metadata } = body as { content?: string; type?: string; metadata?: any };\n    const block = store.getBlock(blockId);\n    if (!block) { json(res, 404, { error: \"block_not_found\" }); return true; }\n    if (content !== undefined) {\n      store.updateBlock(blockId, content, assistant?.id || \"system\");\n    }\n    if (type !== undefined || metadata !== undefined) {\n      const updates: string[] = [];\n      const vals: any[] = [];\n      if (type !== undefined) { updates.push(\"type = ?\"); vals.push(type); }\n      if (metadata !== undefined) { updates.push(\"metadata = ?\"); vals.push(JSON.stringify(metadata)); }\n      vals.push(blockId);\n      store[\"stmt\"](`UPDATE blocks SET ${updates.join(\", \")} WHERE id = ?`).run(...vals);\n    }\n    json(res, 200, { block: store.getBlock(blockId) });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/blocks\\/[^\\/]+$/) && method === \"DELETE\") {\n    const blockId = pathname.replace(\"/api/v1/blocks/\", \"\");\n    const block = store.getBlock(blockId);\n    if (!block) { json(res, 404, { error: \"block_not_found\" }); return true; }\n    const ok = store.deleteBlock(blockId, assistant?.id || \"system\");\n    json(res, ok ? 200 : 400, { success: ok });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport { json, resolveProjectId } from \"../utils.js\";\n\nexport async function handleSearch(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  searchParams: URLSearchParams\n): Promise<boolean> {\n  if (pathname === \"/api/v1/search\" && method === \"GET\") {\n    const projectId = resolveProjectId(store, searchParams.get(\"project_id\") || \"\");\n    const q = (searchParams.get(\"q\") || \"\").toLowerCase();\n    const limit = parseInt(searchParams.get(\"limit\") || \"20\", 10);\n    const semantic = searchParams.get(\"semantic\") === \"true\";\n    if (!q) { json(res, 200, { results: [], count: 0 }); return true; }\n\n    let results: any[] = [];\n\n    if (semantic) {\n      const { embedText } = await import(\"../../server/embedder.js\");\n      const queryEmbedding = await embedText(q);\n      if (queryEmbedding) {\n        results = store.searchHybrid(projectId, q, queryEmbedding, limit);\n      } else {\n        results = store.search(projectId, q, limit);\n      }\n    } else {\n      results = store.search(projectId, q, limit);\n    }\n\n    json(res, 200, { query: q, semantic, count: results.length, results });\n    return true;\n  }\n\n  return false;\n}\n","/**\n * Content-Addressed Storage (CAS)\n * Files stored by SHA256 hash, sharded by first 2 hex chars.\n */\n\nimport { createHash } from \"crypto\";\nimport { mkdirSync, existsSync, writeFileSync, readFileSync } from \"fs\";\nimport { resolve, dirname } from \"path\";\nimport { CONFIG } from \"../config.js\";\n\nconst FILES_DIR = resolve(process.cwd(), CONFIG.storage.files_dir);\n\nfunction ensureDir(path: string): void {\n  if (!existsSync(path)) mkdirSync(path, { recursive: true });\n}\n\nfunction hashPath(hash: string): string {\n  return resolve(FILES_DIR, hash.slice(0, 2), hash.slice(2));\n}\n\nexport function computeHash(buffer: Buffer): string {\n  return createHash(\"sha256\").update(buffer).digest(\"hex\");\n}\n\nexport function saveFile(buffer: Buffer, _fileName: string): { hash: string; size: number; path: string } {\n  const hash = computeHash(buffer);\n  const dest = hashPath(hash);\n\n  if (!existsSync(dest)) {\n    ensureDir(dirname(dest));\n    writeFileSync(dest, buffer);\n  }\n\n  return { hash, size: buffer.length, path: dest };\n}\n\nexport function getFile(hash: string): Buffer | null {\n  try {\n    return readFileSync(hashPath(hash));\n  } catch {\n    return null;\n  }\n}\n\nexport function fileExists(hash: string): boolean {\n  return existsSync(hashPath(hash));\n}\n","import type { Store } from \"../../core/Store.js\";\nimport { saveFile, getFile, computeHash } from \"../../server/files.js\";\nimport { json } from \"../utils.js\";\n\nexport function handleFiles(\n  store: Store,\n  pathname: string,\n  method: string,\n  req: import(\"http\").IncomingMessage,\n  res: import(\"http\").ServerResponse,\n  maxFileSizeMb: number\n): boolean | Promise<boolean> {\n  if (pathname === \"/api/v1/files/upload\" && method === \"POST\") {\n    const fileName = req.headers[\"x-file-name\"] as string || \"upload\";\n    const mimeType = req.headers[\"content-type\"] || \"application/octet-stream\";\n    const chunks: Buffer[] = [];\n    req.on(\"data\", (chunk: Buffer) => chunks.push(chunk));\n    req.on(\"end\", () => {\n      const buffer = Buffer.concat(chunks);\n      const maxBytes = maxFileSizeMb * 1024 * 1024;\n      if (buffer.length > maxBytes) {\n        json(res, 413, { error: \"file_too_large\", max: `${maxFileSizeMb}MB` }); return;\n      }\n      const hash = computeHash(buffer);\n      const existing = store.getAttachmentByHash(hash);\n      if (existing) {\n        json(res, 200, { success: true, hash, file_name: existing.file_name, size: existing.file_size, mime_type: existing.mime_type, dedup: true });\n        return;\n      }\n      const saved = saveFile(buffer, fileName);\n      const attachment = store.createAttachment(hash, fileName, saved.size, mimeType);\n      json(res, 200, { success: true, hash, file_name: fileName, size: saved.size, mime_type: mimeType });\n    });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/files\\/[^\\/]+$/) && method === \"GET\") {\n    const hash = pathname.replace(\"/api/v1/files/\", \"\");\n    const data = getFile(hash);\n    if (!data) { json(res, 404, { error: \"file_not_found\" }); return true; }\n    const attachment = store.getAttachmentByHash(hash);\n    const mime = attachment?.mime_type || \"application/octet-stream\";\n    res.writeHead(200, { \"Content-Type\": mime, \"Content-Length\": data.length });\n    res.end(data);\n    return true;\n  }\n\n  return false;\n}\n","/**\n * .mnemosyne Export Format\n * Creates a ZIP containing: nexus.db + files/ + manifest.json\n */\n\nimport AdmZip from \"adm-zip\";\nimport { createHash } from \"crypto\";\nimport { readFileSync, existsSync, readdirSync, statSync } from \"fs\";\nimport { resolve } from \"path\";\n\nconst DB_PATH = resolve(process.cwd(), \"data\", \"nexus.db\");\nconst FILES_DIR = resolve(process.cwd(), \"data\", \"files\");\n\nfunction sha256File(path: string): string {\n  return createHash(\"sha256\").update(readFileSync(path)).digest(\"hex\");\n}\n\nfunction sha256Dir(dir: string): string {\n  const hash = createHash(\"sha256\");\n  function walk(p: string) {\n    const stat = statSync(p);\n    if (stat.isFile()) {\n      hash.update(readFileSync(p));\n    } else if (stat.isDirectory()) {\n      for (const child of readdirSync(p).sort()) walk(resolve(p, child));\n    }\n  }\n  walk(dir);\n  return hash.digest(\"hex\");\n}\n\nexport function buildMnemosyneExport(projectId?: string, projectName?: string): Buffer {\n  const zip = new AdmZip();\n\n  // Add database\n  zip.addLocalFile(DB_PATH, \"\", \"nexus.db\");\n\n  // Add files directory\n  if (existsSync(FILES_DIR)) {\n    zip.addLocalFolder(FILES_DIR, \"files\");\n  }\n\n  // Build manifest\n  const dbChecksum = sha256File(DB_PATH);\n  const filesChecksum = existsSync(FILES_DIR) ? sha256Dir(FILES_DIR) : \"\";\n\n  const manifest = {\n    version: \"1.1\",\n    app: \"Mnemosyne\",\n    exported_at: new Date().toISOString(),\n    project: projectId ? { id: projectId, name: projectName || \"\" } : null,\n    checksums: { db: dbChecksum, files: filesChecksum },\n  };\n\n  zip.addFile(\"manifest.json\", Buffer.from(JSON.stringify(manifest, null, 2)));\n\n  return zip.toBuffer();\n}\n\nexport function parseMnemosyneImport(zipBuffer: Buffer): { valid: boolean; error?: string; manifest?: any } {\n  try {\n    const zip = new AdmZip(zipBuffer);\n    const manifestEntry = zip.getEntry(\"manifest.json\");\n    if (!manifestEntry) return { valid: false, error: \"Missing manifest.json\" };\n\n    const manifest = JSON.parse(manifestEntry.getData().toString(\"utf-8\"));\n    if (manifest.version !== \"1.0\" && manifest.version !== \"1.1\") return { valid: false, error: `Unsupported version: ${manifest.version}` };\n    if (!zip.getEntry(\"nexus.db\")) return { valid: false, error: \"Missing nexus.db\" };\n\n    return { valid: true, manifest };\n  } catch (err: any) {\n    return { valid: false, error: err.message };\n  }\n}\n","import type { Store } from \"../../core/Store.js\";\nimport type { Assistant } from \"../../core/types.js\";\nimport { buildMnemosyneExport, parseMnemosyneImport } from \"../../server/export-format.js\";\nimport { json, resolveProjectId, exportMarkdown } from \"../utils.js\";\n\nexport function handleExportImport(\n  store: Store,\n  pathname: string,\n  method: string,\n  req: import(\"http\").IncomingMessage,\n  res: import(\"http\").ServerResponse,\n  body: any,\n  searchParams: URLSearchParams,\n  assistant?: Assistant\n): boolean | Promise<boolean> {\n  if (pathname === \"/api/v1/export\" && method === \"GET\") {\n    const format = searchParams.get(\"format\") || \"mnemosyne\";\n    const projectId = resolveProjectId(store, searchParams.get(\"project_id\") || \"\");\n\n    if (format === \"markdown\") {\n      const md = exportMarkdown(store, projectId);\n      res.writeHead(200, { \"Content-Type\": \"text/markdown; charset=utf-8\", \"Content-Disposition\": \"attachment; filename=mnemosyne-export.md\" });\n      res.end(md);\n      return true;\n    }\n\n    if (format === \"mnemosyne\") {\n      const project = projectId ? store.getProject(projectId) : undefined;\n      const zipBuffer = buildMnemosyneExport(projectId, project?.name);\n      res.writeHead(200, {\n        \"Content-Type\": \"application/zip\",\n        \"Content-Disposition\": `attachment; filename=\"${project?.name || \"mnemosyne\"}.mnemosyne\"`,\n        \"Content-Length\": zipBuffer.length,\n      });\n      