@elnora-ai/cli 1.2.1 → 1.3.1

package/dist/cli.js

@@ -398,7 +398,32 @@ function resolveApiKey(profileName) {
   migrateConfigIfNeeded();
   return getApiKey(profileName ?? "default");
 }
-var CONFIG_DIR, PROFILES_FILE, LEGACY_CONFIG_FILE, PROFILE_NAME_RE;
+function truncateForDisplay(value) {
+  if (value.length > 20) return `${value.slice(0, 16)}...${value.slice(-4)}`;
+  return `${value.slice(0, 4)}...`;
+}
+function resolveCredentialHint(profileName) {
+  for (const varName of CREDENTIAL_ENV_VARS) {
+    const val2 = process.env[varName];
+    if (val2) return truncateForDisplay(val2);
+  }
+  migrateConfigIfNeeded();
+  const profiles = loadProfiles();
+  const name = profileName ?? "default";
+  if (!(name in profiles)) {
+    throw new AuthError(`Profile '${name}' not found.`, {
+      suggestion: "Run 'elnora auth login' to set up a profile."
+    });
+  }
+  const val = profiles[name][PROFILE_CREDENTIAL_FIELD] ?? "";
+  if (!val) {
+    throw new AuthError(`Profile '${name}' has no credential.`, {
+      suggestion: `Run: elnora auth login --profile ${name}`
+    });
+  }
+  return truncateForDisplay(val);
+}
+var CONFIG_DIR, PROFILES_FILE, LEGACY_CONFIG_FILE, PROFILE_NAME_RE, CREDENTIAL_ENV_VARS, PROFILE_CREDENTIAL_FIELD;
 var init_profiles = __esm({
   "src/lib/profiles.ts"() {
     "use strict";
@@ -407,6 +432,8 @@ var init_profiles = __esm({
     PROFILES_FILE = join(CONFIG_DIR, "profiles.toml");
     LEGACY_CONFIG_FILE = join(CONFIG_DIR, "config.toml");
     PROFILE_NAME_RE = /^[a-z0-9][a-z0-9-]{0,31}$/;
+    CREDENTIAL_ENV_VARS = ["ELNORA_API_KEY", "ELNORA_MCP_API_KEY"];
+    PROFILE_CREDENTIAL_FIELD = "api_key";
   }
 });
 
@@ -1906,7 +1933,7 @@ function generateZsh(root) {
   lines.push("  if (( CURRENT == 2 )); then");
   lines.push("    commands=(");
   for (const cmd of root.subcommands) {
-    lines.push(`      '${cmd.name}:${cmd.description.replace(/'/g, "")}'`);
+    lines.push(`      '${cmd.name}:${cmd.description.replace(/\\/g, "\\\\").replace(/'/g, "")}'`);
   }
   lines.push("    )");
   lines.push("    _describe 'command' commands");
@@ -1920,7 +1947,7 @@ function generateZsh(root) {
       lines.push("      local -a subcommands");
       lines.push("      subcommands=(");
       for (const sub of group.subcommands) {
-        lines.push(`        '${sub.name}:${sub.description.replace(/'/g, "")}'`);
+        lines.push(`        '${sub.name}:${sub.description.replace(/\\/g, "\\\\").replace(/'/g, "")}'`);
       }
       lines.push("      )");
       lines.push("      _describe 'subcommand' subcommands");
@@ -1941,14 +1968,14 @@ function generateFish(root) {
   ];
   for (const cmd of root.subcommands) {
     lines.push(
-      `complete -c elnora -n "__fish_use_subcommand" -a "${cmd.name}" -d "${cmd.description.replace(/"/g, '\\"')}"`
+      `complete -c elnora -n "__fish_use_subcommand" -a "${cmd.name}" -d "${cmd.description.replace(/\\/g, "\\\\").replace(/"/g, '\\"')}"`
     );
   }
   lines.push("");
   for (const group of root.subcommands) {
     for (const sub of group.subcommands) {
       lines.push(
-        `complete -c elnora -n "__fish_seen_subcommand_from ${group.name}" -a "${sub.name}" -d "${sub.description.replace(/"/g, '\\"')}"`
+        `complete -c elnora -n "__fish_seen_subcommand_from ${group.name}" -a "${sub.name}" -d "${sub.description.replace(/\\/g, "\\\\").replace(/"/g, '\\"')}"`
       );
     }
   }
@@ -1992,10 +2019,10 @@ var CACHE_DIR = join2(homedir2(), ".elnora");
 var CACHE_FILE = join2(CACHE_DIR, ".update-check");
 var CHECK_INTERVAL_MS = 24 * 60 * 60 * 1e3;
 var FETCH_TIMEOUT_MS = 3e3;
-function shouldSkip() {
+var SEMVER_RE = /^\d+\.\d+\.\d+(?:-[\w.]+)?(?:\+[\w.]+)?$/;
+function shouldSkipEntirely() {
   if (process.env.CI || process.env.GITHUB_ACTIONS) return true;
   if (process.env.ELNORA_NO_UPDATE_CHECK) return true;
-  if (!process.stderr.isTTY) return true;
   return false;
 }
 function readCache() {
@@ -2015,13 +2042,14 @@ function writeCache(entry) {
   }
 }
 function showUpdateNotice(latest) {
-  const color = isColorEnabled();
-  const msg = color ? `
+  if (!process.stderr.isTTY) return;
+  const color2 = isColorEnabled();
+  const msg = color2 ? `
 ${pc.yellow(`Update available: v${VERSION} \u2192 v${latest}`)}
-Run: curl -fsSL https://cli.elnora.ai/install.sh | bash
+Run: elnora update
 ` : `
 Update available: v${VERSION} \u2192 v${latest}
-Run: curl -fsSL https://cli.elnora.ai/install.sh | bash
+Run: elnora update
 `;
   process.stderr.write(msg);
 }
@@ -2037,7 +2065,7 @@ function isNewerVersion(a, b) {
