nexus-agents 2.29.1 → 2.29.2

package/dist/{chunk-2UR7YN6T.js → chunk-TL2GJMJ5.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-BC3M4VLP.js";
 import {
   createLogger
-} from "./chunk-ELIFTCYM.js";
+} from "./chunk-HSOPD265.js";
 
 // src/mcp/tools/scanner-registry-fetcher.ts
 import { z } from "zod";
@@ -697,4 +697,4 @@ export {
   generateSecurityPlan,
   buildPlanFromAnalysis
 };
-//# sourceMappingURL=chunk-2UR7YN6T.js.map
+//# sourceMappingURL=chunk-TL2GJMJ5.js.map

package/dist/{chunk-3GXDN4AX.js → chunk-V6MSPUQF.js}

@@ -1,6 +1,6 @@
 import {
   getErrorMessage
-} from "./chunk-ELIFTCYM.js";
+} from "./chunk-HSOPD265.js";
 
 // src/cli/setup-config.ts
 import { existsSync, writeFileSync } from "fs";
@@ -59,4 +59,4 @@ function runConfigInitSync(projectRoot, force, dryRun) {
 export {
   runConfigInitSync
 };
-//# sourceMappingURL=chunk-3GXDN4AX.js.map
+//# sourceMappingURL=chunk-V6MSPUQF.js.map

package/dist/{chunk-7SKAKA4I.js → chunk-VZ2YOQWU.js}

@@ -2,7 +2,7 @@ import {
   createLogger,
   err,
   ok
-} from "./chunk-ELIFTCYM.js";
+} from "./chunk-HSOPD265.js";
 
 // src/scm/token-resolver.ts
 import { execFile } from "child_process";
@@ -87,4 +87,4 @@ export {
   hasToken,
   getTokenEnvVars
 };
-//# sourceMappingURL=chunk-7SKAKA4I.js.map
+//# sourceMappingURL=chunk-VZ2YOQWU.js.map

package/dist/{chunk-3EVVQ32X.js → chunk-WSYJN7BI.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-633WH2ML.js";
 import {
   createAllAdapters
-} from "./chunk-4AGPR6XZ.js";
+} from "./chunk-CW2Z773T.js";
 import {
   DEFAULT_CAPABILITIES,
   DEFAULT_MODEL_CAPABILITIES,
@@ -15,7 +15,7 @@ import {
   ok,
   symbols,
   writeLine
-} from "./chunk-ELIFTCYM.js";
+} from "./chunk-HSOPD265.js";
 import {
   LEARNING_DIR,
   OUTCOMES_FILE,
@@ -24,7 +24,7 @@ import {
 } from "./chunk-CLYZ7FWP.js";
 
 // src/version.ts
-var VERSION = true ? "2.29.1" : "dev";
+var VERSION = true ? "2.29.2" : "dev";
 
 // src/cli/setup-data-dir.ts
 import { mkdirSync, existsSync as existsSync2 } from "fs";
@@ -170,6 +170,7 @@ async function startStdioServer(config) {
   }
   const { server, logger: logger2 } = serverResult.value;
   try {
+    logger2.setDestination?.("stderr");
     logger2.info("Starting stdio transport");
     const transport = new StdioServerTransport();
     const connectResult = await connectTransport(server, transport, logger2);
@@ -757,7 +758,7 @@ async function runDoctorFix(result) {
   writeLine2("\u2500".repeat(40));
   let fixCount = 0;
   if (!result.dataDirectory.rootExists || result.dataDirectory.subdirectories.some((d) => !d.exists || !d.writable)) {
-    const { runSetup } = await import("./setup-command-E6MXO5RZ.js");
+    const { runSetup } = await import("./setup-command-CMCQRBJF.js");
     const setupResult = runSetup({
       skipMcp: true,
       skipRules: true,
@@ -771,7 +772,7 @@ async function runDoctorFix(result) {
     }
   }
   if (!result.configFile.found) {
-    const { runConfigInitSync } = await import("./setup-config-O5F3AZBL.js");
+    const { runConfigInitSync } = await import("./setup-config-KITOPV7V.js");
     const configResult = runConfigInitSync(process.cwd(), false, false);
     if (configResult.success && configResult.created) {
       writeLine2(`\u2713 Generated config: ${configResult.path}`);
@@ -835,4 +836,4 @@ export {
   startStdioServer,
   closeServer
 };
-//# sourceMappingURL=chunk-3EVVQ32X.js.map
+//# sourceMappingURL=chunk-WSYJN7BI.js.map