res.end(zipBuffer);\n      return true;\n    }\n\n    if (!assistant || !store.can(assistant.role, \"export\", \"/system\")) {\n      json(res, 403, { error: \"permission_denied\" }); return true;\n    }\n    const snapshot = store.exportSnapshot();\n    json(res, 200, snapshot);\n    return true;\n  }\n\n  if (pathname === \"/api/v1/import\" && method === \"POST\") {\n    if (!assistant || !store.can(assistant.role, \"import\", \"/system\")) {\n      json(res, 403, { error: \"permission_denied\" }); return true;\n    }\n    const format = searchParams.get(\"format\") || \"mnemosyne\";\n\n    if (format === \"mnemosyne\") {\n      const contentType = req.headers[\"content-type\"] || \"\";\n      if (contentType.includes(\"application/zip\") || contentType.includes(\"multipart\") || contentType.includes(\"application/octet-stream\")) {\n        const chunks: Buffer[] = [];\n        req.on(\"data\", (chunk: Buffer) => chunks.push(chunk));\n        req.on(\"end\", () => {\n          const buffer = Buffer.concat(chunks);\n          const parsed = parseMnemosyneImport(buffer);\n          if (!parsed.valid) { json(res, 400, { success: false, error: parsed.error }); return; }\n          const result = store.importMnemosyneZip(buffer, assistant.id);\n          if (result.success) {\n            json(res, 200, { success: true, atomsRestored: result.atomsRestored });\n          } else {\n            json(res, 400, { success: false, error: result.error });\n          }\n        });\n        return true;\n      }\n      json(res, 400, { success: false, error: \"expected_zip_body\" });\n      return true;\n    }\n\n    if (format === \"markdown\") {\n      const projectId = resolveProjectId(store, searchParams.get(\"project_id\") || \"\");\n      if (!projectId) { json(res, 400, { error: \"project_id_required\" }); return true; }\n      const md = typeof body === \"string\" ? body : (body.content || \"\");\n      const title = body.title || undefined;\n      const result = store.importMarkdown(md, projectId, assistant.id, { title });\n      if (result.success) {\n        json(res, 200, { success: true, atomId: result.atomId, bondsCreated: result.bondsCreated });\n      } else {\n        json(res, 400, { success: false, error: result.error });\n      }\n      return true;\n    }\n\n    json(res, 400, { success: false, error: \"unsupported_import_format\" });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport { json } from \"../utils.js\";\n\nexport function handleEvents(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  searchParams: URLSearchParams\n): boolean {\n  if (pathname === \"/api/v1/events\" && method === \"GET\") {\n    const since = parseInt(searchParams.get(\"since\") || \"0\", 10);\n    const projectId = searchParams.get(\"project_id\") || undefined;\n    const limit = parseInt(searchParams.get(\"limit\") || \"50\", 10);\n    json(res, 200, { events: store.getEvents(since, projectId, limit) });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/events$/) && method === \"GET\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/events\", \"\");\n    const limit = parseInt(searchParams.get(\"limit\") || \"50\", 10);\n    json(res, 200, { events: store.getEventsByAtom(atomId, limit) });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport { json } from \"../utils.js\";\n\nconst PKG_VERSION = (() => {\n  try {\n    const pkg = JSON.parse(require(\"fs\").readFileSync(require(\"path\").resolve(__dirname, \"../../../package.json\"), \"utf-8\"));\n    return pkg.version;\n  } catch {\n    return \"2.0.1\";\n  }\n})();\n\nexport function handleHealth(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse\n): boolean {\n  if ((pathname === \"/health\" || pathname === \"/api/v1/health\") && method === \"GET\") {\n    const stats = store.getStats();\n    json(res, 200, {\n      status: \"ok\",\n      version: PKG_VERSION,\n      storage: \"sqlite\",\n      database: store.config.database.path,\n      uptime: process.uptime(),\n      counts: stats,\n    });\n    return true;\n  }\n\n  return false;\n}\n","/**\n * Mnemosyne Core Types\n * Shared TypeScript interfaces and constants used across all modules.\n */\n\nexport const VALID_STATUSES = ['draft', 'review', 'approved', 'archived', 'deprecated', 'hot'];\n\nexport const ALLOWED_TRANSITIONS: Record<string, string[]> = {\n  draft: ['review', 'archived', 'hot'],\n  review: ['draft', 'approved', 'archived'],\n  approved: ['review', 'deprecated', 'archived'],\n  archived: ['draft'],\n  deprecated: ['draft', 'archived'],\n  hot: ['draft', 'review']\n};\n\nexport type PermissionLevel = \"none\" | \"view\" | \"suggest\" | \"edit\" | \"create\" | \"admin\";\n\nexport type Action =\n  | \"create\" | \"read\" | \"write\" | \"update\" | \"delete\"\n  | \"lock\" | \"manage_queue\" | \"force_release\"\n  | \"peek\" | \"export\" | \"import\" | \"suggest\";\n\nexport type AssistantRole = \"owner\" | \"admin\" | \"manager\" | \"lead\" | \"developer\" | \"worker\" | \"reviewer\" | \"observer\" | \"bot\" | \"guest\";\n\nexport interface Project {\n  id: string;\n  name: string;\n  description: string | null;\n  icon: string;\n  color: string;\n  created_at: number;\n  updated_at: number;\n  owner: string;\n  metadata: Record<string, any>;\n}\n\nexport interface Atom {\n  id: string;\n  project_id: string;\n  parent_id: string | null;\n  title: string;\n  summary: string | null;\n  icon: string;\n  color: string | null;\n  x: number | null;\n  y: number | null;\n  created_at: number;\n  updated_at: number;\n  version: number;\n  locked_by: string | null;\n  locked_at: number | null;\n  locked_reason: string | null;\n  owner: string;\n  status: string;\n  metadata: Record<string, any>;\n  auto_path?: string;\n  path_overridden?: boolean;\n  status_updated_at?: number;\n  block_count?: number;\n  bond_count?: number;\n  template_id?: string | null;\n  embedding_status?: string | null;\n}\n\nexport interface Block {\n  id: string;\n  atom_id: string;\n  type: string;\n  content: string | null;\n  order_index: number;\n  created_at: number;\n  updated_at: number;\n  metadata: Record<string, any>;\n}\n\nexport interface Bond {\n  id: string;\n  source_id: string;\n  target_id: string;\n  label: string;\n  color: string | null;\n  created_at: number;\n}\n\nexport interface Assistant {\n  id: string;\n  name: string;\n  role: AssistantRole;\n  permissions: Record<string, any>;\n  status: string;\n  provider: string | null;\n  connected_at: number;\n  last_seen: number;\n  metadata: Record<string, any>;\n}\n\nexport interface QueueEntry {\n  id: string;\n  atom_id: string;\n  assistant_id: string;\n  requested_at: number;\n  priority: number;\n  status: string;\n  reason: string | null;\n}\n\nexport interface EventLogEntry {\n  id: string;\n  timestamp: number;\n  event_type: string;\n  project_id: string | null;\n  atom_id: string | null;\n  block_id: string | null;\n  bond_id: string | null;\n  actor: string;\n  actor_type: string;\n  diff: string | null;\n  trigger: string | null;\n  metadata: Record<string, any>;\n}\n\nexport interface Config {\n  server: {\n    port: number;\n    host: string;\n    version: string;\n  };\n  database: {\n    path: string;\n    wal_mode: boolean;\n    vec_extension_path: string;\n  };\n  storage: {\n    files_dir: string;\n    max_file_size_mb: number;\n    backups_dir: string;\n    backup_interval_hours: number;\n    max_backups: number;\n  };\n  limits: {\n    max_atoms_per_project: number;\n    rate_limit_requests: number;\n    rate_limit_window_ms: number;\n  };\n  embeddings: {\n    model: string;\n    dimension: number;\n    max_text_length: number;\n  };\n  features: {\n    mcp_enabled: boolean;\n    auto_index_enabled: boolean;\n    file_processing_enabled: boolean;\n  };\n  index: {\n    debounce_ms: number;\n  };\n  search: {\n    semantic_weight: number;\n    fts_weight: number;\n  };\n  bonds: {\n    default_type: string;\n  };\n}\n\nexport const TEMPLATES: Record<string, { name: string; blocks: { type: string; content: string }[] }> = {\n  blank: { name: \"Blank\", blocks: [] },\n  \"meeting-notes\": { name: \"Meeting Notes\", blocks: [\n    { type: \"Attendees\", content: \"\" },\n    { type: \"Agenda\", content: \"\" },\n    { type: \"Notes\", content: \"\" },\n    { type: \"Action Items\", content: \"\" }\n  ]},\n  \"decision-record\": { name: \"Decision Record\", blocks: [\n    { type: \"Context\", content: \"\" },\n    { type: \"Options\", content: \"\" },\n    { type: \"Decision\", content: \"\" },\n    { type: \"Consequences\", content: \"\" }\n  ]},\n  \"bug-report\": { name: \"Bug Report\", blocks: [\n    { type: \"Repro Steps\", content: \"\" },\n    { type: \"Expected\", content: \"\" },\n    { type: \"Actual\", content: \"\" },\n    { type: \"Environment\", content: \"\" }\n  ]},\n  \"api-design\": { name: \"API Design\", blocks: [\n    { type: \"Endpoint\", content: \"\" },\n    { type: \"Request\", content: \"\" },\n    { type: \"Response\", content: \"\" },\n    { type: \"Auth\", content: \"\" },\n    { type: \"Errors\", content: \"\" }\n  ]},\n  persona: { name: \"Persona\", blocks: [\n    { type: \"Name\", content: \"\" },\n    { type: \"Role\", content: \"\" },\n    { type: \"Goals\", content: \"\" },\n    { type: \"Pain Points\", content: \"\" },\n    { type: \"Quotes\", content: \"\" }\n  ]},\n  \"project-spec\": { name: \"Project Spec\", blocks: [\n    { type: \"Overview\", content: \"\" },\n    { type: \"Goals\", content: \"\" },\n    { type: \"Non-Goals\", content: \"\" },\n    { type: \"Timeline\", content: \"\" }\n  ]},\n  \"daily-journal\": { name: \"Daily Journal\", blocks: [\n    { type: \"Date\", content: \"\" },\n    { type: \"Wins\", content: \"\" },\n    { type: \"Blockers\", content: \"\" },\n    { type: \"Tomorrow\", content: \"\" }\n  ]}\n};\n\nexport const ROLE_PERMISSIONS: Record<AssistantRole, { actions: Action[]; pattern: string }> = {\n  owner:       { actions: [\"create\",\"read\",\"write\",\"update\",\"delete\",\"lock\",\"manage_queue\",\"force_release\",\"peek\",\"export\",\"import\"], pattern: \"/**\" },\n  admin:       { actions: [\"create\",\"read\",\"write\",\"update\",\"delete\",\"lock\",\"manage_queue\",\"force_release\",\"peek\",\"export\",\"import\"], pattern: \"/**\" },\n  manager:     { actions: [\"create\",\"read\",\"write\",\"update\",\"delete\",\"lock\",\"manage_queue\",\"force_release\",\"peek\",\"export\",\"import\"], pattern: \"/**\" },\n  lead:        { actions: [\"create\",\"read\",\"write\",\"update\",\"delete\",\"lock\",\"manage_queue\",\"force_release\",\"peek\",\"export\"], pattern: \"/**\" },\n  developer:   { actions: [\"create\",\"read\",\"write\",\"update\",\"delete\",\"lock\",\"peek\",\"export\"], pattern: \"/**\" },\n  worker:      { actions: [\"read\",\"write\",\"lock\",\"peek\"], pattern: \"/**\" },\n  reviewer:    { actions: [\"read\",\"peek\",\"export\"], pattern: \"/**\" },\n  observer:    { actions: [\"read\",\"peek\"], pattern: \"/**\" },\n  bot:         { actions: [\"read\",\"write\",\"peek\"], pattern: \"/**\" },\n  guest:       { actions: 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 return false;\n}\n","/**\n * Mnemosyne API Router\n * Modular HTTP router combining all domain routes.