   return false;
 }
 function registerUpdateCheck() {
-  if (shouldSkip()) return;
+  if (shouldSkipEntirely()) return;
   const cached = readCache();
   if (cached) {
     const elapsed = Date.now() - new Date(cached.checkedAt).getTime();
@@ -2050,7 +2078,9 @@ function registerUpdateCheck() {
       return;
     }
   }
-  setTimeout(async () => {
+  const keepAlive = setInterval(() => {
+  }, 6e4);
+  (async () => {
     try {
       const response = await fetch(NPM_REGISTRY_URL, {
         signal: AbortSignal.timeout(FETCH_TIMEOUT_MS)
@@ -2058,22 +2088,25 @@ function registerUpdateCheck() {
       if (!response.ok) return;
       const data = await response.json();
       const latest = data.version ?? "unknown";
+      if (latest !== "unknown" && !SEMVER_RE.test(latest)) return;
       writeCache({ checkedAt: (/* @__PURE__ */ new Date()).toISOString(), latest });
       if (latest !== VERSION && latest !== "unknown" && isNewerVersion(latest, VERSION)) {
         showUpdateNotice(latest);
       }
     } catch {
+    } finally {
+      clearInterval(keepAlive);
     }
-  }, 0);
+  })();
 }
 
 // src/commands/doctor.ts
 function addDoctorCommand(program2) {
   program2.command("doctor").description("Check Elnora CLI configuration and connectivity").action(async () => {
-    const color = isColorEnabled();
-    const ok = (msg) => color ? `  ${pc2.green("\u2713")} ${msg}` : `  \u2713 ${msg}`;
-    const fail = (msg) => color ? `  ${pc2.red("\u2717")} ${msg}` : `  \u2717 ${msg}`;
-    const warn = (msg) => color ? `  ${pc2.yellow("!")} ${msg}` : `  ! ${msg}`;
+    const color2 = isColorEnabled();
+    const ok2 = (msg) => color2 ? `  ${pc2.green("\u2713")} ${msg}` : `  \u2713 ${msg}`;
+    const fail2 = (msg) => color2 ? `  ${pc2.red("\u2717")} ${msg}` : `  \u2717 ${msg}`;
+    const warn = (msg) => color2 ? `  ${pc2.yellow("!")} ${msg}` : `  ! ${msg}`;
     console.error(`
 Elnora CLI v${VERSION}
 `);
@@ -2085,12 +2118,12 @@ Elnora CLI v${VERSION}
       const res = await fetch("https://platform.elnora.ai/health", { signal: AbortSignal.timeout(5e3) });
       const ms = Date.now() - start;
       if (res.ok) {
-        console.error(ok(`API reachable         platform.elnora.ai (${res.status} OK, ${ms}ms)`));
+        console.error(ok2(`API reachable         platform.elnora.ai (${res.status} OK, ${ms}ms)`));
         passed++;
-      } else console.error(fail(`API unreachable       platform.elnora.ai (HTTP ${res.status})`));
+      } else console.error(fail2(`API unreachable       platform.elnora.ai (HTTP ${res.status})`));
     } catch (e) {
       console.error(
-        fail(`API unreachable       platform.elnora.ai (${e instanceof Error ? e.message : "network error"})`)
+        fail2(`API unreachable       platform.elnora.ai (${e instanceof Error ? e.message : "network error"})`)
       );
     }
     total++;
@@ -2101,10 +2134,10 @@ Elnora CLI v${VERSION}
         queryParams: { page: 1, pageSize: 1 }
       });
       const count = result?.totalCount ?? result?.items?.length ?? 0;
-      console.error(ok(`Authenticated         profile: default (${count} projects accessible)`));
+      console.error(ok2(`Authenticated         profile: default (${count} projects accessible)`));
       passed++;
     } catch (e) {
-      console.error(fail(`Authentication failed ${e instanceof Error ? e.message : "no API key"}`));
+      console.error(fail2(`Authentication failed ${e instanceof Error ? e.message : "no API key"}`));
     }
     total++;
     try {
@@ -2115,29 +2148,29 @@ Elnora CLI v${VERSION}
         const data = await res.json();
         const latest = data.version ?? "unknown";
         if (latest === VERSION || latest === "unknown" || !isNewerVersion(latest, VERSION)) {
-          console.error(ok(`Version current       v${VERSION} (latest: v${latest})`));
+          console.error(ok2(`Version current       v${VERSION} (latest: v${latest})`));
         } else {
           console.error(warn(`Update available      v${VERSION} \u2192 v${latest}`));
         }
         passed++;
       } else {
-        console.error(ok(`Version               v${VERSION} (registry check failed)`));
+        console.error(ok2(`Version               v${VERSION} (registry check failed)`));
         passed++;
       }
     } catch {
-      console.error(ok(`Version               v${VERSION} (registry unreachable)`));
+      console.error(ok2(`Version               v${VERSION} (registry unreachable)`));
       passed++;
     }
     total++;
     if (process.platform === "win32") {