package/dist/chunk-WSYJN7BI.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/version.ts","../src/cli/setup-data-dir.ts","../src/cli/doctor.ts","../src/mcp/server.ts","../src/mcp/task-store.ts","../src/cli/doctor-formatting.ts"],"sourcesContent":["/**\n * nexus-agents - Version constant\n *\n * Injected at build time via tsup define from package.json.\n * Do NOT edit this value manually — it is replaced during build.\n */\n\ndeclare const __NEXUS_VERSION__: string;\n\nexport const VERSION: string = typeof __NEXUS_VERSION__ !== 'undefined' ? __NEXUS_VERSION__ : 'dev';\n","/**\n * nexus-agents data directory initialization\n *\n * Pre-creates ~/.nexus-agents/ directory structure with proper permissions.\n * Used by `nexus-agents setup` to ensure data directories exist before first use.\n *\n * @module cli/setup-data-dir\n * (Source: Issue #1249 - Developer experience improvements)\n */\n\nimport { mkdirSync, existsSync } from 'node:fs';\nimport { homedir } from 'node:os';\nimport { join } from 'node:path';\nimport { DATA_SUBDIRECTORIES } from './doctor.js';\n\n/** Root data directory path. */\nexport const NEXUS_DATA_DIR = join(homedir(), '.nexus-agents');\n\n/** Subdirectories requiring restricted permissions (owner-only). */\nconst RESTRICTED_DIRS = new Set(['auth']);\n\n/**\n * Result of data directory initialization.\n */\nexport interface DataDirInitResult {\n  readonly success: boolean;\n  readonly rootPath: string;\n  readonly created: readonly string[];\n  readonly alreadyExisted: readonly string[];\n  readonly error: string | null;\n}\n\n/**\n * Creates the ~/.nexus-agents/ directory structure.\n * Sets restrictive permissions (0o700) on auth/ directory.\n *\n * @param dryRun - If true, reports what would be created without creating.\n * @returns Result of initialization.\n */\nexport function initDataDirectories(dryRun: boolean = false): DataDirInitResult {\n  const created: string[] = [];\n  const alreadyExisted: string[] = [];\n\n  try {\n    ensureDir(NEXUS_DATA_DIR, dryRun, created, alreadyExisted);\n\n    for (const subdir of DATA_SUBDIRECTORIES) {\n      const mode = RESTRICTED_DIRS.has(subdir) ? 0o700 : undefined;\n      ensureDir(join(NEXUS_DATA_DIR, subdir), dryRun, created, alreadyExisted, mode);\n    }\n\n    return { success: true, rootPath: NEXUS_DATA_DIR, created, alreadyExisted, error: null };\n  } catch (error: unknown) {\n    const msg = error instanceof Error ? error.message : String(error);\n    return { success: false, rootPath: NEXUS_DATA_DIR, created, alreadyExisted, error: msg };\n  }\n}\n\n/** Creates a single directory if it doesn't exist, tracking the result. */\nfunction ensureDir(\n  dirPath: string,\n  dryRun: boolean,\n  created: string[],\n  alreadyExisted: string[],\n  mode?: number\n): void {\n  if (existsSync(dirPath)) {\n    alreadyExisted.push(dirPath);\n    return;\n  }\n  if (!dryRun) {\n    mkdirSync(dirPath, { recursive: true, ...(mode !== undefined ? { mode } : {}) });\n  }\n  created.push(dirPath);\n}\n","/* eslint-disable max-lines -- Cohesive doctor command module (governance: 400-600 OK if cohesive) */\n/**\n * nexus-agents doctor command\n *\n * Health check utility for CLI integration validation.\n * Verifies CLI installations, versions, authentication, Node.js version,\n * API keys, configuration files, and MCP server readiness.\n *\n * (Source: Issue #91, cli-project_plan.md DevEx amendment)\n * (Source: Issue #422 - Doctor command validations)\n */\n\nimport { existsSync, readFileSync, accessSync, constants as fsConstants } from 'node:fs';\nimport { homedir } from 'node:os';\nimport { join } from 'node:path';\nimport { getTimeProvider, getErrorMessage } from '../core/index.js';\nimport {\n  isPersistenceEnabled,\n  LEARNING_DIR,\n  OUTCOMES_FILE,\n  RULES_FILE,\n} from '../config/learning-persistence.js';\nimport { createAllAdapters } from '../cli-adapters/factory.js';\nimport type { CliName, HealthStatus, CapacityStatus } from '../cli-adapters/types.js';\nimport { DEFAULT_MODEL_CAPABILITIES } from '../config/model-capabilities.js';\nimport { createServer } from '../mcp/server.js';\nimport { printDoctorResults } from './doctor-formatting.js';\n\n/** Required Node.js major version. */\nconst REQUIRED_NODE_MAJOR = 22;\n\n/** API key environment variable names. */\nconst API_KEY_VARS = ['ANTHROPIC_API_KEY', 'OPENAI_API_KEY', 'GOOGLE_AI_API_KEY'] as const;\n\n/** Configuration file paths to check (in order of priority). */\nconst CONFIG_FILE_PATHS = ['./nexus-agents.yaml', './nexus-agents.yml'] as const;\n\n/**\n * Check result for a single CLI.\n */\nexport interface CliCheckResult {\n  readonly name: CliName;\n  readonly installed: boolean;\n  readonly version: string;\n  readonly versionStatus: 'supported' | 'outdated' | 'unsupported' | 'breaking';\n  readonly authenticated: boolean;\n  readonly authMethod?: string;\n  readonly capacity?: CapacityStatus;\n  readonly error?: string;\n  readonly fix?: string;\n}\n\n/**\n * Node.js version check result.\n */\nexport interface NodeVersionCheck {\n  readonly version: string;\n  readonly major: number;\n  readonly supported: boolean;\n}\n\n/**\n * API key check result.\n */\nexport interface ApiKeyCheck {\n  readonly name: string;\n  readonly configured: boolean;\n}\n\n/**\n * Configuration file check result.\n */\nexport interface ConfigFileCheck {\n  readonly found: boolean;\n  readonly path: string | null;\n}\n\n/**\n * Model availability advisory entry (#890).\n */\nexport interface ModelAdvisory {\n  readonly modelId: string;\n  readonly displayName: string;\n  readonly cliName: string;\n  readonly available: boolean;\n  readonly reason: string;\n}\n\n/**\n * Learning persistence health check result (#1017).\n */\nexport interface LearningPersistenceCheck {\n  readonly enabled: boolean;\n  readonly dirExists: boolean;\n  readonly dirWritable: boolean;\n  readonly outcomeCount: number;\n  readonly ruleCount: number;\n  readonly rulesLastSaved: string | null;\n  readonly error: string | null;\n}\n\n/**\n * Registry advisory summary (#890).\n */\nexport interface RegistryAdvisory {\n  readonly totalModels: number;\n  readonly availableModels: number;\n  readonly unavailableModels: number;\n  readonly models: readonly ModelAdvisory[];\n  /** Days since the registry was last updated. */\n  readonly registryAgeDays: number;\n  /** True if the registry is >30 days old and may have stale model data. */\n  readonly registryStale: boolean;\n}\n\n/**\n * SQLite (better-sqlite3) availability check (#1249).\n */\nexport interface SqliteCheck {\n  readonly available: boolean;\n  readonly error: string | null;\n}\n\n/**\n * Data directory health check (#1249).\n * Reports status of ~/.nexus-agents/ and its subdirectories.\n */\nexport interface DataDirectoryCheck {\n  readonly rootExists: boolean;\n  readonly rootPath: string;\n  readonly subdirectories: readonly DataSubdirStatus[];\n}\n\n/**\n * Status of a single data subdirectory.\n */\nexport interface DataSubdirStatus {\n  readonly name: string;\n  readonly path: string;\n  readonly exists: boolean;\n  readonly writable: boolean;\n}\n\n/** Standard data subdirectories under ~/.nexus-agents/. */\nexport const DATA_SUBDIRECTORIES = [\n  'memory',\n  'memory/beliefs',\n  'learning',\n  'sessions',\n  'audit',\n  'voting',\n  'auth',\n  'research',\n  'checkpoints',\n] as const;\n\n/**\n * Complete doctor check results.\n */\nexport interface DoctorResult {\n  readonly clis: CliCheckResult[];\n  readonly nodeVersion: NodeVersionCheck;\n  readonly apiKeys: ApiKeyCheck[];\n  readonly configFile: ConfigFileCheck;\n  readonly mcpServerReady: boolean;\n  readonly mcpClientReady: boolean;\n  /** Model registry advisory — which models are available (#890). */\n  readonly registryAdvisory: RegistryAdvisory;\n  /** Learning persistence health check (#1017). */\n  readonly learningPersistence: LearningPersistenceCheck;\n  /** SQLite (better-sqlite3) availability (#1249). */\n  readonly sqliteCheck: SqliteCheck;\n  /** Data directory health (#1249). */\n  readonly dataDirectory: DataDirectoryCheck;\n  readonly allHealthy: boolean;\n  readonly timestamp: Date;\n}\n\n/**\n * Gets the CLI install/upgrade fix command.