\n */\n\nimport type { Store } from \"../core/Store.js\";\nimport { McpServer, McpHttpTransport } from \"../server/mcp.js\";\nimport { RateLimiter, setCorsHeaders, authenticate } from \"./middleware.js\";\nimport { readBody, json } from \"./utils.js\";\nimport { handleAssistants } from \"./routes/assistants.js\";\nimport { handleProjects } from \"./routes/projects.js\";\nimport { handleAtoms } from \"./routes/atoms.js\";\nimport { handleBonds } from \"./routes/bonds.js\";\nimport { handleBlocks } from \"./routes/blocks.js\";\nimport { handleSearch } from \"./routes/search.js\";\nimport { handleFiles } from \"./routes/files.js\";\nimport { handleExportImport } from \"./routes/export-import.js\";\nimport { handleEvents } from \"./routes/events.js\";\nimport { handleHealth } from \"./routes/health.js\";\nimport { handleTree } from \"./routes/tree.js\";\n\nexport class ApiRouter {\n  private store: Store;\n  private rateLimiter: RateLimiter;\n  private mcpServer: McpServer;\n  private mcpTransport: McpHttpTransport;\n\n  constructor(store: Store) {\n    this.store = store;\n    this.rateLimiter = new RateLimiter(\n      store.config.limits.rate_limit_requests,\n      store.config.limits.rate_limit_window_ms\n    );\n    this.mcpServer = new McpServer(store);\n    this.mcpTransport = new McpHttpTransport(this.mcpServer);\n  }\n\n  async handle(req: import(\"http\").IncomingMessage, res: import(\"http\").ServerResponse): Promise<void> {\n    const url = new URL(req.url || \"/\", `http://${req.headers.host}`);\n    const pathname = url.pathname;\n    const method = req.method || \"GET\";\n\n    setCorsHeaders(res);\n    if (method === \"OPTIONS\") { res.writeHead(204); res.end(); return; }\n\n    try {\n      const assistant = authenticate(this.store, req);\n      const token = req.headers.authorization?.replace(\"Bearer \", \"\");\n\n      if (token && !this.rateLimiter.check(token)) {\n        json(res, 429, { error: \"rate_limit\" }); return;\n      }\n\n      // File upload (raw body)\n      const filesResult = handleFiles(this.store, pathname, method, req, res, this.store.config.storage.max_file_size_mb);\n      if (filesResult === true) return;\n\n      const body = method !== \"GET\" && method !== \"DELETE\" ? await readBody(req) : {};\n\n      // MCP\n      if (pathname === \"/mcp/manifest\" && method === \"GET\") {\n        json(res, 200, this.mcpServer.getManifest()); return;\n      }\n      if (pathname === \"/mcp/sse\" && method === \"GET\") {\n        this.mcpTransport.handleSse(req, res); return;\n      }\n      if (pathname === \"/mcp/messages\" && method === \"POST\") {\n        this.mcpTransport.handleMessage(req, res, body); return;\n      }\n\n      // Domain routes\n      if (handleAssistants(this.store, pathname, method, res, body)) return;\n      if (handleProjects(this.store, pathname, method, res, body, 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{\n        target.push(parseValue(valueStr));\n      }\n      continue;\n    }\n\n    const colonIdx = trimmed.indexOf(\":\");\n    if (colonIdx === -1) continue;\n\n    const key = trimmed.slice(0, colonIdx).trim();\n    const valueStr = trimmed.slice(colonIdx + 1).trim();\n\n    if (!valueStr) {\n      const newObj: any = {};\n      parent.obj[key] = newObj;\n      stack.push({ obj: newObj, indent, isArray: false });\n    } else {\n      parent.obj[key] = parseValue(valueStr);\n    }\n  }\n\n  return root;\n}\n\nfunction loadConfig(): Config {\n  const configPath = resolve(process.cwd(), \"config.yaml\");\n  if (!existsSync(configPath)) {\n    console.warn(\"[Config] config.yaml not found, using defaults\");\n    return defaultConfig();\n  }\n  try {\n    const raw = readFileSync(configPath, \"utf-8\");\n    const parsed = parseYaml(raw);\n    return mergeDeep(defaultConfig(), parsed) as Config;\n  } catch (err: any) {\n    console.error(\"[Config] Failed to parse config.yaml:\", err.message);\n    return defaultConfig();\n  }\n}\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\nfunction defaultConfig(): Config {\n  return {\n    server: { port: 7321, host: \"localhost\", version: getVersion() },\n    database: { path: \"data/nexus.db\", wal_mode: true, vec_extension_path: \"data/vec0\" },\n    storage: { files_dir: \"data/files\", max_file_size_mb: 50, backups_dir: \"data/backups\", backup_interval_hours: 24, max_backups: 7 },\n    limits: { max_atoms_per_project: 10000, rate_limit_requests: 100, rate_limit_window_ms: 60000 },\n    embeddings: { model: \"Xenova/all-MiniLM-L6-v2\", dimension: 384, max_text_length: 10000 },\n    features: { mcp_enabled: true, auto_index_enabled: true, file_processing_enabled: true },\n    index: { debounce_ms: 30000 },\n    search: { semantic_weight: 0.6, fts_weight: 0.4 },\n    bonds: { default_type: \"relates\" },\n  };\n}\n\nfunction mergeDeep(target: any, source: any): any {\n  if (!source || typeof source !== \"object\") return target;\n  const output = { ...target };\n  for (const key of Object.keys(source)) {\n    if (source[key] && typeof source[key] === \"object\" && !Array.isArray(source[key])) {\n      output[key] = mergeDeep(target[key] || {}, source[key]);\n    } else {\n      output[key] = source[key];\n    }\n  }\n  return output;\n}\n\n// ─── Typed Config Interface ───\nexport interface Config {\n  server: {\n    port: number;\n    host: string;\n    version: string;\n  };\n  database: {\n    path: string;\n    wal_mode: boolean;\n    vec_extension_path: string;\n  };\n  storage: {\n    files_dir: string;\n    max_file_size_mb: number;\n    backups_dir: string;\n    backup_interval_hours: number;\n    max_backups: number;\n  };\n  limits: {\n    max_atoms_per_project: number;\n    rate_limit_requests: number;\n    rate_limit_window_ms: number;\n  };\n  embeddings: {\n    model: string;\n    dimension: number;\n    max_text_length: number;\n  };\n  features: {\n    mcp_enabled: boolean;\n    auto_index_enabled: boolean;\n    file_processing_enabled: boolean;\n  };\n  index: {\n    debounce_ms: number;\n  };\n  search: {\n    semantic_weight: number;\n    fts_weight: number;\n  };\n  bonds: {\n    default_type: string;\n  };\n}\n\nlet _config: Config | null = null;\nfunction getConfig(): Config {\n  if (!_config) _config = loadConfig();\n  return _config;\n}\nexport const CONFIG = new Proxy({} as Config, {\n  get(_, prop) {\n    return getConfig()[prop as keyof Config];\n  },\n});\n","/**\n * Mnemosyne Embedder\n * Lazy-loaded semantic embedding using @xenova/transformers.\n * Model: all-MiniLM-L6-v2 (384 dimensions)\n * Downloads model on first use (~50MB).\n */\n\nimport { pipeline, type FeatureExtractionPipeline } from \"@xenova/transformers\";\nimport { CONFIG } from \"../config.js\";\n\nlet extractor: FeatureExtractionPipeline | null = null;\nlet loading = false;\nlet loadError: Error | null = null;\n\nasync function getExtractor(): Promise<FeatureExtractionPipeline | null> {\n  if (extractor) return extractor;\n  if (loadError) return null;\n  if (loading) {\n    // Wait for existing load\n    while (loading) await new Promise(r => setTimeout(r, 100));\n    return extractor;\n  }\n\n  loading = true;\n  try {\n    // Use Xenova's hosted model (no local path needed)\n    extractor = await pipeline(\"feature-extraction\", CONFIG.embeddings.model, {\n      quantized: true, // Use quantized model for faster download\n    });\n    console.log(`[Embedder] Model loaded: ${CONFIG.embeddings.model}`);\n    return extractor;\n  } catch (err: any) {\n    loadError = err;\n    console.error(\"[Embedder] Failed to load model:\", err.message);\n    return null;\n  } finally {\n    loading = false;\n  }\n}\n\n/**\n * Embed a single text string into a 384-dim float array.\n * Returns null if embedder is unavailable.\n */\nexport async function embedText(text: string): Promise<number[] | null> {\n  const ext = await getExtractor();\n  if (!ext) return null;\n\n  // Truncate very long text\n  const truncated = text.slice(0, CONFIG.embeddings.max_text_length);\n  if (!truncated.trim()) return null;\n\n  try {\n    const output = await ext(truncated, { pooling: \"mean\", normalize: true });\n    // output.data is a TypedArray of 384 floats\n    return Array.from(output.data as Float32Array);\n  } catch (err: any) {\n    console.error(\"[Embedder] Embedding failed:\", err.message);\n    return null;\n  }\n}\n\n/**\n * Batch embed multiple texts.