-      console.error(ok("Config permissions    (skipped on Windows)"));
+      console.error(ok2("Config permissions    (skipped on Windows)"));
       passed++;
     } else if (!existsSync3(PROFILES_FILE)) {
       console.error(warn("Config permissions    ~/.elnora/profiles.toml not found"));
     } else {
       const mode = statSync(PROFILES_FILE).mode & 511;
       if (mode === 384) {
-        console.error(ok(`Config permissions    ${PROFILES_FILE} (0600)`));
+        console.error(ok2(`Config permissions    ${PROFILES_FILE} (0600)`));
         passed++;
       } else {
         console.error(warn(`Config permissions    ${PROFILES_FILE} (0${mode.toString(8)}) \u2014 should be 0600`));
@@ -2149,11 +2182,11 @@ Elnora CLI v${VERSION}
       const res = await fetch(`${AI_SERVER_URL}/health`, { signal: AbortSignal.timeout(5e3) });
       const ms = Date.now() - start;
       if (res.ok) {
-        console.error(ok(`AI Server reachable   ${new URL(AI_SERVER_URL).hostname} (${res.status} OK, ${ms}ms)`));
+        console.error(ok2(`AI Server reachable   ${new URL(AI_SERVER_URL).hostname} (${res.status} OK, ${ms}ms)`));
         passed++;
-      } else console.error(fail(`AI Server unreachable ${new URL(AI_SERVER_URL).hostname} (HTTP ${res.status})`));
+      } else console.error(fail2(`AI Server unreachable ${new URL(AI_SERVER_URL).hostname} (HTTP ${res.status})`));
     } catch {
-      console.error(fail(`AI Server unreachable ${AI_SERVER_URL}`));
+      console.error(fail2(`AI Server unreachable ${AI_SERVER_URL}`));
     }
     console.error("");
     if (passed === total) {
@@ -4094,42 +4127,31 @@ function registerSearchCommands() {
   return [searchTasks, searchFiles, searchAll, searchFileContent];
 }
 
-// src/commands/setup-claude.ts
-init_config();
-import { cpSync, existsSync as existsSync4, mkdirSync as mkdirSync3, readFileSync as readFileSync5, writeFileSync as writeFileSync3 } from "node:fs";
+// src/commands/setup.ts
+init_profiles();
+
+// src/lib/setup/claude.ts
+import { existsSync as existsSync5 } from "node:fs";
+
+// src/lib/setup/common.ts
+import { existsSync as existsSync4, mkdirSync as mkdirSync3, readFileSync as readFileSync5, writeFileSync as writeFileSync3 } from "node:fs";
 import { homedir as homedir3 } from "node:os";
-import { dirname, join as join3 } from "node:path";
-import { fileURLToPath } from "node:url";
+import { join as join3 } from "node:path";
 import pc3 from "picocolors";
-var __script_dir;
-try {
-  __script_dir = dirname(fileURLToPath(import.meta.url));
-} catch {
-  __script_dir = typeof __dirname !== "undefined" ? __dirname : process.cwd();
-}
-var ELNORA_DIR = join3(homedir3(), ".elnora");
-var PLUGIN_DIR = join3(ELNORA_DIR, "plugin", "elnora");
-var CLAUDE_DIR = join3(homedir3(), ".claude");
-var MARKETPLACES_FILE = join3(CLAUDE_DIR, "plugins", "known_marketplaces.json");
-var SETTINGS_FILE = join3(CLAUDE_DIR, "settings.json");
-var MARKETPLACE_NAME = "elnora-local";
+var HOME = homedir3();
+var ELNORA_DIR = join3(HOME, ".elnora");
+var CLAUDE_DIR = join3(HOME, ".claude");
+var CLAUDE_MARKETPLACES_FILE = join3(CLAUDE_DIR, "plugins", "known_marketplaces.json");
+var CLAUDE_SETTINGS_FILE = join3(CLAUDE_DIR, "settings.json");
+var CURSOR_DIR = join3(HOME, ".cursor");
+var CURSOR_MCP_GLOBAL = join3(HOME, ".cursor", "mcp.json");
+var VSCODE_DIR = join3(HOME, ".vscode");
+var CODEX_DIR = join3(HOME, ".codex");
+var MARKETPLACE_NAME = "elnora-ai";
+var MARKETPLACE_REPO = "Elnora-AI/elnora-plugins";
 var PLUGIN_ID = `elnora@${MARKETPLACE_NAME}`;
-function findSkillsDir() {
-  const candidates = [
-    join3(__script_dir, "../../skills"),
-    join3(__script_dir, "../skills"),
-    // When running from source via tsx
-    join3(__script_dir, "../../../skills"),
-    // Standalone binary: skills extracted to ~/.elnora/skills/
-    join3(ELNORA_DIR, "skills")
-  ];
-  for (const dir of candidates) {
-    if (existsSync4(join3(dir, "elnora-platform", "SKILL.md"))) {
-      return dir;
-    }
-  }
-  return null;
-}
+var LEGACY_PLUGIN_IDS = ["elnora@elnora-local"];
+var LEGACY_MARKETPLACE_NAMES = ["elnora-local"];
 function readJsonFile(path) {
   try {
     return JSON.parse(readFileSync5(path, "utf-8"));
@@ -4142,63 +4164,225 @@ function writeJsonFile(path, data) {
   writeFileSync3(path, `${JSON.stringify(data, null, 2)}
 `, "utf-8");
 }
-function addSetupClaudeCommand(program2) {
-  program2.command("setup-claude").description("Install Elnora skills for Claude Code").action(() => {
-    const color = isColorEnabled();