\n */\nfunction getFixCommand(name: CliName, issue: 'install' | 'upgrade' | 'auth'): string {\n  const commands: Record<CliName, Record<string, string>> = {\n    claude: {\n      install: 'npm install -g @anthropic-ai/claude-code',\n      upgrade: 'npm update -g @anthropic-ai/claude-code',\n      auth: 'claude auth login',\n    },\n    gemini: {\n      install: 'npm install -g @google/gemini-cli',\n      upgrade: 'npm update -g @google/gemini-cli',\n      auth: 'gemini auth login',\n    },\n    codex: {\n      install: 'npm install -g @openai/codex',\n      upgrade: 'npm update -g @openai/codex',\n      auth: 'codex auth login',\n    },\n    opencode: {\n      install: 'npm install -g opencode-ai',\n      upgrade: 'npm update -g opencode-ai',\n      auth: 'opencode auth login',\n    },\n  };\n  return commands[name][issue] ?? '';\n}\n\n/**\n * Creates a result for when a CLI is not found.\n */\nfunction createNotFoundResult(name: CliName, errorMsg: string): CliCheckResult {\n  return {\n    name,\n    installed: false,\n    version: 'N/A',\n    versionStatus: 'unsupported',\n    authenticated: false,\n    error: errorMsg,\n    fix: getFixCommand(name, 'install'),\n  };\n}\n\n/**\n * Determines the authentication method based on CLI name.\n * CLIs use their own auth mechanisms - we report the method type\n * rather than assuming a specific one like 'OAuth'.\n */\nfunction detectAuthMethod(name: CliName): string {\n  const authMethods: Record<CliName, string> = {\n    claude: 'CLI auth',\n    gemini: 'ADC/CLI auth',\n    codex: 'CLI auth',\n    opencode: 'CLI auth',\n  };\n  return authMethods[name];\n}\n\n/**\n * Creates a result from a successful health check.\n */\nfunction createHealthyResult(\n  name: CliName,\n  health: HealthStatus,\n  capacity?: CapacityStatus\n): CliCheckResult {\n  const authenticated = health.healthy;\n\n  const result: CliCheckResult = {\n    name,\n    installed: true,\n    version: health.version,\n    versionStatus: health.versionStatus,\n    authenticated,\n    ...(authenticated && { authMethod: detectAuthMethod(name) }),\n    ...(capacity !== undefined && { capacity }),\n  };\n\n  if (health.message !== undefined && health.message !== '') {\n    return { ...result, error: health.message };\n  }\n  if (!authenticated) {\n    return { ...result, fix: getFixCommand(name, 'auth') };\n  }\n  if (health.versionStatus === 'outdated') {\n    return { ...result, fix: getFixCommand(name, 'upgrade') };\n  }\n\n  return result;\n}\n\n/**\n * Runs health check on a single CLI adapter.\n */\nasync function checkCli(name: CliName): Promise<CliCheckResult> {\n  const adapters = createAllAdapters();\n  const adapter = adapters.get(name);\n\n  if (!adapter) {\n    return createNotFoundResult(name, 'Adapter not available');\n  }\n\n  try {\n    const health: HealthStatus = await adapter.healthCheck();\n    let capacity: CapacityStatus | undefined;\n\n    try {\n      capacity = await adapter.getCapacity();\n    } catch (capErr: unknown) {\n      // Capacity check is optional — some adapters don't support it\n      void capErr; // Logged at debug via adapter internals\n    }\n\n    return createHealthyResult(name, health, capacity);\n  } catch (error) {\n    const message = getErrorMessage(error);\n    const isNotFound = message.includes('ENOENT') || message.includes('not found');\n    return createNotFoundResult(name, isNotFound ? 'Not found in PATH' : message);\n  }\n}\n\n/**\n * Checks the Node.js version against the required version.\n */\nfunction checkNodeVersion(): NodeVersionCheck {\n  const version = process.version;\n  const major = Number(version.slice(1).split('.')[0]);\n  return {\n    version,\n    major,\n    supported: major >= REQUIRED_NODE_MAJOR,\n  };\n}\n\n/**\n * Checks which API keys are configured in the environment.\n * Does NOT expose the actual key values - only reports presence.\n */\nfunction checkApiKeys(): ApiKeyCheck[] {\n  return API_KEY_VARS.map((name) => ({\n    name,\n    configured: typeof process.env[name] === 'string' && process.env[name] !== '',\n  }));\n}\n\n/**\n * Checks for the existence of a configuration file.\n */\nfunction checkConfigFile(): ConfigFileCheck {\n  for (const configPath of CONFIG_FILE_PATHS) {\n    if (existsSync(configPath)) {\n      return { found: true, path: configPath };\n    }\n  }\n  return { found: false, path: null };\n}\n\n/**\n * Validates that the MCP server can be created successfully.\n * This is a lightweight check that verifies server instantiation works.\n */\nfunction checkMcpServerReady(): boolean {\n  try {\n    const result = createServer({ name: 'nexus-agents-doctor-check' });\n    return result.ok;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Builds model registry advisory based on detected CLI availability (#890).\n */\nfunction buildRegistryAdvisory(cliResults: CliCheckResult[]): RegistryAdvisory {\n  const installedClis = new Set(cliResults.filter((c) => c.installed).map((c) => c.name));\n\n  const models: ModelAdvisory[] = DEFAULT_MODEL_CAPABILITIES.models\n    .filter((m) => m.cliName !== undefined)\n    .map((m) => {\n      const cliName = m.cliName ?? '';\n      const available = cliName.length > 0 && installedClis.has(cliName as CliName);\n      const reason = available ? `${cliName} CLI is installed` : `${cliName} CLI is not installed`;\n      return { modelId: m.id, displayName: m.displayName, cliName, available, reason };\n    });\n\n  // Registry staleness check (#1549)\n  const STALE_THRESHOLD_DAYS = 30;\n  const updatedAt = new Date(DEFAULT_MODEL_CAPABILITIES.updatedAt);\n  const nowMs = getTimeProvider().now();\n  const ageDays = Math.floor((nowMs - updatedAt.getTime()) / (1000 * 60 * 60 * 24));\n\n  return {\n    totalModels: models.length,\n    availableModels: models.filter((m) => m.available).length,\n    unavailableModels: models.filter((m) => !m.available).length,\n    models,\n    registryAgeDays: ageDays,\n    registryStale: ageDays > STALE_THRESHOLD_DAYS,\n  };\n}\n\n/** Counts non-empty lines in a JSONL file. Returns 0 if file doesn't exist. */\nfunction countJsonlLines(filePath: string): number {\n  if (!existsSync(filePath)) return 0;\n  return readFileSync(filePath, 'utf-8')\n    .split('\\n')\n    .filter((l) => l.trim().length > 0).length;\n}\n\n/** Reads rules snapshot metadata. Returns count and savedAt. */\nfunction readRulesMetadata(filePath: string): { count: number; savedAt: string | null } {\n  if (!existsSync(filePath)) return { count: 0, savedAt: null };\n  try {\n    const raw = JSON.parse(readFileSync(filePath, 'utf-8')) as Record<string, unknown>;\n    const rules = raw['rules'];\n    const saved = raw['savedAt'];\n    return {\n      count: Array.isArray(rules) ? rules.length : 0,\n      savedAt: typeof saved === 'string' ? saved : null,\n    };\n  } catch {\n    return { count: 0, savedAt: null };\n  }\n}\n\n/** Checks if a directory exists and is writable. */\nfunction checkDirAccess(dir: string): { exists: boolean; writable: boolean } {\n  const exists = existsSync(dir);\n  if (!exists) return { exists: false, writable: false };\n  try {\n    accessSync(dir, fsConstants.W_OK);\n    return { exists: true, writable: true };\n  } catch {\n    return { exists: true, writable: false };\n  }\n}\n\nconst DISABLED_CHECK: LearningPersistenceCheck = {\n  enabled: false,\n  dirExists: false,\n  dirWritable: false,\n  outcomeCount: 0,\n  ruleCount: 0,\n  rulesLastSaved: null,\n  error: null,\n};\n\n/** Checks learning persistence health (#1017). */\nfunction checkLearningPersistence(): LearningPersistenceCheck {\n  if (!isPersistenceEnabled()) return DISABLED_CHECK;\n  try {\n    const { exists: dirExists, writable: dirWritable } = checkDirAccess(LEARNING_DIR);\n    const outcomeCount = countJsonlLines(OUTCOMES_FILE);\n    const { count: ruleCount, savedAt: rulesLastSaved } = readRulesMetadata(RULES_FILE);\n    return {\n      enabled: true,\n      dirExists,\n      dirWritable,\n      outcomeCount,\n      ruleCount,\n      rulesLastSaved,\n      error: null,\n    };\n  } catch (error: unknown) {\n    return {\n      enabled: true,\n      dirExists: false,\n      dirWritable: false,\n      outcomeCount: 0,\n      ruleCount: 0,\n      rulesLastSaved: null,\n      error: getErrorMessage(error),\n    };\n  }\n}\n\n/**\n * Checks if better-sqlite3 is available (#1249).