\n */\nexport async function embedTexts(texts: string[]): Promise<(number[] | null)[]> {\n  const ext = await getExtractor();\n  if (!ext) return texts.map(() => null);\n\n  const results: (number[] | null)[] = [];\n  for (const text of texts) {\n    const truncated = text.slice(0, CONFIG.embeddings.max_text_length);\n    if (!truncated.trim()) {\n      results.push(null);\n      continue;\n    }\n    try {\n      const output = await ext(truncated, { pooling: \"mean\", normalize: true });\n      results.push(Array.from(output.data as Float32Array));\n    } catch {\n      results.push(null);\n    }\n  }\n  return results;\n}\n\nexport function isReady(): boolean {\n  return extractor !== null;\n}\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 * API Middleware\n * Rate limiting, CORS, auth helpers.\n */\n\nimport type { Store } from \"../core/Store.js\";\nimport type { Assistant } from \"../core/types.js\";\n\ninterface RateWindow {\n  count: number;\n  resetAt: number;\n}\n\nexport class RateLimiter {\n  private rates = new Map<string, RateWindow>();\n  private limit: number;\n  private windowMs: number;\n\n  constructor(limit: number, windowMs: number) {\n    this.limit = limit;\n    this.windowMs = windowMs;\n    setInterval(() => this.cleanup(), 60000);\n  }\n\n  check(token: string): boolean {\n    const now = Date.now();\n    let window = this.rates.get(token);\n    if (!window || window.resetAt < now) {\n      window = { count: 0, resetAt: now + this.windowMs };\n      this.rates.set(token, window);\n    }\n    if (window.count >= this.limit) return false;\n    window.count++;\n    return true;\n  }\n\n  private cleanup(): void {\n    const now = Date.now();\n    for (const [key, window] of this.rates.entries()) {\n      if (window.resetAt < now) this.rates.delete(key);\n    }\n  }\n}\n\nexport function setCorsHeaders(res: import(\"http\").ServerResponse): void {\n  res.setHeader(\"Access-Control-Allow-Origin\", \"*\");\n  res.setHeader(\"Access-Control-Allow-Methods\", \"GET, POST, PATCH, DELETE, OPTIONS\");\n  res.setHeader(\"Access-Control-Allow-Headers\", \"Content-Type, Authorization\");\n  res.setHeader(\"Cache-Control\", \"no-store, no-cache, must-revalidate, proxy-revalidate\");\n  res.setHeader(\"Pragma\", \"no-cache\");\n  res.setHeader(\"Expires\", \"0\");\n}\n\nexport function authenticate(store: Store, req: import(\"http\").IncomingMessage): Assistant | undefined {\n  const token = req.headers.authorization?.replace(\"Bearer \", \"\");\n  return token ? store.getAssistant(token) : undefined;\n}\n","/**\n * API Utilities\n * Shared helpers for route handlers.\n */\n\nimport type { Store } from \"../core/Store.js\";\n\nexport function json(res: import(\"http\").ServerResponse, status: number, data: any): void {\n  res.writeHead(status, { \"Content-Type\": \"application/json\" });\n  res.end(JSON.stringify(data));\n}\n\nexport function readBody(req: import(\"http\").IncomingMessage): Promise<any> {\n  return new Promise((resolve) => {\n    let body = \"\";\n    req.on(\"data\", chunk => body += chunk);\n    req.on(\"end\", () => { try { resolve(JSON.parse(body)); } catch { resolve({}); } });\n  });\n}\n\nexport function resolveProjectId(store: Store, idOrName: string): string {\n  if (!idOrName) return \"\";\n  if (/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(idOrName)) return idOrName;\n  const p = store.getProjectByName(idOrName);\n  return p?.id || idOrName;\n}\n\nexport function serializeAtom(store: Store, atom: any, compact = false): any {\n  if (compact) {\n    return {\n      id: atom.id,\n      title: atom.title,\n      type: atom.metadata?.type || \"memory\",\n      status: atom.status,\n    };\n  }\n  const blockCount = atom.block_count ?? store.getBlocksByAtom(atom.id).length;\n  return {\n    id: atom.id,\n    project_id: atom.project_id,\n    parent_id: atom.parent_id,\n    title: atom.title,\n    summary: atom.summary,\n    type: atom.metadata?.type || \"memory\",\n    icon: atom.icon,\n    color: atom.color,\n    metadata: atom.metadata,\n    auto_path: atom.auto_path,\n    path_overridden: atom.path_overridden,\n    status: atom.status,\n    status_updated_at: atom.status_updated_at,\n    block_count: atom.block_count,\n    bond_count: atom.bond_count,\n    template_id: atom.template_id,\n    embedding_status: atom.embedding_status,\n    state: {\n      lock: atom.locked_by ? { assistantId: atom.locked_by, reason: atom.locked_reason } : null,\n      queue: [],\n      blockCount: blockCount,\n      lastActivity: atom.updated_at,\n    },\n  };\n}\n\nexport function pickFields(obj: any, fields: string[]): any {\n  const result: any = {};\n  for (const f of fields) {\n    if (f.includes(\".\")) {\n      const [head, ...tail] = f.split(\".\");\n      if (obj[head] != null) {\n        result[head] = result[head] || (Array.isArray(obj[head]) ? [] : {});\n        if (Array.isArray(obj[head])) {\n          result[head] = obj[head].map((item: any) => pickFields(item, [tail.join(\".\")]));\n        } else {\n          const nested = pickFields(obj[head], [tail.join(\".\")]);\n          Object.assign(result[head], nested);\n        }\n      }\n    } else if (obj[f] !== undefined) {\n      result[f] = obj[f];\n    }\n  }\n  return result;\n}\n\nexport function exportAtomMarkdown(store: Store, atom: any): string {\n  const blocks = store.getBlocksByAtom(atom.id).sort((a: any, b: any) => (a.order_index || 0) - (b.order_index || 0));\n  const bonds = store.getBondsByAtom(atom.id);\n  const parent = atom.parent_id ? store.getAtom(atom.parent_id) : null;\n\n  let md = `---\\n`;\n  md += `title: \"${atom.title}\"\\n`;\n  md += `type: ${atom.type || \"memory\"}\\n`;\n  md += `status: ${atom.status || \"draft\"}\\n`;\n  md += `path: ${atom.auto_path || \"/\"}\\n`;\n  if (atom.summary) md += `summary: \"${atom.summary}\"\\n`;\n  if (atom.metadata?.tags?.length) md += `tags: [${atom.metadata.tags.map((t: string) => `\"${t}\"`).join(\", \")}]\\n`;\n  if (parent) md += `parent: \"${parent.title}\"\\n`;\n  md += `exported_at: ${new Date().toISOString()}\\n`;\n  md += `---\\n\\n`;\n\n  md += `# ${atom.title}\\n\\n`;\n  if (atom.summary) md += `${atom.summary}\\n\\n`;\n\n  for (const b of blocks) {\n    const content = b.content || \"\";\n    if (b.type === \"text\") {\n      try { const p = JSON.parse(content); md += `${p.text || content}\\n\\n`; } catch { md += `${content}\\n\\n`; }\n    } else if (b.type === \"code\") {\n      const lines = content.split(\"\\n\");\n      const first = lines[0]?.trim() || \"\";\n      let lang = \"\";\n      let code = content;\n      if (first.startsWith(\"```\")) { lang = first.replace(/```/g, \"\").trim(); code = lines.slice(1).join(\"\\n\").replace(/```$/, \"\").trim(); }\n      md += `\\`\\`\\`${lang}\\n${code}\\n\\`\\`\\`\\n\\n`;\n    } else if (b.type === \"checklist\") {\n      try {\n        const items = JSON.parse(content);\n        if (Array.isArray(items)) {\n          for (const item of items) md += `- [${item.checked ? \"x\" : \" \"}] ${item.text}\\n`;\n          md += \"\\n\";\n        }\n      } catch { md += `${content}\\n\\n`; }\n    } else if (b.type === \"table\") {\n      try {\n        const rows = JSON.parse(content);\n        if (Array.isArray(rows) && rows.length) {\n          const headers = Object.keys(rows[0]);\n          md += `| ${headers.join(\" | \")} |\\n`;\n          md += `| ${headers.map(() => \"---\").join(\" | \")} |\\n`;\n          for (const row of rows) md += `| ${headers.map(h => String(row[h] ?? \"\")).join(\" | \")} |\\n`;\n          md += \"\\n\";\n        }\n      } catch { md += `${content}\\n\\n`; }\n    } else if (b.type === \"image\" || b.type === \"file\") {\n      try {\n        const meta = JSON.parse(content);\n        if (b.type === \"image\") md += `![${meta.file_name || \"image\"}](${meta.hash})\\n\\n`;\n        else md += `[${meta.file_name || \"file\"}](${meta.hash})\\n\\n`;\n      } catch { md += `${content}\\n\\n`; }\n    } else if (b.type === \"link\") {\n      const url = content.trim().startsWith(\"http\") ? content.trim() : \"https://\" + content.trim();\n      md += `[${content.trim()}](${url})\\n\\n`;\n    } else {\n      md += `${content}\\n\\n`;\n    }\n  }\n\n  const allBonds = [...(bonds.outgoing || []), ...(bonds.incoming || [])];\n  if (allBonds.length) {\n    md += `---\\n\\n## Connections\\n\\n`;\n    for (const b of allBonds) {\n      const otherId = b.source_id === atom.id ? b.target_id : b.source_id;\n      const other = store.getAtom(otherId);\n      const dir = b.source_id === atom.id ? \"→\" : \"←\";\n      md += `- ${dir} [[${other ? other.title : otherId}]] (${b.label})\\n`;\n    }\n    md += \"\\n\";\n  }\n\n  return md;\n}\n\nexport function exportMarkdown(store: Store, projectId: string): string {\n  const project = projectId ? store.getProject(projectId) : undefined;\n  const atoms = projectId ? store.getAtomsByProject(projectId) : [];\n  const bonds = projectId ? store.getGraph(projectId).bonds : [];\n  const blockMap = new Map<string, any>();\n  for (const atom of atoms) {\n    for (const b of store.getBlocksByAtom(atom.id)) {\n      blockMap.set(b.id, b);\n    }\n  }\n\n  let md = `# ${project ? project.name : \"Mnemosyne Export\"}\\n\\n`;\n  md += `*Exported on ${new Date().toISOString()}*\\n\\n`;\n\n  const atomMap = new Map(atoms.map(a => [a.id, a]));\n  const rootAtoms = atoms.filter(a => !a.parent_id);\n\n  function renderAtom(atom: any, depth: number) {\n    const indent = \"  \".repeat(depth);\n    md += `${indent}## ${atom.title}\\n\\n`;\n    if (atom.summary) md += `${indent}${atom.summary}\\n\\n`;\n    if (atom.metadata?.tags?.length) md += `${indent}*Tags: ${atom.metadata.tags.join(\", \")}*\\n\\n`;\n\n    const atomBlocks = Array.from(blockMap.values()).filter(b => b.atom_id === atom.id).sort((a, b) => a.order_index - b.order_index);\n    for (const b of atomBlocks) {\n      try {\n        const parsed = JSON.parse(b.content || \"{}\");\n        if (parsed.text) md += `${indent}${parsed.text}\\n\\n`;\n        else md += `${indent}\\`\\`\\`json\\n${indent}${JSON.stringify(parsed, null, 2).split(\"\\n\").join(\"\\n\" + indent)}\\n${indent}\\`\\`\\`\\n\\n`;\n      } catch {\n        md += `${indent}${b.content || \"\"}\\n\\n`;\n      }\n    }\n\n    const children = atoms.filter(a => a.parent_id === atom.id);\n    for (const child of children) renderAtom(child, depth + 1);\n  }\n\n  for (const root of rootAtoms) renderAtom(root, 0);\n\n  if (bonds.length) {\n    md += `---\\n\\n## Bonds\\n\\n`;\n    for (const b of bonds) {\n      const src = atomMap.get(b.source_id);\n      const tgt = atomMap.get(b.target_id);\n      md += `- [[${src ? src.title : b.source_id}]] —${b.label}→ [[${tgt ? tgt.title : b.target_id}]]\\n`;\n    }\n    md += \"\\n\";\n  }\n\n  return md;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport type { AssistantRole } from \"../../core/types.js\";\nimport { json } from \"../utils.js\";\n\nexport function handleAssistants(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  body: any\n): boolean {\n  if (pathname === \"/api/v1/assistants/register\" && method === \"POST\") {\n    const a = body as { id?: string; name: string; role: AssistantRole; capabilities?: string[]; description?: string; provider?: string; instructions?: string; config?: Record<string, any> };\n    const id = a.id || a.name || crypto.randomUUID();\n    const existing = store.getAssistant(id);\n    if (existing) {\n      json(res, 200, { success: true, token: existing.id, assistant: existing });\n      return true;\n    }\n    const newAssistant = store.registerAssistant({ id, name: a.name || id, role: a.role || \"developer\", capabilities: a.capabilities || [], description: a.description, provider: a.provider, instructions: a.instructions, config: a.config });\n    json(res, 200, { success: true, token: newAssistant.id, assistant: newAssistant });\n    return true;\n  }\n\n  if (pathname.startsWith(\"/api/v1/assistants/\") && pathname.endsWith(\"/heartbeat\") && method === \"POST\") {\n    const id = pathname.split(\"/\")[4];\n    store.heartbeat(id);\n    json(res, 200, { success: true });\n    return true;\n  }\n\n  if (pathname === \"/api/v1/assistants\" && method === \"GET\") {\n    const compact = new URL(pathname, \"http://localhost\").searchParams.get(\"compact\") === \"true\";\n    const assistants = store.getAllAssistants().map(a => compact\n      ? { id: a.id, name: a.name, role: a.role, status: a.status }\n      : a\n    );\n    json(res, 200, { assistants });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/assistants\\/[^\\/]+$/) && method === \"PATCH\") {\n    const id = pathname.replace(\"/api/v1/assistants/\", \"\");\n    const a = body as { name?: string; role?: AssistantRole; description?: string; provider?: string; instructions?: string; config?: Record<string, any>; capabilities?: string[]; status?: string };\n    const updated = store.updateAssistant(id, a);\n    if (!updated) { json(res, 404, { error: \"assistant_not_found\" }); return true; }\n    json(res, 200, { assistant: updated });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/assistants\\/[^\\/]+$/) && method === \"DELETE\") {\n    const id = pathname.replace(\"/api/v1/assistants/\", \"\");\n    const ok = store.deleteAssistant(id);\n    json(res, ok ? 200 : 404, { success: ok });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport { json, resolveProjectId } from \"../utils.js\";\n\nexport function handleProjects(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  body: any,\n  searchParams: URLSearchParams\n): boolean {\n  if (pathname === \"/api/v1/projects\" && method === \"GET\") {\n    const compact = searchParams.get(\"compact\") === \"true\";\n    const projects = store.getProjects().map(p => compact\n      ? { id: p.id, name: p.name, description: p.description }\n      : p\n    );\n    json(res, 200, { projects });\n    return true;\n  }\n\n  if (pathname === \"/api/v1/projects\" && method === \"POST\") {\n    const { name, description } = body as { name: string; description?: string };\n    if (!name) { json(res, 400, { error: \"name_required\" }); return true; }\n    const project = store.createProject(name, description);\n    json(res, 200, { success: true, project });\n    return true;\n  }\n\n  // Project Index (__INDEX__ atom)\n  const projectIndexMatch = pathname.match(/^\\/api\\/v1\\/projects\\/([^/]+)\\/index$/);\n  if (projectIndexMatch && method === \"GET\") {\n    const projectId = resolveProjectId(store, projectIndexMatch[1]);\n    const indexAtom = store.getProjectIndexAtom(projectId);\n    if (!indexAtom) {\n      json(res, 404, { error: \"index_not_found\" });\n      return true;\n    }\n    const blocks = store.getBlocksByAtom(indexAtom.id);\n    const manifestBlock = blocks.find(b => b.type === \"text\");\n    let manifest: any = {};\n    try {\n      if (manifestBlock) manifest = JSON.parse(manifestBlock.content || \"{}\");\n    } catch {}\n    json(res, 200, {\n      project_id: projectId,\n      atom_id: indexAtom.id,\n      generated_at: indexAtom.updated_at,\n      manifest,\n    });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport type { Assistant } from \"../../core/types.js\";\nimport { json, resolveProjectId, serializeAtom, pickFields, exportAtomMarkdown } from \"../utils.js\";\n\nexport function handleAtoms(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  body: any,\n  searchParams: URLSearchParams,\n  assistant?: Assistant\n): boolean {\n  if (pathname === \"/api/v1/atoms\" && method === \"POST\") {\n    const { project_id, title, type, parent_id, tags, template, status, auto_path, path_overridden } = body as { project_id: string; title: string; type: string; parent_id?: string; tags?: string[]; template?: string; status?: string; auto_path?: string; path_overridden?: boolean };\n    if (!project_id || !title) { json(res, 400, { error: \"project_id_and_title_required\" }); return true; }\n    const resolvedProjectId = resolveProjectId(store, project_id);\n    if (!resolvedProjectId) { json(res, 400, { error: \"project_not_found\" }); return true; }\n    if (!assistant || !store.can(assistant.role, \"create\", undefined, assistant.id)) {\n      json(res, 403, { error: \"permission_denied\" }); return true; }\n    const atom = store.createAtom(resolvedProjectId, title, type || \"text\", assistant.id, { parentId: parent_id, tags, template, status, auto_path, path_overridden });\n    json(res, 200, { atom: serializeAtom(store, atom) });\n    return true;\n  }\n\n  if (pathname === \"/api/v1/atoms\" && method === \"GET\") {\n    const projectId = resolveProjectId(store, searchParams.get(\"project_id\") || \"\");\n    const compact = searchParams.get(\"compact\") === \"true\";\n    const atoms = projectId\n      ? store.getAtomsByProject(projectId).map(d => serializeAtom(store, d, compact))\n      : [];\n    json(res, 200, { atoms });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+$/) && method === \"GET\" && !pathname.includes(\"/blocks\") && !pathname.includes(\"/bonds\") && !pathname.includes(\"/checkout\") && !pathname.includes(\"/queue\")) {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\");\n    const atom = store.getAtom(atomId);\n    if (!atom) { json(res, 404, { error: \"atom_not_found\" }); return true; }\n    const fieldsParam = searchParams.get(\"fields\");\n    const children = store.getAtomChildren(atomId).map(a => ({ id: a.id, title: a.title, type: a.metadata?.type || \"memory\", blockCount: store.getBlocksByAtom(a.id).length }));\n    const full = {\n      atom: serializeAtom(store, atom),\n      children,\n      blocks: store.getBlocksByAtom(atomId),\n      bonds: store.getBondsByAtom(atomId),\n    };\n    const response = fieldsParam ? pickFields(full, fieldsParam.split(\",\")) : full;\n    json(res, 200, response);\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+$/) && (method === \"PATCH\" || method === \"POST\") && !pathname.includes(\"/blocks\") && !pathname.includes(\"/bonds\")) {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\");\n    const { parent_id, title, summary, tags, status, auto_path, path_overridden } = body as { parent_id?: string | null; title?: string; summary?: string; tags?: string[]; status?: string; auto_path?: string; path_overridden?: boolean };\n    if (!assistant || !store.can(assistant.role, \"update\", atomId, assistant.id)) {\n      json(res, 403, { error: \"permission_denied\" }); return true; }\n    if (parent_id !== undefined) {\n      const updated = store.updateAtomParent(atomId, parent_id ?? null, assistant.id);\n      if (!updated) { json(res, 400, { error: \"invalid_parent\" }); return true; }\n      json(res, 200, { atom: serializeAtom(store, updated) });\n      return true;\n    }\n    try {\n      const updated = store.updateAtom(atomId, { title, summary, tags, status, auto_path, path_overridden }, assistant.id);\n      if (!updated) { json(res, 404, { error: \"atom_not_found\" }); return true; }\n      json(res, 200, { atom: serializeAtom(store, updated) });\n    } catch (err: any) {\n      json(res, 400, { error: err.message });\n    }\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+$/) && method === \"DELETE\" && !pathname.includes(\"/blocks\") && !pathname.includes(\"/bonds\") && !pathname.includes(\"/checkout\")) {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\");\n    if (!assistant || !store.can(assistant.role, \"delete\", atomId, assistant.id)) {\n      json(res, 403, { error: \"permission_denied\" }); return true; }\n    const ok = store.deleteAtom(atomId, assistant.id);\n    json(res, ok ? 