-    const ok = (msg) => color ? `  ${pc3.green("\u2713")} ${msg}` : `  \u2713 ${msg}`;
-    const fail = (msg) => color ? `  ${pc3.red("\u2717")} ${msg}` : `  \u2717 ${msg}`;
+var color = isColorEnabled();
+function ok(msg) {
+  return color ? `  ${pc3.green("\u2713")} ${msg}` : `  \u2713 ${msg}`;
+}
+function fail(msg) {
+  return color ? `  ${pc3.red("\u2717")} ${msg}` : `  \u2717 ${msg}`;
+}
+function info(msg) {
+  return color ? `  ${pc3.dim(msg)}` : `  ${msg}`;
+}
+function detectPlatforms() {
+  return [
+    { name: "claude", label: "Claude Code", installed: existsSync4(CLAUDE_DIR) },
+    { name: "cursor", label: "Cursor", installed: existsSync4(CURSOR_DIR) },
+    { name: "vscode", label: "VS Code", installed: existsSync4(VSCODE_DIR) },
+    { name: "codex", label: "OpenAI Codex", installed: existsSync4(CODEX_DIR) }
+  ];
+}
+
+// src/lib/setup/claude.ts
+function setupClaude() {
+  if (!existsSync5(CLAUDE_DIR)) {
+    console.error(fail("Claude Code not found (~/.claude/ does not exist)"));
     console.error("");
-    if (!existsSync4(CLAUDE_DIR)) {
-      console.error(fail("Claude Code not found (~/.claude/ does not exist)"));
-      console.error("");
-      console.error("  Install Claude Code first: https://claude.ai/code");
-      process.exit(1);
+    console.error("  Install Claude Code first: https://claude.ai/code");
+    return false;
+  }
+  console.error(ok("Claude Code found"));
+  const marketplaces = readJsonFile(CLAUDE_MARKETPLACES_FILE);
+  for (const old of LEGACY_MARKETPLACE_NAMES) {
+    delete marketplaces[old];
+  }
+  marketplaces[MARKETPLACE_NAME] = {
+    source: {
+      source: "github",
+      repo: MARKETPLACE_REPO
     }
-    console.error(ok("Claude Code found"));
-    const skillsDir = findSkillsDir();
-    if (!skillsDir) {
-      console.error(fail("Skills not found"));
-      console.error("");
-      console.error("  Skills may not be bundled with your install method.");
-      console.error("  Try: npm install -g @elnora-ai/cli");
-      process.exit(1);
+  };
+  writeJsonFile(CLAUDE_MARKETPLACES_FILE, marketplaces);
+  console.error(ok(`Marketplace registered (GitHub: ${MARKETPLACE_REPO})`));
+  const settings = readJsonFile(CLAUDE_SETTINGS_FILE);
+  if (!settings.enabledPlugins || typeof settings.enabledPlugins !== "object") {
+    settings.enabledPlugins = {};
+  }
+  const plugins = settings.enabledPlugins;
+  for (const old of LEGACY_PLUGIN_IDS) {
+    delete plugins[old];
+  }
+  plugins[PLUGIN_ID] = true;
+  writeJsonFile(CLAUDE_SETTINGS_FILE, settings);
+  console.error(ok(`Plugin enabled (${PLUGIN_ID})`));
+  console.error("");
+  console.error("  Elnora skills are now available in Claude Code.");
+  console.error("  Restart Claude Code if it's currently running.");
+  return true;
+}
+
+// src/lib/setup/codex.ts
+import { existsSync as existsSync6 } from "node:fs";
+import { join as join4 } from "node:path";
+var CODEX_MCP_FILE = join4(CODEX_DIR, "mcp.json");
+function setupCodex(apiKey) {
+  if (!existsSync6(CODEX_DIR)) {
+    console.error(fail("Codex CLI not found (~/.codex/ does not exist)"));
+    console.error("");
+    console.error("  Install Codex first: https://github.com/openai/codex");
+    return false;
+  }
+  console.error(ok("Codex CLI found"));
+  const config = readJsonFile(CODEX_MCP_FILE);
+  if (!config.mcpServers || typeof config.mcpServers !== "object") {
+    config.mcpServers = {};
+  }
+  config.mcpServers.elnora = {
+    url: "https://mcp.elnora.ai/mcp",
+    headers: {
+      "X-API-Key": apiKey
     }
-    console.error(ok(`Skills found at ${skillsDir}`));
-    mkdirSync3(PLUGIN_DIR, { recursive: true });
-    writeJsonFile(join3(PLUGIN_DIR, ".claude-plugin", "plugin.json"), {
-      name: "elnora",
-      version: VERSION,
-      description: "AI-powered bioprotocol generation and lab workflow management. Connect to the Elnora AI Platform to generate, optimize, and manage bioprotocols.",
-      author: { name: "Elnora AI", url: "https://elnora.ai" },
-      repository: "https://github.com/Elnora-AI/elnora-cli",
-      homepage: "https://elnora.ai",
-      license: "Apache-2.0",
-      keywords: ["bioprotocol", "lab", "pharma", "life-sciences"]
-    });
-    cpSync(skillsDir, join3(PLUGIN_DIR, "skills"), { recursive: true });
-    console.error(ok("Skills installed to ~/.elnora/plugin/"));
-    const marketplaces = readJsonFile(MARKETPLACES_FILE);
-    marketplaces[MARKETPLACE_NAME] = {
-      source: {
-        source: "directory",
-        path: join3(ELNORA_DIR, "plugin")
-      },