\n * Memory backends (agentic, adaptive, typed, mobimem, decay) require it.\n */\nasync function checkSqlite(): Promise<SqliteCheck> {\n  try {\n    await import('better-sqlite3');\n    return { available: true, error: null };\n  } catch (error: unknown) {\n    const msg = getErrorMessage(error);\n    const isNotFound = msg.includes('Cannot find') || msg.includes('MODULE_NOT_FOUND');\n    return {\n      available: false,\n      error: isNotFound\n        ? 'better-sqlite3 not installed — 5 memory backends unavailable'\n        : `better-sqlite3 load error: ${msg}`,\n    };\n  }\n}\n\n/**\n * Checks the ~/.nexus-agents/ data directory health (#1249).\n */\nfunction checkDataDirectory(): DataDirectoryCheck {\n  const rootPath = join(homedir(), '.nexus-agents');\n  const rootExists = existsSync(rootPath);\n\n  const subdirectories: DataSubdirStatus[] = DATA_SUBDIRECTORIES.map((name) => {\n    const fullPath = join(rootPath, name);\n    const exists = existsSync(fullPath);\n    return { name, path: fullPath, exists, writable: exists && isWritable(fullPath) };\n  });\n\n  return { rootExists, rootPath, subdirectories };\n}\n\n/** Checks if a directory is writable by the current user. */\nfunction isWritable(dirPath: string): boolean {\n  try {\n    accessSync(dirPath, fsConstants.W_OK);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Runs the complete doctor check.\n */\nexport async function runDoctor(): Promise<DoctorResult> {\n  const clis = await Promise.all([\n    checkCli('claude'),\n    checkCli('gemini'),\n    checkCli('codex'),\n    checkCli('opencode'),\n  ]);\n  const nodeVersion = checkNodeVersion();\n  const apiKeys = checkApiKeys();\n  const configFile = checkConfigFile();\n  const mcpServerReady = checkMcpServerReady();\n  const codexCheck = clis.find((c) => c.name === 'codex');\n  const mcpClientReady = codexCheck?.installed ?? false;\n  const registryAdvisory = buildRegistryAdvisory(clis);\n  const learningPersistence = checkLearningPersistence();\n  const sqliteCheck = await checkSqlite();\n  const dataDirectory = checkDataDirectory();\n\n  // At least one API key configured or one CLI authenticated\n  const hasAuthMethod =\n    apiKeys.some((k) => k.configured) || clis.some((c) => c.installed && c.authenticated);\n\n  const allHealthy =\n    nodeVersion.supported &&\n    hasAuthMethod &&\n    mcpServerReady &&\n    clis.every((c) => c.installed && c.authenticated && c.versionStatus !== 'unsupported');\n\n  return {\n    clis,\n    nodeVersion,\n    apiKeys,\n    configFile,\n    mcpServerReady,\n    mcpClientReady,\n    registryAdvisory,\n    learningPersistence,\n    sqliteCheck,\n    dataDirectory,\n    allHealthy,\n    timestamp: new Date(getTimeProvider().now()),\n  };\n}\n\n/** Doctor command options. */\nexport interface DoctorOptions {\n  /** Auto-fix safe issues (run setup, generate config). */\n  readonly fix?: boolean;\n}\n\n/**\n * Runs the doctor command and prints results.\n * Returns exit code (0 = healthy, 1 = issues found).\n */\nexport async function doctorCommand(options: DoctorOptions = {}): Promise<number> {\n  const result = await runDoctor();\n  printDoctorResults(result);\n\n  if (options.fix === true) {\n    await runDoctorFix(result);\n  }\n\n  return result.allHealthy ? 0 : 1;\n}\n\n/**\n * Auto-fixes safe issues found by doctor (#1254).\n * Only runs our own code — never execs external package managers.\n */\nasync function runDoctorFix(result: DoctorResult): Promise<void> {\n  const writeLine = (text: string): void => {\n    process.stdout.write(text + '\\n');\n  };\n\n  writeLine('');\n  writeLine('\\x1b[1mAuto-fix\\x1b[0m');\n  writeLine('─'.repeat(40));\n\n  let fixCount = 0;\n\n  // Fix: data directories (missing or not writable)\n  if (\n    !result.dataDirectory.rootExists ||\n    result.dataDirectory.subdirectories.some((d) => !d.exists || !d.writable)\n  ) {\n    const { runSetup } = await import('./setup-command.js');\n    const setupResult = runSetup({\n      skipMcp: true,\n      skipRules: true,\n      skipHooks: true,\n      skipConfig: true,\n      skipOpencode: true,\n    });\n    if (setupResult.success) {\n      writeLine('✓ Created missing data directories');\n      fixCount++;\n    }\n  }\n\n  // Fix: config file\n  if (!result.configFile.found) {\n    const { runConfigInitSync } = await import('./setup-config.js');\n    const configResult = runConfigInitSync(process.cwd(), false, false);\n    if (configResult.success && configResult.created) {\n      writeLine(`✓ Generated config: ${configResult.path}`);\n      fixCount++;\n    }\n  }\n\n  // Display-only: better-sqlite3\n  if (!result.sqliteCheck.available) {\n    writeLine('');\n    writeLine('⚠ better-sqlite3 not installed (manual step required):');\n    writeLine('  npm install -g better-sqlite3');\n  }\n\n  if (fixCount > 0) {\n    writeLine('');\n    writeLine(\n      `\\x1b[32m${String(fixCount)} issue(s) fixed.\\x1b[0m Re-run \\x1b[1mnexus-agents doctor\\x1b[0m to verify.`\n    );\n  } else {\n    writeLine('No auto-fixable issues found.');\n  }\n  writeLine('');\n}\n\n// Re-export printDoctorResults for backward compatibility\nexport { printDoctorResults } from './doctor-formatting.js';\n","/**\n * nexus-agents/mcp - MCP Server\n *\n * Main MCP server implementation for Nexus Agents orchestration.\n * Provides factory functions to create and start the server with\n * stdio or custom transports.\n *\n * (Source: MCP Protocol 2025-11-25)\n */\n\nimport { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';\nimport { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';\nimport type { Transport } from '@modelcontextprotocol/sdk/shared/transport.js';\n\nimport {\n  getErrorMessage,\n  createLogger,\n  type Result,\n  ok,\n  err,\n  type ILogger,\n} from '../core/index.js';\nimport { VERSION } from '../version.js';\nimport { getTaskStore } from './task-store.js';\nimport { initDataDirectories } from '../cli/setup-data-dir.js';\n\n/**\n * Server configuration options.\n */\nexport interface ServerConfig {\n  /** Server name (default: \"nexus-agents\") */\n  readonly name?: string;\n  /** Server version (default: package version) */\n  readonly version?: string;\n  /** Logger instance */\n  readonly logger?: ILogger;\n}\n\n/**\n * Server creation result containing the server and logger.\n */\nexport interface ServerInstance {\n  /** The MCP server instance */\n  readonly server: McpServer;\n  /** The logger instance for this server */\n  readonly logger: ILogger;\n}\n\n/**\n * Error type for server operations.\n */\nexport interface ServerError {\n  code: 'SERVER_CREATION_FAILED' | 'SERVER_START_FAILED' | 'SERVER_STOP_FAILED';\n  message: string;\n  cause?: Error;\n}\n\nconst DEFAULT_SERVER_NAME = 'nexus-agents';\n\n/**\n * Creates a ServerError with the given code, message, and optional cause.\n */\nfunction createServerError(\n  code: ServerError['code'],\n  message: string,\n  error: unknown\n): ServerError {\n  const serverError: ServerError = { code, message };\n  if (error instanceof Error) {\n    serverError.cause = error;\n  }\n  return serverError;\n}\n\n/**\n * Creates a new MCP server instance.\n *\n * @param config - Optional server configuration\n * @returns Result containing the server instance or an error\n *\n * @example\n * ```typescript\n * const result = createServer({ name: 'my-server' });\n * if (result.ok) {\n *   const { server, logger } = result.value;\n *   // Register tools on server\n * }\n * ```\n */\nexport function createServer(config?: ServerConfig): Result<ServerInstance, ServerError> {\n  const serverName = config?.name ?? DEFAULT_SERVER_NAME;\n  const serverVersion = config?.version ?? VERSION;\n  const logger = config?.logger ?? createLogger({ component: 'mcp-server' });\n\n  try {\n    // Ensure data directories exist on first MCP server startup (#1398)\n    initDataDirectories();\n\n    logger.info('Creating MCP server', {\n      name: serverName,\n      version: serverVersion,\n    });\n\n    const server = new McpServer(\n      {\n        name: serverName,\n        version: serverVersion,\n      },\n      {\n        capabilities: {\n          logging: {},\n          prompts: {},\n          resources: {},\n          tasks: {},\n        },\n        taskStore: getTaskStore(),\n      }\n    );\n\n    logger.debug('MCP server created successfully');\n\n    return ok({ server, logger });\n  } catch (error) {\n    const errorMessage = getErrorMessage(error);\n    logger.error('Failed to create MCP server', error instanceof Error ? error : undefined);\n    return err(\n      createServerError(\n        'SERVER_CREATION_FAILED',\n        `Failed to create MCP server: ${errorMessage}`,\n        error\n      )\n    );\n  }\n}\n\n/**\n * Connects the server to a transport.