200 : 404, { success: ok });\n    return true;\n  }\n\n  // Checkout\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/checkout$/) && method === \"POST\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/checkout\", \"\");\n    const { mode, reason } = body as { mode: any; reason: string };\n    if (!assistant || !store.can(assistant.role, \"lock\", atomId, assistant.id)) {\n      json(res, 403, { error: \"permission_denied\" }); return true; }\n    const result = store.checkout(atomId, assistant.id, mode || \"exclusive\", reason || \"\");\n    json(res, result.success ? 200 : 423, result);\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/checkout$/) && method === \"DELETE\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/checkout\", \"\");\n    if (!assistant) { json(res, 403, { error: \"unauthorized\" }); return true; }\n    const success = store.releaseCheckout(atomId, assistant.id);\n    json(res, success ? 200 : 400, { success });\n    return true;\n  }\n\n  // Queue\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/queue$/) && method === \"GET\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/queue\", \"\");\n    const status = store.getQueueStatus(atomId);\n    json(res, status ? 200 : 404, status || { error: \"atom_not_found\" });\n    return true;\n  }\n\n  const queueGrantMatch = pathname.match(/^\\/api\\/v1\\/atoms\\/([^\\/]+)\\/queue\\/([^\\/]+)\\/grant$/);\n  if (queueGrantMatch && method === \"POST\") {\n    const atomId = queueGrantMatch[1];\n    const queueId = queueGrantMatch[2];\n    const ok = store.grantQueueItem(atomId, queueId);\n    json(res, ok ? 200 : 400, { success: ok });\n    return true;\n  }\n\n  const queueRejectMatch = pathname.match(/^\\/api\\/v1\\/atoms\\/([^\\/]+)\\/queue\\/([^\\/]+)\\/reject$/);\n  if (queueRejectMatch && method === \"POST\") {\n    const atomId = queueRejectMatch[1];\n    const queueId = queueRejectMatch[2];\n    const ok = store.rejectQueueItem(atomId, queueId);\n    json(res, ok ? 200 : 400, { success: ok });\n    return true;\n  }\n\n  const queueBumpMatch = pathname.match(/^\\/api\\/v1\\/atoms\\/([^\\/]+)\\/queue\\/([^\\/]+)\\/bump$/);\n  if (queueBumpMatch && method === \"POST\") {\n    const atomId = queueBumpMatch[1];\n    const queueId = queueBumpMatch[2];\n    const ok = store.bumpQueueItem(atomId, queueId);\n    json(res, ok ? 200 : 400, { success: ok });\n    return true;\n  }\n\n  // Permissions\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/permissions$/) && method === \"GET\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/permissions\", \"\");\n    const perms = store.getAtomPermissions(atomId);\n    json(res, 200, { atom_id: atomId, permissions: perms });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/permissions$/) && method === \"POST\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/permissions\", \"\");\n    const { assistant_id, level } = body as { assistant_id: string; level: string };\n    if (!assistant_id || !level) { json(res, 400, { error: \"assistant_id_and_level_required\" }); return true; }\n    store.setAtomPermission(atomId, assistant_id, level as any, assistant?.id);\n    json(res, 200, { success: true });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/permissions\\/[^\\/]+$/) && method === \"DELETE\") {\n    const parts = pathname.replace(\"/api/v1/atoms/\", \"\").split(\"/\");\n    const atomId = parts[0];\n    const assistantId = parts[2];\n    const ok = store.removeAtomPermission(atomId, assistantId);\n    json(res, ok ? 200 : 404, { success: ok });\n    return true;\n  }\n\n  // History\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/history$/) && method === \"GET\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/history\", \"\");\n    const history = store.getAtomHistory(atomId);\n    json(res, 200, { atom_id: atomId, history });\n    return true;\n  }\n\n  // Export\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/export$/) && method === \"GET\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/export\", \"\");\n    const format = searchParams.get(\"format\") || \"markdown\";\n    const atom = store.getAtom(atomId);\n    if (!atom) { json(res, 404, { error: \"atom_not_found\" }); return true; }\n    if (format === \"markdown\") {\n      const md = exportAtomMarkdown(store, atom);\n      const safeName = (atom.title || \"memory\").replace(/[^a-z0-9\\-_]/gi, \"_\").toLowerCase();\n      res.writeHead(200, { \"Content-Type\": \"text/markdown; charset=utf-8\", \"Content-Disposition\": `attachment; filename=\"${safeName}.md\"` });\n      res.end(md);\n      return true;\n    }\n    json(res, 400, { error: \"unsupported_format\" });\n    return true;\n  }\n\n  // Force Release\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/force-release$/) && method === \"POST\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/force-release\", \"\");\n    const atom = store.getAtom(atomId);\n    if (!atom) { json(res, 404, { error: \"atom_not_found\" }); return true; }\n    if (!atom.locked_by) { json(res, 200, { success: true, note: \"not_locked\" }); return true; }\n    const ok = store.forceRelease(atomId, assistant?.id || \"system\");\n    json(res, ok ? 200 : 400, { success: ok });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport { json } from \"../utils.js\";\n\nexport function handleBonds(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  body: any\n): boolean {\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/bonds$/) && method === \"GET\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/bonds\", \"\");\n    json(res, 200, store.getBondsByAtom(atomId));\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/bonds$/) && method === \"POST\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/bonds\", \"\");\n    const { target_id, label, color } = body as { target_id: string; label: string; color?: string };\n    if (!target_id) { json(res, 400, { error: \"target_id_required\" }); return true; }\n    const bond = store.createBond(atomId, target_id, label || \"connects\", color);\n    json(res, 200, { bond });\n    return true;\n  }\n\n  if (pathname === \"/api/v1/bonds\" && method === \"DELETE\") {\n    const { bond_id } = body as { bond_id: string };\n    const ok = store.deleteBond(bond_id);\n    json(res, ok ? 200 : 404, { success: ok });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/bonds\\/[^\\/]+$/) && method === \"DELETE\") {\n    const bondId = pathname.replace(\"/api/v1/bonds/\", \"\");\n    const ok = store.deleteBond(bondId);\n    json(res, ok ? 200 : 404, { success: ok });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/bonds\\/[^\\/]+$/) && method === \"PATCH\") {\n    const bondId = pathname.replace(\"/api/v1/bonds/\", \"\");\n    const { label, color } = body as { label?: string; color?: string };\n    const updated = store.updateBond(bondId, { label, color });\n    if (!updated) { json(res, 404, { error: \"bond_not_found\" }); return true; }\n    json(res, 200, { bond: updated });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport type { Assistant } from \"../../core/types.js\";\nimport { json } from \"../utils.js\";\n\nexport function handleBlocks(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  body: any,\n  assistant?: Assistant\n): boolean {\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/blocks$/) && method === \"POST\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/blocks\", \"\");\n    const { type, content, tags } = body as { type: string; content: string; tags?: string[] };\n    const isSuggestion = type === \"suggestion\";\n    const requiredAction = isSuggestion ? \"suggest\" : \"write\";\n    if (!assistant || !store.can(assistant.role, requiredAction as any, atomId, assistant.id)) {\n      json(res, 403, { error: \"permission_denied\" }); return true;\n    }\n    const block = store.createBlock(atomId, type || \"text\", content || \"\", assistant.id, { tags });\n    if (type === \"file\" || type === \"image\") {\n      store.processFileBlock(atomId, content || \"\").catch(() => {});\n    }\n    json(res, 200, { block });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/blocks\\/[^\\/]+$/) && method === \"GET\") {\n    const blockId = pathname.replace(\"/api/v1/blocks/\", \"\");\n    const block = store.getBlock(blockId);\n    if (!block) { json(res, 404, { error: \"block_not_found\" }); return true; }\n    json(res, 200, { block });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/blocks\\/[^\\/]+$/) && method === \"PATCH\") {\n    const blockId = pathname.replace(\"/api/v1/blocks/\", \"\");\n    const { content, type, metadata } = body as { content?: string; type?: string; metadata?: any };\n    const block = store.getBlock(blockId);\n    if (!block) { json(res, 404, { error: \"block_not_found\" }); return true; }\n    if (content !== undefined) {\n      store.updateBlock(blockId, content, assistant?.id || \"system\");\n    }\n    if (type !== undefined || metadata !== undefined) {\n      const updates: string[] = [];\n      const vals: any[] = [];\n      if (type !== undefined) { updates.push(\"type = ?\"); vals.push(type); }\n      if (metadata !== undefined) { updates.push(\"metadata = ?\"); vals.push(JSON.stringify(metadata)); }\n      vals.push(blockId);\n      store[\"stmt\"](`UPDATE blocks SET ${updates.join(\", \")} WHERE id = ?`).run(...vals);\n    }\n    json(res, 200, { block: store.getBlock(blockId) });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/blocks\\/[^\\/]+$/) && method === \"DELETE\") {\n    const blockId = pathname.replace(\"/api/v1/blocks/\", \"\");\n    const block = store.getBlock(blockId);\n    if (!block) { json(res, 404, { error: \"block_not_found\" }); return true; }\n    const ok = store.deleteBlock(blockId, assistant?.id || \"system\");\n    json(res, ok ? 