-      installLocation: join3(ELNORA_DIR, "plugin"),
-      lastUpdated: (/* @__PURE__ */ new Date()).toISOString()
-    };
-    writeJsonFile(MARKETPLACES_FILE, marketplaces);
-    console.error(ok("Marketplace registered in Claude Code"));
-    const settings = readJsonFile(SETTINGS_FILE);
-    if (!settings.enabledPlugins || typeof settings.enabledPlugins !== "object") {
-      settings.enabledPlugins = {};
+  };
+  writeJsonFile(CODEX_MCP_FILE, config);
+  console.error(ok("MCP server configured in ~/.codex/mcp.json"));
+  console.error("");
+  console.error("  Elnora MCP server is now available in Codex.");
+  return true;
+}
+
+// src/lib/setup/cursor.ts
+import { existsSync as existsSync7 } from "node:fs";
+function setupCursor(apiKey) {
+  if (!existsSync7(CURSOR_DIR)) {
+    console.error(fail("Cursor not found (~/.cursor/ does not exist)"));
+    console.error("");
+    console.error("  Install Cursor first: https://cursor.com");
+    return false;
+  }
+  console.error(ok("Cursor found"));
+  const config = readJsonFile(CURSOR_MCP_GLOBAL);
+  if (!config.mcpServers || typeof config.mcpServers !== "object") {
+    config.mcpServers = {};
+  }
+  config.mcpServers.elnora = {
+    url: "https://mcp.elnora.ai/mcp",
+    headers: {
+      "X-API-Key": apiKey
     }
-    settings.enabledPlugins[PLUGIN_ID] = true;
-    writeJsonFile(SETTINGS_FILE, settings);
-    console.error(ok("Plugin enabled"));
+  };
+  writeJsonFile(CURSOR_MCP_GLOBAL, config);
+  console.error(ok("MCP server configured in ~/.cursor/mcp.json"));
+  console.error("");
+  console.error("  Elnora MCP server is now available in Cursor.");
+  console.error("  Restart Cursor if it's currently running.");
+  return true;
+}
+
+// src/lib/setup/vscode.ts
+import { existsSync as existsSync8 } from "node:fs";
+import { join as join5 } from "node:path";
+var VSCODE_MCP_GLOBAL = join5(HOME, ".vscode", "mcp.json");
+function setupVscode(apiKey) {
+  if (!existsSync8(VSCODE_DIR)) {
+    console.error(fail("VS Code not found (~/.vscode/ does not exist)"));
     console.error("");
-    console.error("  Elnora skills are now available in Claude Code.");
-    console.error("  Restart Claude Code if it's currently running.");
+    console.error("  Install VS Code first: https://code.visualstudio.com");
+    return false;
+  }
+  console.error(ok("VS Code found"));
+  const config = readJsonFile(VSCODE_MCP_GLOBAL);
+  if (!config.servers || typeof config.servers !== "object") {
+    config.servers = {};
+  }
+  config.servers.elnora = {
+    type: "http",
+    url: "https://mcp.elnora.ai/mcp",
+    headers: {
+      "X-API-Key": apiKey
+    }
+  };
+  writeJsonFile(VSCODE_MCP_GLOBAL, config);
+  console.error(ok("MCP server configured in ~/.vscode/mcp.json"));
+  console.error("");
+  console.error("  Elnora MCP server is now available in VS Code Copilot.");
+  console.error("  Restart VS Code if it's currently running.");
+  return true;
+}
+
+// src/commands/setup.ts
+var PLATFORM_SETUP = {
+  claude: () => setupClaude(),
+  cursor: (key) => setupCursor(key),
+  vscode: (key) => setupVscode(key),
+  codex: (key) => setupCodex(key)
+};
+function runSetup(platforms, profileName) {
+  let apiKey;
+  const needsKey = platforms.some((p) => p !== "claude");
+  if (needsKey) {
+    try {
+      apiKey = resolveApiKey(profileName);
+    } catch {
+      if (platforms.every((p) => p !== "claude")) {
+        console.error(fail("No API key found. Run 'elnora auth login' first."));
+        process.exitCode = 1;
+        return;
+      }
+    }
+  }
+  let anyFailed = false;
+  for (const platform of platforms) {
+    const setupFn = PLATFORM_SETUP[platform];
+    const success = setupFn(apiKey ?? "");
+    if (!success) anyFailed = true;
+    console.error("");
+  }
+  if (anyFailed) {
+    process.exitCode = 1;
+  }
+}
+function addSetupCommand(program2) {
+  const setup = program2.command("setup").description("Configure AI coding tools to use Elnora").option("--profile <name>", "API key profile to use", "default");
+  setup.command("claude").description("Set up Claude Code (skills + MCP server)").action(() => {
+    const opts = setup.opts();
     console.error("");
+    runSetup(["claude"], opts.profile);
+  });
+  setup.command("cursor").description("Set up Cursor (MCP server)").action(() => {
+    const opts = setup.opts();
+    console.error("");
+    runSetup(["cursor"], opts.profile);
+  });
+  setup.command("vscode").description("Set up VS Code Copilot (MCP server)").action(() => {
+    const opts = setup.opts();
+    console.error("");