\n *\n * @param server - The MCP server instance\n * @param transport - The transport to connect to\n * @param logger - Logger for the operation\n * @returns Result indicating success or failure\n */\nexport async function connectTransport(\n  server: McpServer,\n  transport: Transport,\n  logger?: ILogger\n): Promise<Result<void, ServerError>> {\n  const log = logger ?? createLogger({ component: 'mcp-server' });\n\n  try {\n    log.info('Connecting server to transport');\n    await server.connect(transport);\n    log.debug('Server connected to transport successfully');\n    return ok(undefined);\n  } catch (error) {\n    const errorMessage = getErrorMessage(error);\n    log.error('Failed to connect to transport', error instanceof Error ? error : undefined);\n    return err(\n      createServerError(\n        'SERVER_START_FAILED',\n        `Failed to connect to transport: ${errorMessage}`,\n        error\n      )\n    );\n  }\n}\n\n/**\n * Starts the MCP server with stdio transport.\n *\n * This is the main entry point for running the server as a standalone process.\n * The server will communicate over stdin/stdout using the MCP protocol.\n *\n * @param config - Optional server configuration\n * @returns Result indicating success or failure\n *\n * @example\n * ```typescript\n * const result = await startStdioServer();\n * if (!result.ok) {\n *   console.error('Failed to start server:', result.error.message);\n *   process.exit(1);\n * }\n * ```\n */\nexport async function startStdioServer(\n  config?: ServerConfig\n): Promise<Result<ServerInstance, ServerError>> {\n  const serverResult = createServer(config);\n  if (!serverResult.ok) {\n    return serverResult;\n  }\n\n  const { server, logger } = serverResult.value;\n\n  try {\n    // Defense-in-depth: stdio transport owns stdout for JSON-RPC frames.\n    logger.setDestination?.('stderr');\n    logger.info('Starting stdio transport');\n    const transport = new StdioServerTransport();\n\n    const connectResult = await connectTransport(server, transport, logger);\n    if (!connectResult.ok) {\n      return connectResult;\n    }\n\n    logger.info('MCP server running with stdio transport');\n    return ok({ server, logger });\n  } catch (error) {\n    const errorMessage = getErrorMessage(error);\n    logger.error('Failed to start stdio server', error instanceof Error ? error : undefined);\n    return err(\n      createServerError(\n        'SERVER_START_FAILED',\n        `Failed to start stdio server: ${errorMessage}`,\n        error\n      )\n    );\n  }\n}\n\n/**\n * Gracefully closes the server connection.\n *\n * @param server - The MCP server to close\n * @param logger - Optional logger\n * @returns Result indicating success or failure\n */\nexport async function closeServer(\n  server: McpServer,\n  logger?: ILogger\n): Promise<Result<void, ServerError>> {\n  const log = logger ?? createLogger({ component: 'mcp-server' });\n\n  try {\n    log.info('Closing MCP server');\n    await server.close();\n    log.info('MCP server closed successfully');\n    return ok(undefined);\n  } catch (error) {\n    const errorMessage = getErrorMessage(error);\n    log.error('Failed to close server', error instanceof Error ? error : undefined);\n    return err(\n      createServerError('SERVER_STOP_FAILED', `Failed to close server: ${errorMessage}`, error)\n    );\n  }\n}\n","/**\n * Nexus-Agents Task Store — wraps SDK InMemoryTaskStore with security controls.\n *\n * Provides:\n * - TTL enforcement (max 10 minutes per task)\n * - Capacity cap (max 50 tasks, FIFO eviction when exceeded)\n * - Singleton access via `getTaskStore()`\n * - Periodic cleanup of expired tasks\n *\n * @module mcp/task-store\n * (Source: Issue #1298 — Layer 2 MCP Tasks async execution)\n */\n\nimport { InMemoryTaskStore } from '@modelcontextprotocol/sdk/experimental/tasks';\nimport type { TaskStore } from '@modelcontextprotocol/sdk/experimental/tasks';\nimport { createLogger } from '../core/index.js';\n\n// ============================================================================\n// Constants\n// ============================================================================\n\n/** Maximum TTL for any task (10 minutes). */\nexport const MAX_TASK_TTL_MS = 600_000;\n\n/** Default TTL applied when none specified (5 minutes). */\nexport const DEFAULT_TASK_TTL_MS = 300_000;\n\n/** Maximum number of tasks before FIFO eviction. */\nexport const MAX_TASK_CAPACITY = 50;\n\n/** Interval for periodic cleanup of expired tasks (60 seconds). */\nconst CLEANUP_INTERVAL_MS = 60_000;\n\n// ============================================================================\n// Singleton\n// ============================================================================\n\nconst logger = createLogger({ component: 'task-store' });\n\nlet singletonStore: InMemoryTaskStore | undefined;\nlet cleanupTimer: ReturnType<typeof setInterval> | undefined;\n\n/**\n * Returns the singleton InMemoryTaskStore, creating it on first call.\n *\n * The SDK's InMemoryTaskStore handles TTL cleanup internally.\n * We enforce our MAX_TASK_TTL_MS via `clampTaskTtl()` at task creation\n * (done by the ToolTaskHandler, not the store itself).\n */\nexport function getTaskStore(): TaskStore {\n  if (singletonStore === undefined) {\n    singletonStore = new InMemoryTaskStore();\n    logger.info('Task store created', { maxCapacity: MAX_TASK_CAPACITY });\n\n    // Periodic cleanup: evict oldest tasks if capacity exceeded\n    cleanupTimer = setInterval(() => {\n      evictExcessTasks();\n    }, CLEANUP_INTERVAL_MS);\n\n    // Prevent cleanup timer from keeping Node alive\n    if (typeof cleanupTimer === 'object' && 'unref' in cleanupTimer) {\n      cleanupTimer.unref();\n    }\n  }\n  return singletonStore;\n}\n\n/**\n * Clamps a requested TTL to the maximum allowed value.\n * Returns DEFAULT_TASK_TTL_MS if no TTL is specified or null.\n */\nexport function clampTaskTtl(requestedTtl?: number | null): number {\n  if (requestedTtl === undefined || requestedTtl === null) {\n    return DEFAULT_TASK_TTL_MS;\n  }\n  if (requestedTtl > MAX_TASK_TTL_MS) {\n    logger.warn('Task TTL clamped to maximum', {\n      requested: requestedTtl,\n      max: MAX_TASK_TTL_MS,\n    });\n    return MAX_TASK_TTL_MS;\n  }\n  return requestedTtl;\n}\n\n/**\n * Evicts oldest tasks when capacity is exceeded (FIFO).\n * Best-effort — logs warnings but does not throw.\n */\nfunction evictExcessTasks(): void {\n  if (singletonStore === undefined) return;\n\n  const allTasks = singletonStore.getAllTasks();\n  if (allTasks.length <= MAX_TASK_CAPACITY) return;\n\n  // Sort by creation time ascending (oldest first)\n  const sorted = [...allTasks].sort(\n    (a, b) => new Date(a.createdAt).getTime() - new Date(b.createdAt).getTime()\n  );\n\n  const evictCount = sorted.length - MAX_TASK_CAPACITY;\n  for (let i = 0; i < evictCount; i++) {\n    const task = sorted[i];\n    if (task === undefined) continue;\n    singletonStore\n      .updateTaskStatus(task.taskId, 'cancelled', 'Evicted: capacity exceeded')\n      .catch((err: unknown) => {\n        logger.debug('Failed to evict task', {\n          taskId: task.taskId,\n          error: String(err),\n        });\n      });\n  }\n\n  logger.info('Evicted excess tasks', { evicted: evictCount, total: sorted.length });\n}\n\n/**\n * Shuts down the task store and cleanup timer.\n * Call during server shutdown. Safe to call multiple times.\n * @internal\n */\nexport function shutdownTaskStore(): void {\n  if (cleanupTimer !== undefined) {\n    clearInterval(cleanupTimer);\n    cleanupTimer = undefined;\n  }\n  if (singletonStore !