200 : 400, { success: ok });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport { json, resolveProjectId } from \"../utils.js\";\n\nexport async function handleSearch(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  searchParams: URLSearchParams\n): Promise<boolean> {\n  if (pathname === \"/api/v1/search\" && method === \"GET\") {\n    const projectId = resolveProjectId(store, searchParams.get(\"project_id\") || \"\");\n    const q = (searchParams.get(\"q\") || \"\").toLowerCase();\n    const limit = parseInt(searchParams.get(\"limit\") || \"20\", 10);\n    const semantic = searchParams.get(\"semantic\") === \"true\";\n    if (!q) { json(res, 200, { results: [], count: 0 }); return true; }\n\n    let results: any[] = [];\n\n    if (semantic) {\n      const { embedText } = await import(\"../../server/embedder.js\");\n      const queryEmbedding = await embedText(q);\n      if (queryEmbedding) {\n        results = store.searchHybrid(projectId, q, queryEmbedding, limit);\n      } else {\n        results = store.search(projectId, q, limit);\n      }\n    } else {\n      results = store.search(projectId, q, limit);\n    }\n\n    json(res, 200, { query: q, semantic, count: results.length, results });\n    return true;\n  }\n\n  return false;\n}\n","/**\n * Content-Addressed Storage (CAS)\n * Files stored by SHA256 hash, sharded by first 2 hex chars.\n */\n\nimport { createHash } from \"crypto\";\nimport { mkdirSync, existsSync, writeFileSync, readFileSync } from \"fs\";\nimport { resolve, dirname } from \"path\";\nimport { CONFIG } from \"../config.js\";\n\nfunction getFilesDir(): string {\n  return resolve(process.cwd(), CONFIG.storage.files_dir);\n}\n\nfunction ensureDir(path: string): void {\n  if (!existsSync(path)) mkdirSync(path, { recursive: true });\n}\n\nfunction hashPath(hash: string): string {\n  return resolve(getFilesDir(), hash.slice(0, 2), hash.slice(2));\n}\n\nexport function computeHash(buffer: Buffer): string {\n  return createHash(\"sha256\").update(buffer).digest(\"hex\");\n}\n\nexport function saveFile(buffer: Buffer, _fileName: string): { hash: string; size: number; path: string } {\n  const hash = computeHash(buffer);\n  const dest = hashPath(hash);\n\n  if (!existsSync(dest)) {\n    ensureDir(dirname(dest));\n    writeFileSync(dest, buffer);\n  }\n\n  return { hash, size: buffer.length, path: dest };\n}\n\nexport function getFile(hash: string): Buffer | null {\n  try {\n    return readFileSync(hashPath(hash));\n  } catch {\n    return null;\n  }\n}\n\nexport function fileExists(hash: string): boolean {\n  return existsSync(hashPath(hash));\n}\n","import type { Store } from \"../../core/Store.js\";\nimport { saveFile, getFile, computeHash } from \"../../server/files.js\";\nimport { json } from \"../utils.js\";\n\nexport function handleFiles(\n  store: Store,\n  pathname: string,\n  method: string,\n  req: import(\"http\").IncomingMessage,\n  res: import(\"http\").ServerResponse,\n  maxFileSizeMb: number\n): boolean | Promise<boolean> {\n  if (pathname === \"/api/v1/files/upload\" && method === \"POST\") {\n    const fileName = req.headers[\"x-file-name\"] as string || \"upload\";\n    const mimeType = req.headers[\"content-type\"] || \"application/octet-stream\";\n    const chunks: Buffer[] = [];\n    req.on(\"data\", (chunk: Buffer) => chunks.push(chunk));\n    req.on(\"end\", () => {\n      const buffer = Buffer.concat(chunks);\n      const maxBytes = maxFileSizeMb * 1024 * 1024;\n      if (buffer.length > maxBytes) {\n        json(res, 413, { error: \"file_too_large\", max: `${maxFileSizeMb}MB` }); return;\n      }\n      const hash = computeHash(buffer);\n      const existing = store.getAttachmentByHash(hash);\n      if (existing) {\n        json(res, 200, { success: true, hash, file_name: existing.file_name, size: existing.file_size, mime_type: existing.mime_type, dedup: true });\n        return;\n      }\n      const saved = saveFile(buffer, fileName);\n      const attachment = store.createAttachment(hash, fileName, saved.size, mimeType);\n      json(res, 200, { success: true, hash, file_name: fileName, size: saved.size, mime_type: mimeType });\n    });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/files\\/[^\\/]+$/) && method === \"GET\") {\n    const hash = pathname.replace(\"/api/v1/files/\", \"\");\n    const data = getFile(hash);\n    if (!data) { json(res, 404, { error: \"file_not_found\" }); return true; }\n    const attachment = store.getAttachmentByHash(hash);\n    const mime = attachment?.mime_type || \"application/octet-stream\";\n    res.writeHead(200, { \"Content-Type\": mime, \"Content-Length\": data.length });\n    res.end(data);\n    return true;\n  }\n\n  return false;\n}\n","/**\n * .mnemosyne Export Format\n * Creates a ZIP containing: nexus.db + files/ + manifest.json\n */\n\nimport AdmZip from \"adm-zip\";\nimport { createHash } from \"crypto\";\nimport { readFileSync, existsSync, readdirSync, statSync } from \"fs\";\nimport { resolve } from \"path\";\n\nconst DB_PATH = resolve(process.cwd(), \"data\", \"nexus.db\");\nconst FILES_DIR = resolve(process.cwd(), \"data\", \"files\");\n\nfunction sha256File(path: string): string {\n  return createHash(\"sha256\").update(readFileSync(path)).digest(\"hex\");\n}\n\nfunction sha256Dir(dir: string): string {\n  const hash = createHash(\"sha256\");\n  function walk(p: string) {\n    const stat = statSync(p);\n    if (stat.isFile()) {\n      hash.update(readFileSync(p));\n    } else if (stat.isDirectory()) {\n      for (const child of readdirSync(p).sort()) walk(resolve(p, child));\n    }\n  }\n  walk(dir);\n  return hash.digest(\"hex\");\n}\n\nexport function buildMnemosyneExport(projectId?: string, projectName?: string): Buffer {\n  const zip = new AdmZip();\n\n  // Add database\n  zip.addLocalFile(DB_PATH, \"\", \"nexus.db\");\n\n  // Add files directory\n  if (existsSync(FILES_DIR)) {\n    zip.addLocalFolder(FILES_DIR, \"files\");\n  }\n\n  // Build manifest\n  const dbChecksum = sha256File(DB_PATH);\n  const filesChecksum = existsSync(FILES_DIR) ? sha256Dir(FILES_DIR) : \"\";\n\n  const manifest = {\n    version: \"1.1\",\n    app: \"Mnemosyne\",\n    exported_at: new Date().toISOString(),\n    project: projectId ? { id: projectId, name: projectName || \"\" } : null,\n    checksums: { db: dbChecksum, files: filesChecksum },\n  };\n\n  zip.addFile(\"manifest.json\", Buffer.from(JSON.stringify(manifest, null, 2)));\n\n  return zip.toBuffer();\n}\n\nexport function parseMnemosyneImport(zipBuffer: Buffer): { valid: boolean; error?: string; manifest?: any } {\n  try {\n    const zip = new AdmZip(zipBuffer);\n    const manifestEntry = zip.getEntry(\"manifest.json\");\n    if (!manifestEntry) return { valid: false, error: \"Missing manifest.json\" };\n\n    const manifest = JSON.parse(manifestEntry.getData().toString(\"utf-8\"));\n    if (manifest.version !== \"1.0\" && manifest.version !== \"1.1\") return { valid: false, error: `Unsupported version: ${manifest.version}` };\n    if (!zip.getEntry(\"nexus.db\")) return { valid: false, error: \"Missing nexus.db\" };\n\n    return { valid: true, manifest };\n  } catch (err: any) {\n    return { valid: false, error: err.message };\n  }\n}\n","import type { Store } from \"../../core/Store.js\";\nimport type { Assistant } from \"../../core/types.js\";\nimport { buildMnemosyneExport, parseMnemosyneImport } from \"../../server/export-format.js\";\nimport { json, resolveProjectId, exportMarkdown } from \"../utils.js\";\n\nexport function handleExportImport(\n  store: Store,\n  pathname: string,\n  method: string,\n  req: import(\"http\").IncomingMessage,\n  res: import(\"http\").ServerResponse,\n  body: any,\n  searchParams: URLSearchParams,\n  assistant?: Assistant\n): boolean | Promise<boolean> {\n  if (pathname === \"/api/v1/export\" && method === \"GET\") {\n    const format = searchParams.get(\"format\") || \"mnemosyne\";\n    const projectId = resolveProjectId(store, searchParams.get(\"project_id\") || \"\");\n\n    if (format === \"markdown\") {\n      const md = exportMarkdown(store, projectId);\n      res.writeHead(200, { \"Content-Type\": \"text/markdown; charset=utf-8\", \"Content-Disposition\": \"attachment; filename=mnemosyne-export.md\" });\n      res.end(md);\n      return true;\n    }\n\n    if (format === \"mnemosyne\") {\n      const project = projectId ? store.getProject(projectId) : undefined;\n      const zipBuffer = buildMnemosyneExport(projectId, project?.name);\n      res.writeHead(200, {\n        \"Content-Type\": \"application/zip\",\n        \"Content-Disposition\": `attachment; filename=\"${project?.name || \"mnemosyne\"}.mnemosyne\"`,\n        \"Content-Length\": zipBuffer.length,\n      });\n      res.end(zipBuffer);\n      return true;\n    }\n\n    if (!assistant || !store.can(assistant.role, \"export\", \"/system\")) {\n      json(res, 403, { error: \"permission_denied\" }); return true;\n    }\n    const snapshot = store.exportSnapshot();\n    json(res, 200, snapshot);\n    return true;\n  }\n\n  if (pathname === \"/api/v1/import\" && method === \"POST\") {\n    if (!assistant || !store.can(assistant.role, \"import\", \"/system\")) {\n      json(res, 403, { error: \"permission_denied\" }); return true;\n    }\n    const format = searchParams.get(\"format\") || \"mnemosyne\";\n\n    if (format === \"mnemosyne\") {\n      const contentType = req.headers[\"content-type\"] || \"\";\n      if (contentType.includes(\"application/zip\") || contentType.includes(\"multipart\") || contentType.includes(\"application/octet-stream\")) {\n        const chunks: Buffer[] = [];\n        req.on(\"data\", (chunk: Buffer) => chunks.push(chunk));\n        req.on(\"end\", () => {\n          const buffer = Buffer.concat(chunks);\n          const parsed = parseMnemosyneImport(buffer);\n          if (!parsed.valid) { json(res, 400, { success: false, error: parsed.error }); return; }\n          const result = store.importMnemosyneZip(buffer, assistant.id);\n          if (result.success) {\n            json(res, 200, { success: true, atomsRestored: result.atomsRestored });\n          } else {\n            json(res, 400, { success: false, error: result.error });\n          }\n        });\n        