+    runSetup(["vscode"], opts.profile);
+  });
+  setup.command("codex").description("Set up OpenAI Codex (MCP server)").action(() => {
+    const opts = setup.opts();
+    console.error("");
+    runSetup(["codex"], opts.profile);
+  });
+  setup.action(() => {
+    const opts = setup.opts();
+    console.error("");
+    const detected = detectPlatforms();
+    const installed = detected.filter((p) => p.installed);
+    if (installed.length === 0) {
+      console.error(fail("No supported AI coding tools detected."));
+      console.error("");
+      console.error("  Supported: Claude Code, Cursor, VS Code, OpenAI Codex");
+      console.error("  Install one first, then run 'elnora setup' again.");
+      process.exitCode = 1;
+      return;
+    }
+    console.error(ok(`Detected ${installed.length} platform(s):`));
+    for (const p of installed) {
+      console.error(info(`${p.label}`));
+    }
+    console.error("");
+    const platforms = installed.map((p) => p.name);
+    runSetup(platforms, opts.profile);
   });
 }
 
@@ -4689,10 +4873,34 @@ import { execFileSync } from "node:child_process";
 import { createHash } from "node:crypto";
 import { chmodSync as chmodSync2, copyFileSync, createWriteStream, mkdirSync as mkdirSync4, readFileSync as readFileSync6, rmSync } from "node:fs";
 import { tmpdir } from "node:os";
-import { join as join4 } from "node:path";
+import { join as join6 } from "node:path";
 import { Readable } from "node:stream";
 import { pipeline } from "node:stream/promises";
 import pc5 from "picocolors";
+
+// src/lib/install-method.ts
+function detectInstallMethod() {
+  const execPath = process.argv[1] ?? "";
+  if (execPath.includes("node_modules")) {
+    return "npm";
+  }
+  if (execPath.includes("/Cellar/") || execPath.includes("/homebrew/")) {
+    return "homebrew";
+  }
+  return "binary";
+}
+function getUpdateInstruction(method) {
+  switch (method) {
+    case "npm":
+      return "npm update -g @elnora-ai/cli";
+    case "homebrew":
+      return "brew upgrade elnora";
+    case "binary":
+      return "elnora update --install";
+  }
+}
+
+// src/commands/update.ts
 var NPM_REGISTRY_URL2 = "https://registry.npmjs.org/@elnora-ai/cli/latest";
 var GITHUB_REPO = "Elnora-AI/elnora-cli";
 function getPlatformTarget() {
@@ -4708,8 +4916,11 @@ function getPlatformTarget() {
       return null;
   }
 }
-function getManualHint() {
-  return process.platform === "win32" ? "  irm https://cli.elnora.ai/install.ps1 | iex" : "  curl -fsSL https://cli.elnora.ai/install.sh | bash";
+async function fetchLatestVersion() {
+  const res = await fetch(NPM_REGISTRY_URL2, { signal: AbortSignal.timeout(5e3) });
+  if (!res.ok) throw new Error(`Registry returned HTTP ${res.status}`);
+  const data = await res.json();
+  return data.version ?? "unknown";
 }
 async function downloadToFile(url, dest) {
   const res = await fetch(url, { signal: AbortSignal.timeout(12e4), redirect: "follow" });
@@ -4717,98 +4928,121 @@ async function downloadToFile(url, dest) {
   const nodeStream = Readable.fromWeb(res.body);
   await pipeline(nodeStream, createWriteStream(dest));
 }
+async function installBinaryUpdate(latest) {
+  const color2 = isColorEnabled();
+  const platformInfo = getPlatformTarget();
+  if (!platformInfo) {
+    console.error(`Unsupported platform: ${process.platform}.`);
+    console.error("Try: npm update -g @elnora-ai/cli");
+    process.exitCode = 1;
+    return;
+  }
+  const { target, ext } = platformInfo;
+  const binaryUrl = `https://github.com/${GITHUB_REPO}/releases/download/v${latest}/${target}.${ext}`;
+  const checksumUrl = `https://github.com/${GITHUB_REPO}/releases/download/v${latest}/${target}.sha256`;
+  const tmp = join6(tmpdir(), `elnora-update-${Date.now()}`);
+  mkdirSync4(tmp, { recursive: true });
+  const archivePath = join6(tmp, `${target}.${ext}`);
+  try {
+    console.error("Downloading...");
+    await downloadToFile(binaryUrl, archivePath);
+    let checksumVerified = false;
+    try {
+      const checksumRes = await fetch(checksumUrl, { signal: AbortSignal.timeout(15e3) });
+      if (checksumRes.ok) {
+        const checksumText = await checksumRes.text();
+        const expected = checksumText.split(/\s/)[0].trim();
+        if (expected.length === 64) {
+          const actual = createHash("sha256").update(readFileSync6(archivePath)).digest("hex");
+          if (actual.toLowerCase() !== expected.toLowerCase()) {
+            console.error("Checksum verification failed. The download may be corrupted.");