== undefined) {\n    singletonStore.cleanup();\n    singletonStore = undefined;\n    logger.info('Task store shut down');\n  }\n}\n\n/** Resets the singleton for testing. @internal */\nexport function resetTaskStore(): void {\n  shutdownTaskStore();\n}\n","/**\n * nexus-agents doctor command - Formatting utilities\n *\n * Terminal output formatting for doctor command results.\n * Extracted to comply with 400-line file limit.\n *\n * (Source: Issue #422 - Doctor command validations)\n */\n\nimport { DEFAULT_CAPABILITIES } from '../cli-adapters/types.js';\nimport type { CapacityStatus } from '../cli-adapters/types.js';\nimport type {\n  CliCheckResult,\n  NodeVersionCheck,\n  ApiKeyCheck,\n  ConfigFileCheck,\n  RegistryAdvisory,\n  LearningPersistenceCheck,\n  SqliteCheck,\n  DataDirectoryCheck,\n  DoctorResult,\n} from './doctor.js';\nimport { colors, symbols, writeLine } from './ansi-output.js';\nimport { capitalize } from '../utils/text-utils.js';\n\n/** Required Node.js major version (for warning message). */\nconst REQUIRED_NODE_MAJOR = 22;\n\n/**\n * Formats a status symbol with color.\n */\nfunction formatStatus(healthy: boolean, warn = false): string {\n  if (healthy) return `${colors.green}${symbols.check}${colors.reset}`;\n  if (warn) return `${colors.yellow}${symbols.warn}${colors.reset}`;\n  return `${colors.red}${symbols.cross}${colors.reset}`;\n}\n\n/**\n * Formats version status with color.\n */\nfunction formatVersionStatus(status: string): string {\n  switch (status) {\n    case 'supported':\n      return `${colors.green}supported${colors.reset}`;\n    case 'outdated':\n      return `${colors.yellow}outdated${colors.reset}`;\n    case 'unsupported':\n    case 'breaking':\n      return `${colors.red}${status}${colors.reset}`;\n    default:\n      return status;\n  }\n}\n\n/**\n * Formats capacity as percentage string.\n */\nfunction formatCapacity(capacity?: CapacityStatus): string {\n  if (capacity === undefined) return 'Unknown';\n  const remaining = 100 - capacity.utilizationPercent;\n  const remainingStr = String(remaining);\n  if (remaining > 80) return `${colors.green}${remainingStr}% remaining${colors.reset}`;\n  if (remaining > 20) return `${colors.yellow}${remainingStr}% remaining${colors.reset}`;\n  return `${colors.red}${remainingStr}% remaining${colors.reset}`;\n}\n\n/**\n * Prints details for an installed CLI.\n */\nfunction printInstalledCliDetails(cli: CliCheckResult): void {\n  writeLine(`  Version: ${cli.version} (${formatVersionStatus(cli.versionStatus)})`);\n\n  const authText = cli.authenticated\n    ? `${colors.green}${cli.authMethod ?? 'Authenticated'}${colors.reset}`\n    : `${colors.red}Not authenticated${colors.reset}`;\n  writeLine(`  Auth: ${authText}`);\n\n  if (cli.capacity !== undefined) {\n    writeLine(`  Capacity: ${formatCapacity(cli.capacity)}`);\n  }\n}\n\n/**\n * Prints a single CLI result.\n */\nfunction printCliResult(cli: CliCheckResult): void {\n  const status = cli.installed && cli.authenticated;\n  const warn = cli.installed && (!cli.authenticated || cli.versionStatus === 'outdated');\n\n  writeLine(\n    `${formatStatus(status, warn)} ${colors.bold}${capitalize(cli.name)} CLI${colors.reset}`\n  );\n\n  if (cli.installed) {\n    printInstalledCliDetails(cli);\n  } else {\n    const errorText = cli.error ?? 'Not installed';\n    writeLine(`  ${colors.red}Error: ${errorText}${colors.reset}`);\n  }\n\n  if (cli.fix !== undefined && cli.fix !== '') {\n    writeLine(`  ${colors.dim}Fix: ${cli.fix}${colors.reset}`);\n  }\n\n  writeLine('');\n}\n\n/**\n * Prints capability summary for installed CLIs.\n */\nfunction printCapabilities(clis: CliCheckResult[]): void {\n  const installedClis = clis.filter((c) => c.installed);\n\n  if (installedClis.length === 0) {\n    writeLine(`${formatStatus(false)} No CLIs installed`);\n    return;\n  }\n\n  const caps = DEFAULT_CAPABILITIES;\n  const bestReasoning = installedClis.reduce((best, c) =>\n    caps[c.name].reasoning > caps[best.name].reasoning ? c : best\n  );\n  const bestContext = installedClis.reduce((best, c) =>\n    caps[c.name].contextWindow > caps[best.name].contextWindow ? c : best\n  );\n  const bestSpeed = installedClis.reduce((best, c) =>\n    caps[c.name].speed > caps[best.name].speed ? c : best\n  );\n\n  const contextTokensK = (caps[bestContext.name].contextWindow / 1000).toFixed(0);\n\n  writeLine(\n    `${formatStatus(true)} Complex reasoning: ${colors.bold}${capitalize(bestReasoning.name)}${colors.reset}`\n  );\n  writeLine(\n    `${formatStatus(true)} Large context: ${colors.bold}${capitalize(bestContext.name)}${colors.reset} (${contextTokensK}K tokens)`\n  );\n  writeLine(\n    `${formatStatus(true)} Fast execution: ${colors.bold}${capitalize(bestSpeed.name)}${colors.reset}`\n  );\n}\n\n/**\n * Prints Node.js version check result.\n */\nfunction printNodeVersionCheck(check: NodeVersionCheck): void {\n  const versionText = check.supported\n    ? `${colors.green}${check.version}${colors.reset}`\n    : `${colors.yellow}${check.version}${colors.reset}`;\n  writeLine(`${formatStatus(check.supported, !check.supported)} Node.js version: ${versionText}`);\n  if (!check.supported) {\n    writeLine(\n      `  ${colors.dim}Warning: Node.js ${String(REQUIRED_NODE_MAJOR)}.x LTS required${colors.reset}`\n    );\n  }\n}\n\n/**\n * Prints API key configuration check results.\n */\nfunction printApiKeysCheck(keys: ApiKeyCheck[]): void {\n  const configuredCount = keys.filter((k) => k.configured).length;\n  const configuredNames = keys.filter((k) => k.configured).map((k) => k.name);\n  const hasAny = configuredCount > 0;\n\n  writeLine(\n    `${formatStatus(hasAny, !hasAny)} API keys configured: ${String(configuredCount)} of ${String(keys.length)}`\n  );\n  if (hasAny) {\n    writeLine(`  ${colors.dim}Keys: ${configuredNames.join(', ')}${colors.reset}`);\n  } else {\n    writeLine(\n      `  ${colors.dim}Set ANTHROPIC_API_KEY, OPENAI_API_KEY, or GOOGLE_AI_API_KEY${colors.reset}`\n    );\n  }\n}\n\n/**\n * Prints configuration file check result.\n */\nfunction printConfigFileCheck(check: ConfigFileCheck): void {\n  if (check.found && check.path !== null) {\n    writeLine(`${formatStatus(true)} Configuration loaded: ${check.path}`);\n  } else {\n    writeLine(`${formatStatus(false, true)} Configuration file: Not found`);\n    writeLine(`  ${colors.dim}Run: nexus-agents config init${colors.reset}`);\n  }\n}\n\n/**\n * Prints model registry advisory (#890).\n */\nfunction printRegistryAdvisory(advisory: RegistryAdvisory): void {\n  const allAvailable = advisory.unavailableModels === 0;\n  const countText = `${String(advisory.availableModels)} of ${String(advisory.totalModels)}`;\n  writeLine(`${formatStatus(allAvailable, !allAvailable)} Models available: ${countText}`);\n  if (advisory.unavailableModels > 0) {\n    const missing = advisory.models.filter((m) => !m.available);\n    for (const m of missing) {\n      writeLine(`  ${colors.dim}${m.displayName} — ${m.reason}${colors.reset}`);\n    }\n  }\n  // Registry staleness warning (#1549)\n  const ageText = `${String(advisory.registryAgeDays)} days old`;\n  if (advisory.registryStale) {\n    writeLine(\n      `${colors.yellow}${symbols.warn}${colors.reset} Model registry is ${ageText} — may have stale model data`\n    );\n    writeLine(`  ${colors.dim}Run: npx tsx scripts/probe-models.ts${colors.reset}`);\n  } else {\n    writeLine(`${formatStatus(true)} Model registry: ${ageText}`);\n  }\n}\n\n/**\n * Prints learning persistence health check (#1017).\n */\nfunction printLearningPersistence(check: LearningPersistenceCheck): void {\n  if (!check.enabled) {\n    writeLine(`${formatStatus(true)} Learning persistence: ${colors.dim}Disabled${colors.reset}`);\n    writeLine(`  ${colors.dim}Set NEXUS_PERSIST_LEARNING=true to enable${colors.reset}`);\n    return;\n  }\n\n  const healthy = check.dirExists && check.dirWritable && check.error === null;\n  writeLine(`${formatStatus(healthy, !healthy)} Learning persistence: Enabled`);\n\n  if (check.error !== null) {\n    writeLine(`  ${colors.red}Error: ${check.error}${colors.reset}`);\n    return;\n  }\n\n  const dirStatus = check.dirExists\n    ? 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package/dist/{chunk-LLGUX44Z.js → chunk-Y477EGI4.js}