return true;\n      }\n      json(res, 400, { success: false, error: \"expected_zip_body\" });\n      return true;\n    }\n\n    if (format === \"markdown\") {\n      const projectId = resolveProjectId(store, searchParams.get(\"project_id\") || \"\");\n      if (!projectId) { json(res, 400, { error: \"project_id_required\" }); return true; }\n      const md = typeof body === \"string\" ? body : (body.content || \"\");\n      const title = body.title || undefined;\n      const result = store.importMarkdown(md, projectId, assistant.id, { title });\n      if (result.success) {\n        json(res, 200, { success: true, atomId: result.atomId, bondsCreated: result.bondsCreated });\n      } else {\n        json(res, 400, { success: false, error: result.error });\n      }\n      return true;\n    }\n\n    json(res, 400, { success: false, error: \"unsupported_import_format\" });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport { json } from \"../utils.js\";\n\nexport function handleEvents(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse,\n  searchParams: URLSearchParams\n): boolean {\n  if (pathname === \"/api/v1/events\" && method === \"GET\") {\n    const since = parseInt(searchParams.get(\"since\") || \"0\", 10);\n    const projectId = searchParams.get(\"project_id\") || undefined;\n    const limit = parseInt(searchParams.get(\"limit\") || \"50\", 10);\n    json(res, 200, { events: store.getEvents(since, projectId, limit) });\n    return true;\n  }\n\n  if (pathname.match(/^\\/api\\/v1\\/atoms\\/[^\\/]+\\/events$/) && method === \"GET\") {\n    const atomId = pathname.replace(\"/api/v1/atoms/\", \"\").replace(\"/events\", \"\");\n    const limit = parseInt(searchParams.get(\"limit\") || \"50\", 10);\n    json(res, 200, { events: store.getEventsByAtom(atomId, limit) });\n    return true;\n  }\n\n  return false;\n}\n","import type { Store } from \"../../core/Store.js\";\nimport { json } from \"../utils.js\";\n\nconst PKG_VERSION = (() => {\n  try {\n    const pkg = JSON.parse(require(\"fs\").readFileSync(require(\"path\").resolve(__dirname, \"../../../package.json\"), \"utf-8\"));\n    return pkg.version;\n  } catch {\n    return \"2.0.3\";\n  }\n})();\n\nexport function handleHealth(\n  store: Store,\n  pathname: string,\n  method: string,\n  res: import(\"http\").ServerResponse\n): boolean {\n  if ((pathname === \"/health\" || pathname === \"/api/v1/health\") && method === \"GET\") {\n    const stats = store.getStats();\n    json(res, 200, {\n      status: \"ok\",\n      version: PKG_VERSION,\n      storage: \"sqlite\",\n      database: store.config.database.path,\n      uptime: process.uptime(),\n      counts: stats,\n    });\n    return true;\n  }\n\n  return false;\n}\n","/**\n * Mnemosyne Core Types\n * Shared TypeScript interfaces and constants used across all modules.\n */\n\nexport const VALID_STATUSES = ['draft', 'review', 'approved', 'archived', 'deprecated', 'hot'];\n\nexport const ALLOWED_TRANSITIONS: Record<string, string[]> = {\n  draft: ['review', 'archived', 'hot'],\n  review: ['draft', 'approved', 'archived'],\n  approved: ['review', 'deprecated', 'archived'],\n  archived: ['draft'],\n  deprecated: ['draft', 'archived'],\n  hot: ['draft', 'review']\n};\n\nexport type PermissionLevel = \"none\" | \"view\" | \"suggest\" | \"edit\" | \"create\" | \"admin\";\n\nexport type Action =\n  | \"create\" | \"read\" | \"write\" | \"update\" | \"delete\"\n  | \"lock\" | \"manage_queue\" | \"force_release\"\n  | \"peek\" | \"export\" | \"import\" | \"suggest\";\n\nexport type AssistantRole = \"owner\" | \"admin\" | \"manager\" | \"lead\" | \"developer\" | \"worker\" | \"reviewer\" | \"observer\" | \"bot\" | \"guest\";\n\nexport interface Project {\n  id: string;\n  name: string;\n  description: string | null;\n  icon: string;\n  color: string;\n  created_at: number;\n  updated_at: number;\n  owner: string;\n  metadata: Record<string, any>;\n}\n\nexport interface Atom {\n  id: string;\n  project_id: string;\n  parent_id: string | null;\n  title: string;\n  summary: string | null;\n  icon: string;\n  color: string | null;\n  x: number | null;\n  y: number | null;\n  created_at: number;\n  updated_at: number;\n  version: number;\n  locked_by: string | null;\n  locked_at: number | null;\n  locked_reason: string | null;\n  owner: string;\n  status: string;\n  metadata: Record<string, any>;\n  auto_path?: string;\n  path_overridden?: boolean;\n  status_updated_at?: number;\n  block_count?: number;\n  bond_count?: number;\n  template_id?: string | null;\n  embedding_status?: string | null;\n}\n\nexport interface Block {\n  id: string;\n  atom_id: string;\n  type: string;\n  content: string | null;\n  order_index: number;\n  created_at: number;\n  updated_at: number;\n  metadata: Record<string, any>;\n}\n\nexport interface Bond {\n  id: string;\n  source_id: string;\n  target_id: string;\n  label: string;\n  color: string | null;\n  created_at: number;\n}\n\nexport interface Assistant {\n  id: string;\n  name: string;\n  role: AssistantRole;\n  permissions: Record<string, any>;\n  status: string;\n  provider: string | null;\n  connected_at: number;\n  last_seen: number;\n  metadata: Record<string, any>;\n}\n\nexport interface QueueEntry {\n  id: string;\n  atom_id: string;\n  assistant_id: string;\n  requested_at: number;\n  priority: number;\n  status: string;\n  reason: string | null;\n}\n\nexport interface EventLogEntry {\n  id: string;\n  timestamp: number;\n  event_type: string;\n  project_id: string | null;\n  atom_id: string | null;\n  block_id: string | null;\n  bond_id: string | null;\n  actor: string;\n  actor_type: string;\n  diff: string | null;\n  trigger: string | null;\n  metadata: Record<string, any>;\n}\n\nexport interface Config {\n  server: {\n    port: number;\n    host: string;\n    version: string;\n  };\n  database: {\n    path: string;\n    wal_mode: boolean;\n    vec_extension_path: string;\n  };\n  storage: {\n    files_dir: string;\n    max_file_size_mb: number;\n    backups_dir: string;\n    backup_interval_hours: number;\n    max_backups: number;\n  };\n  limits: {\n    max_atoms_per_project: number;\n    rate_limit_requests: number;\n    rate_limit_window_ms: number;\n  };\n  embeddings: {\n    model: string;\n    dimension: number;\n    max_text_length: number;\n  };\n  features: {\n    mcp_enabled: boolean;\n    auto_index_enabled: boolean;\n    file_processing_enabled: boolean;\n  };\n  index: {\n    debounce_ms: number;\n  };\n  search: {\n    semantic_weight: number;\n    fts_weight: number;\n  };\n  bonds: {\n    default_type: string;\n  };\n}\n\nexport const TEMPLATES: Record<string, { name: string; blocks: { type: string; content: string }[] }> = {\n  blank: { name: \"Blank\", blocks: [] },\n  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persona: { name: \"Persona\", blocks: [\n    { type: \"Name\", content: \"\" },\n    { type: \"Role\", content: \"\" },\n    { type: \"Goals\", content: \"\" },\n    { type: \"Pain Points\", content: \"\" },\n    { type: \"Quotes\", content: \"\" }\n  ]},\n  \"project-spec\": { name: \"Project Spec\", blocks: [\n    { type: \"Overview\", content: \"\" },\n    { type: \"Goals\", content: \"\" },\n    { type: \"Non-Goals\", content: \"\" },\n    { type: \"Timeline\", content: \"\" }\n  ]},\n  \"daily-journal\": { name: \"Daily Journal\", blocks: [\n    { type: \"Date\", content: \"\" },\n    { type: \"Wins\", content: \"\" },\n    { type: \"Blockers\", content: \"\" },\n    { type: \"Tomorrow\", content: \"\" }\n  ]}\n};\n\nexport const ROLE_PERMISSIONS: Record<AssistantRole, { actions: Action[]; pattern: string }> = {\n  owner:       { actions: [\"create\",\"read\",\"write\",\"update\",\"delete\",\"lock\",\"manage_queue\",\"force_release\",\"peek\",\"export\",\"import\"], pattern: 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 return false;\n}\n","/**\n * Mnemosyne API Router\n * Modular HTTP router combining all domain routes.\n */\n\nimport type { Store } from \"../core/Store.js\";\nimport { McpServer, McpHttpTransport } from \"../server/mcp.js\";\nimport { RateLimiter, setCorsHeaders, authenticate } from \"./middleware.js\";\nimport { readBody, json } from \"./utils.js\";\nimport { handleAssistants } from \"./routes/assistants.js\";\nimport { handleProjects } from \"./routes/projects.js\";\nimport { handleAtoms } from \"./routes/atoms.js\";\nimport { handleBonds } from \"./routes/bonds.js\";\nimport { handleBlocks } from \"./routes/blocks.js\";\nimport { handleSearch } from \"./routes/search.js\";\nimport { handleFiles } from \"./routes/files.js\";\nimport { handleExportImport } from \"./routes/export-import.js\";\nimport { handleEvents } from \"./routes/events.js\";\nimport { handleHealth } from \"./routes/health.js\";\nimport { handleTree } from \"./routes/tree.js\";\n\nexport class ApiRouter {\n  private store: Store;\n  private rateLimiter: RateLimiter;\n  private mcpServer: McpServer;\n  private mcpTransport: McpHttpTransport;\n\n  constructor(store: Store) {\n    this.store = store;\n    this.rateLimiter = new RateLimiter(\n      store.config.limits.rate_limit_requests,\n      store.config.limits.rate_limit_window_ms\n    );\n    this.mcpServer = new McpServer(store);\n    this.mcpTransport = new McpHttpTransport(this.mcpServer);\n  }\n\n  async handle(req: import(\"http\").IncomingMessage, res: import(\"http\").ServerResponse): Promise<void> {\n    const url = new URL(req.url || \"/\", `http://${req.headers.host}`);\n    const pathname = url.pathname;\n    const method = req.method || \"GET\";\n\n    setCorsHeaders(res);\n    if (method === \"OPTIONS\") { res.writeHead(204); res.end(); return; }\n\n    try {\n      const assistant = authenticate(this.store, req);\n      const token = req.headers.authorization?.replace(\"Bearer \", \"\");\n\n      if (token && 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