+            process.exitCode = 1;
+            return;
+          }
+          checksumVerified = true;
+        }
+      }
+    } catch {
+    }
+    if (!checksumVerified) {
+      console.error("Warning: Could not verify download checksum. Proceeding anyway.");
+    }
+    if (process.platform === "win32") {
+      const extractDir = join6(tmp, "extracted");
+      execFileSync("powershell", [
+        "-NoProfile",
+        "-Command",
+        `Expand-Archive -Path '${archivePath}' -DestinationPath '${extractDir}' -Force`
+      ]);
+      const installDir = join6(process.env.USERPROFILE ?? process.env.HOME ?? "", ".elnora", "bin");
+      mkdirSync4(installDir, { recursive: true });
+      copyFileSync(join6(extractDir, target), join6(installDir, "elnora.exe"));
+    } else {
+      execFileSync("tar", ["-xzf", archivePath, "-C", tmp]);
+      const installDir = process.env.ELNORA_INSTALL_DIR ?? join6(process.env.HOME ?? "", ".local", "bin");
+      mkdirSync4(installDir, { recursive: true });
+      const dest = join6(installDir, "elnora");
+      copyFileSync(join6(tmp, target), dest);
+      chmodSync2(dest, 493);
+    }
+    const done = color2 ? `${pc5.green("\u2713")} Updated to v${latest}` : `\u2713 Updated to v${latest}`;
+    console.error(done);
+  } finally {
+    try {
+      rmSync(tmp, { recursive: true, force: true });
+    } catch {
+    }
+  }
+}
 function addUpdateCommand(program2) {
-  program2.command("update").description("Update Elnora CLI to the latest version").action(async () => {
-    const color = isColorEnabled();
-    const hint = getManualHint();
+  program2.command("update").description("Check for updates (use --install to apply)").option("--install", "Download and install the update").action(async (opts) => {
+    const color2 = isColorEnabled();
+    const method = detectInstallMethod();
     let latest;
     try {
-      const res = await fetch(NPM_REGISTRY_URL2, { signal: AbortSignal.timeout(5e3) });
-      if (!res.ok) {
-        console.error("Failed to check for updates. Try manually:");
-        console.error(hint);
-        process.exit(1);
-      }
-      const data = await res.json();
-      latest = data.version ?? "unknown";
+      latest = await fetchLatestVersion();
     } catch {
-      console.error("Failed to reach registry. Try manually:");
-      console.error(hint);
-      process.exit(1);
+      console.error("Failed to check for updates.");
+      process.exitCode = 1;
+      return;
+    }
+    if (latest === "unknown") {
+      console.error("Could not determine latest version.");
+      process.exitCode = 1;
+      return;
     }
     if (latest === VERSION || !isNewerVersion(latest, VERSION)) {
-      const msg2 = color ? `${pc5.green("\u2713")} Already on the latest version (v${VERSION})` : `\u2713 Already on the latest version (v${VERSION})`;
+      const msg2 = color2 ? `${pc5.green("\u2713")} Already on the latest version (v${VERSION})` : `\u2713 Already on the latest version (v${VERSION})`;
       console.error(msg2);
       return;
     }
-    const msg = color ? `Updating Elnora CLI ${pc5.dim(`v${VERSION}`)} \u2192 ${pc5.green(`v${latest}`)}...` : `Updating Elnora CLI v${VERSION} \u2192 v${latest}...`;
+    const instruction = getUpdateInstruction(method);
+    if (!opts.install) {
+      const msg2 = color2 ? `${pc5.yellow("Update available:")} v${VERSION} \u2192 v${latest}` : `Update available: v${VERSION} \u2192 v${latest}`;
+      console.error(msg2);
+      console.error(`Run: ${instruction}`);
+      return;
+    }
+    const msg = color2 ? `Updating Elnora CLI ${pc5.dim(`v${VERSION}`)} \u2192 ${pc5.green(`v${latest}`)}...` : `Updating Elnora CLI v${VERSION} \u2192 v${latest}...`;
     console.error(msg);
-    const platformInfo = getPlatformTarget();
-    if (!platformInfo) {
-      console.error(`
-Unsupported platform: ${process.platform}. Try manually:`);
-      console.error("  npm update -g @elnora-ai/cli");
-      process.exit(1);
+    if (method === "npm") {
+      console.error("Installed via npm. Run:");
+      console.error(`  npm update -g @elnora-ai/cli`);
+      return;
+    }
+    if (method === "homebrew") {
+      console.error("Installed via Homebrew. Run:");
+      console.error(`  brew upgrade elnora`);
+      return;
     }
-    const { target, ext } = platformInfo;
-    const binaryUrl = `https://github.com/${GITHUB_REPO}/releases/download/v${latest}/${target}.${ext}`;
-    const checksumUrl = `https://github.com/${GITHUB_REPO}/releases/download/v${latest}/${target}.sha256`;