@@ -5,7 +5,7 @@ import {
   getErrorMessage,
   getTimeProvider,
   ok
-} from "./chunk-ELIFTCYM.js";
+} from "./chunk-HSOPD265.js";
 
 // src/cli-adapters/circuit-breaker-types.ts
 var CircuitErrorCode = {
@@ -353,4 +353,4 @@ export {
   CircuitBreakerRegistry,
   mapCliErrorToCategory
 };
-//# sourceMappingURL=chunk-LLGUX44Z.js.map
+//# sourceMappingURL=chunk-Y477EGI4.js.map

package/dist/{chunk-VKRMXD62.js → chunk-Z4OZ25VS.js}

@@ -1,10 +1,10 @@
 import {
   runConfigInitSync
-} from "./chunk-3GXDN4AX.js";
+} from "./chunk-V6MSPUQF.js";
 import {
   VERSION,
   initDataDirectories
-} from "./chunk-3EVVQ32X.js";
+} from "./chunk-WSYJN7BI.js";
 import {
   CLI_SUBPROCESS_TIMEOUTS,
   createLogger,
@@ -13,7 +13,7 @@ import {
   formatStatus,
   getErrorMessage,
   getTimeProvider
-} from "./chunk-ELIFTCYM.js";
+} from "./chunk-HSOPD265.js";
 
 // src/cli/setup-command.ts
 import { existsSync as existsSync4 } from "fs";
@@ -1523,4 +1523,4 @@ export {
   setupCommand,
   setupCommandAsync
 };
-//# sourceMappingURL=chunk-VKRMXD62.js.map
+//# sourceMappingURL=chunk-Z4OZ25VS.js.map

package/dist/{cli-circuit-breaker-5FAODXVY.js → cli-circuit-breaker-6EJO3PPU.js}

@@ -1,13 +1,13 @@
 import {
   CliCircuitBreakerIntegration,
   createCliCircuitBreakerIntegration
-} from "./chunk-C2C5ONFR.js";
-import "./chunk-LLGUX44Z.js";
-import "./chunk-ELIFTCYM.js";
+} from "./chunk-66NNHMVB.js";
+import "./chunk-Y477EGI4.js";
+import "./chunk-HSOPD265.js";
 import "./chunk-CLYZ7FWP.js";
 import "./chunk-UP2VWCW5.js";
 export {
   CliCircuitBreakerIntegration,
   createCliCircuitBreakerIntegration
 };
-//# sourceMappingURL=cli-circuit-breaker-5FAODXVY.js.map
+//# sourceMappingURL=cli-circuit-breaker-6EJO3PPU.js.map

package/dist/cli.js

@@ -12,11 +12,11 @@ import {
   parseFindings,
   sumFindings
 } from "./chunk-6E3NMMEY.js";
-import "./chunk-XU3NADFE.js";
+import "./chunk-63AJLNKU.js";
 import {
   setupCommandAsync
-} from "./chunk-VKRMXD62.js";
-import "./chunk-3GXDN4AX.js";
+} from "./chunk-Z4OZ25VS.js";
+import "./chunk-V6MSPUQF.js";
 import {
   AuthHandler,
   CustomExpertDefinitionSchema,
@@ -150,10 +150,10 @@ import {
   validateNexusEnv,
   validateWorkflow,
   wrapInMarkdownFence
-} from "./chunk-FZFZ77UJ.js";
+} from "./chunk-QSNAFOE6.js";
 import {
   resolveToken
-} from "./chunk-7SKAKA4I.js";
+} from "./chunk-VZ2YOQWU.js";
 import {
   CATEGORY_DISPLAY_NAMES,
   DEFAULT_PR_REVIEW_CONFIG
@@ -169,29 +169,29 @@ import {
   registerConsensusVoteTool,
   shutdownToolMemory,
   validateTimeout
-} from "./chunk-CGWRJ4EM.js";
+} from "./chunk-J245RJGW.js";
 import {
   loadPapersRegistry,
   loadTechniquesRegistry,
   savePapersRegistry,
   synthesizeResearch
-} from "./chunk-MRU6L7YJ.js";
+} from "./chunk-GX436VRU.js";
 import {
   classifyTrust,
   createFullGitHubProvider,
   evaluatePolicy,
   parsePRUrl,
   sanitizeInput
-} from "./chunk-IECE6DBS.js";
-import "./chunk-4HA5PAL7.js";
-import "./chunk-2UR7YN6T.js";
+} from "./chunk-5COIDGQJ.js";
+import "./chunk-EPMBGZQX.js";
+import "./chunk-TL2GJMJ5.js";
 import "./chunk-BC3M4VLP.js";
 import "./chunk-AP2FD37C.js";
 import "./chunk-BQ4YXGGQ.js";
 import "./chunk-ED6VQWNG.js";
 import {
   BUILT_IN_EXPERTS
-} from "./chunk-OOIPRRPX.js";
+} from "./chunk-LDIN2PLV.js";
 import {
   VERSION,
   closeServer,
@@ -200,25 +200,25 @@ import {
   doctorCommand,
   initDataDirectories,
   runDoctor
-} from "./chunk-3EVVQ32X.js";
-import "./chunk-SRECH7OQ.js";
+} from "./chunk-WSYJN7BI.js";
+import "./chunk-KQIDTE52.js";
 import {
   MemoryError
-} from "./chunk-FYJVXQHX.js";
+} from "./chunk-DDQGAVQA.js";
 import {
   capitalize,
   capitalizeKebab,
   truncateSentence
 } from "./chunk-633WH2ML.js";
-import "./chunk-2UUUKVNR.js";
-import "./chunk-C2C5ONFR.js";
-import "./chunk-YSTJEMQX.js";
+import "./chunk-LKDHAJJB.js";
+import "./chunk-66NNHMVB.js";
+import "./chunk-QGODFK36.js";
 import {
   createAllAdapters,
   getAvailableClis,
   isRecord
-} from "./chunk-4AGPR6XZ.js";
-import "./chunk-LLGUX44Z.js";
+} from "./chunk-CW2Z773T.js";
+import "./chunk-Y477EGI4.js";
 import {
   API_TIMEOUTS,
   AgentCapability,
@@ -279,7 +279,7 @@ import {
   toError,
   writeEmptyLine,
   writeLine
-} from "./chunk-ELIFTCYM.js";
+} from "./chunk-HSOPD265.js";
 import "./chunk-CLYZ7FWP.js";
 import "./chunk-UP2VWCW5.js";
 
@@ -453,7 +453,9 @@ logging:
   format: json
 
   # Destination: stdout, stderr, file
-  destination: stdout
+  # NOTE: stdout is unsafe when running as an MCP stdio server (corrupts
+  # JSON-RPC frames). Keep stderr unless you have a specific need.
+  destination: stderr
 
   # Log file path (required if destination is 'file')
   # filePath: ./logs/nexus-agents.log
@@ -19326,6 +19328,8 @@ async function initializeAndLogSandbox(logger17, sandboxConfig) {
   });
 }
 async function connectToStdioTransport(server, logger17, serverLogger) {
+  logger17.setDestination?.("stderr");
+  serverLogger.setDestination?.("stderr");
   logger17.info("Connecting to stdio transport");
   const transport = new StdioServerTransport();
   const connectResult = await connectTransport(server, transport, serverLogger);
@@ -19848,7 +19852,7 @@ async function handleVerifyCommand(args) {
 async function handleDoctorCommand(args) {
   const exitCode = await doctorCommand({ fix: args.options.fix });
   if (args.options.deep) {
-    const { runDeepDiagnostics: runDeepDiagnostics2, formatDeepDiagnostics: formatDeepDiagnostics2 } = await import("./doctor-deep-LMCEAFU4.js");
+    const { runDeepDiagnostics: runDeepDiagnostics2, formatDeepDiagnostics: formatDeepDiagnostics2 } = await import("./doctor-deep-4A4X5X6U.js");
     const diag = runDeepDiagnostics2();
     process.stdout.write(formatDeepDiagnostics2(diag) + "\n");
   }