-    const tmp = join4(tmpdir(), `elnora-update-${Date.now()}`);
-    mkdirSync4(tmp, { recursive: true });
-    const archivePath = join4(tmp, `${target}.${ext}`);
     try {
-      await downloadToFile(binaryUrl, archivePath);
-      let checksumVerified = false;
-      try {
-        const checksumRes = await fetch(checksumUrl, { signal: AbortSignal.timeout(15e3) });
-        if (checksumRes.ok) {
-          const checksumText = await checksumRes.text();
-          const expected = checksumText.split(/\s/)[0].trim();
-          if (expected.length === 64) {
-            const actual = createHash("sha256").update(readFileSync6(archivePath)).digest("hex");
-            if (actual.toLowerCase() !== expected.toLowerCase()) {
-              console.error("\nChecksum verification failed. The download may be corrupted.");
-              console.error("Try again, or install manually:");
-              console.error(hint);
-              process.exit(1);
-            }
-            checksumVerified = true;
-          }
-        }
-      } catch {
-      }
-      if (!checksumVerified) {
-        console.error("Warning: Could not verify download checksum. Proceeding anyway.");
-      }
-      if (process.platform === "win32") {
-        const extractDir = join4(tmp, "extracted");
-        execFileSync("powershell", [
-          "-NoProfile",
-          "-Command",
-          `Expand-Archive -Path '${archivePath}' -DestinationPath '${extractDir}' -Force`
-        ]);
-        const installDir = join4(process.env.USERPROFILE ?? process.env.HOME ?? "", ".elnora", "bin");
-        mkdirSync4(installDir, { recursive: true });
-        copyFileSync(join4(extractDir, target), join4(installDir, "elnora.exe"));
-      } else {
-        execFileSync("tar", ["-xzf", archivePath, "-C", tmp]);
-        const installDir = process.env.ELNORA_INSTALL_DIR ?? join4(process.env.HOME ?? "", ".local", "bin");
-        mkdirSync4(installDir, { recursive: true });
-        const dest = join4(installDir, "elnora");
-        copyFileSync(join4(tmp, target), dest);
-        chmodSync2(dest, 493);
-      }
-      const done = color ? `${pc5.green("\u2713")} Updated to v${latest}` : `\u2713 Updated to v${latest}`;
-      console.error(done);
+      await installBinaryUpdate(latest);
     } catch {
-      console.error("\nUpdate failed. Try manually:");
-      console.error(hint);
-      process.exit(1);
-    } finally {
-      try {
-        rmSync(tmp, { recursive: true, force: true });
-      } catch {
-      }
+      console.error("Update failed. Try manually:");
+      console.error(
+        process.platform === "win32" ? "  irm https://cli.elnora.ai/install.ps1 | iex" : "  curl -fsSL https://cli.elnora.ai/install.sh | bash"
+      );
+      process.exitCode = 1;
     }
   });
 }
@@ -4821,22 +5055,21 @@ function addWhoamiCommand(program2) {
     const parentOpts = program2.opts();
     const profileName = parentOpts.profile ?? "default";
     try {
-      const key = resolveApiKey(profileName);
-      const masked = key.length > 20 ? `${key.slice(0, 16)}...${key.slice(-4)}` : `${key.slice(0, 4)}...`;
+      const hint = resolveCredentialHint(profileName);
       let orgName = "unknown";
       try {
-        const client = new ElnoraApiClient(key);
+        const client = new ElnoraApiClient(resolveApiKey(profileName));
         const orgs = await client.get("organizations");
         const orgList = Array.isArray(orgs) ? orgs : orgs?.items ?? [];
         if (orgList.length > 0) orgName = orgList[0]?.name ?? "unknown";
       } catch {
       }
       if (parentOpts.json) {
-        console.log(JSON.stringify({ profile: profileName, apiKey: masked, orgName }, null, 2));
+        console.log(JSON.stringify({ profile: profileName, credential: hint, orgName }, null, 2));
       } else {
         console.log(`
-Profile:  ${profileName}`);
-        console.log(`API Key:  ${masked}`);
+Profile:     ${profileName}`);
+        console.log(`Credential:  ${hint}`);
         console.log(`Org:      ${orgName}`);
         console.log("");
       }
@@ -4925,7 +5158,7 @@ addMcpCommands(program, registry);
 addDoctorCommand(program);
 addWhoamiCommand(program);
 addOpenCommand(program);
-addSetupClaudeCommand(program);
+addSetupCommand(program);
 addUpdateCommand(program);
 addCompletionCommand(program);
 registerUpdateCheck();

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@elnora-ai/cli",
-  "version": "1.2.1",
+  "version": "1.3.1",
   "description": "Elnora AI Platform CLI",
   "type": "module",
   "bin": {