@dosu/cli 0.13.2 → 0.14.0

package/bin/dosu.js

@@ -4341,7 +4341,7 @@ function getSupabaseAnonKey() {
 function getVersionString() {
   return `v${VERSION}`;
 }
-var VERSION = "0.13.2";
+var VERSION = "0.14.0";
 
 // src/debug/logger.ts
 import {
@@ -4353,6 +4353,17 @@ import {
   writeFileSync as writeFileSync2
 } from "node:fs";
 import { join as join2 } from "node:path";
+function redactSecrets(message) {
+  let redacted = message;
+  for (const key of SECRET_QUERY_KEYS) {
+    const queryPattern = new RegExp(`([?&]${key}=)[^\\s&#]+`, "gi");
+    redacted = redacted.replace(queryPattern, `$1${REDACTED}`);
+  }
+  redacted = redacted.replace(/(\b(?:access_token|refresh_token|api_key|apikey|id_token|token)\b\s*[:=]\s*)("[^"]+"|'[^']+'|[^\s,]+)/gi, `$1${REDACTED}`);
+  redacted = redacted.replace(/(X-Dosu-API-Key:\s*)[^\s,]+/gi, `$1${REDACTED}`);
+  redacted = redacted.replace(/(Authorization:\s*Bearer\s+)[^\s,]+/gi, `$1${REDACTED}`);
+  return redacted;
+}
 function ensureInit() {
   if (!initialized) {
     initLogger({});
@@ -4409,7 +4420,8 @@ function initLogger(opts) {
 function writeEntry(level, mod, message) {
   ensureInit();
   const timestamp = new Date().toISOString();
-  const line = `[${timestamp}] [${level}] [${mod}] ${message}
+  const safeMessage = redactSecrets(message);
+  const line = `[${timestamp}] [${level}] [${mod}] ${safeMessage}
 `;
   try {
     appendFileSync(resolveLogPath(), line, { mode: 384 });
@@ -4424,10 +4436,19 @@ function writeEntry(level, mod, message) {
     console.error(colorize(line.trimEnd()));
   }
 }
-var import_picocolors, MAX_LOG_SIZE = 1048576, TRUNCATE_KEEP = 524288, LOG_FILENAME = "debug.log", initialized = false, debugToConsole = false, logFilePath = null, logger;
+var import_picocolors, MAX_LOG_SIZE = 1048576, TRUNCATE_KEEP = 524288, LOG_FILENAME = "debug.log", REDACTED = "[REDACTED]", SECRET_QUERY_KEYS, initialized = false, debugToConsole = false, logFilePath = null, logger;
 var init_logger = __esm(() => {
   init_config();
   import_picocolors = __toESM(require_picocolors(), 1);
+  SECRET_QUERY_KEYS = [
+    "access_token",
+    "refresh_token",
+    "api_key",
+    "apikey",
+    "token",
+    "id_token",
+    "code"
+  ];
   logger = {
     init: initLogger,
     getLogPath() {
@@ -6635,7 +6656,8 @@ var init_skill = __esm(() => {
 });
 
 // src/mcp/config-helpers.ts
-import { existsSync as existsSync4, mkdirSync as mkdirSync4, readFileSync as readFileSync5, writeFileSync as writeFileSync4 } from "node:fs";
+import { existsSync as existsSync4, mkdirSync as mkdirSync4, readFileSync as readFileSync5 } from "node:fs";
+import { createRequire as createRequire2 } from "node:module";
 import { dirname } from "node:path";
 function mcpURL(deploymentID) {
   return `${getBackendURL()}/v1/mcp/deployments/${deploymentID}`;
@@ -6644,6 +6666,9 @@ function mcpBaseURL() {
   return `${getBackendURL()}/v1/mcp`;
 }
 function mcpHeaders(apiKey) {
+  if (!apiKey) {
+    throw new Error("API key is required. Run 'dosu setup' to create one.");
+  }
   return { "X-Dosu-API-Key": apiKey };
 }
 function loadJSONConfig(path) {
@@ -6708,11 +6733,14 @@ function stripJSONComments(data) {
   return result.join("");
 }
 function saveJSONConfig(path, cfg) {
+  writeSecureFile(path, JSON.stringify(cfg, null, 2));
+}
+function writeSecureFile(path, content) {
   const dir = dirname(path);
   if (!existsSync4(dir)) {
-    mkdirSync4(dir, { recursive: true });
+    mkdirSync4(dir, { recursive: true, mode: 448 });
   }
-  writeFileSync4(path, JSON.stringify(cfg, null, 2));
+  writeFileAtomic.sync(path, content, { mode: 384, chown: false });
 }
 function isJSONKeyConfigured(configPath, topLevelKey) {
   const cfg = loadJSONConfig(configPath);
@@ -6744,7 +6772,11 @@ function removeJSONServer(configPath, topKey) {
   }
   saveJSONConfig(configPath, jsonCfg);
 }
-var init_config_helpers = () => {};
+var require2, writeFileAtomic;
+var init_config_helpers = __esm(() => {
+  require2 = createRequire2(import.meta.url);
+  writeFileAtomic = require2("write-file-atomic");
+});
 
 // src/mcp/detect.ts
 import { existsSync as existsSync5 } from "node:fs";
@@ -6938,8 +6970,8 @@ var init_cline_cli = __esm(() => {
 });
 
 // src/mcp/providers/codex.ts
-import { existsSync as existsSync6, mkdirSync as mkdirSync5, readFileSync as readFileSync6, writeFileSync as writeFileSync5 } from "node:fs";
-import { dirname as dirname2, join as join9 } from "node:path";
+import { existsSync as existsSync6, readFileSync as readFileSync6 } from "node:fs";
+import { join as join9 } from "node:path";
 function codexHome() {
   return process.env.CODEX_HOME ?? expandHome("~/.codex");
 }
@@ -6954,10 +6986,7 @@ function readTOML(path) {
   return readFileSync6(path, "utf-8");
 }
 function writeTOML(path, content) {
-  const dir = dirname2(path);
-  if (!existsSync6(dir))
-    mkdirSync5(dir, { recursive: true });
-  writeFileSync5(path, content);
+  writeSecureFile(path, content);
 }
 function mcpEndpoint(cfg) {
   if (cfg.mode === MODE_OSS)
@@ -7139,17 +7168,29 @@ function mcpEndpoint3(cfg) {
     throw new Error("deployment ID is required");
   return mcpURL(cfg.deployment_id);
 }
+function maskSecret(secret) {
+  if (secret.length <= 8)
+    return "[hidden]";
+  const visibleChars = Math.min(4, Math.floor(secret.length / 4));
+  return `${secret.slice(0, visibleChars)}...${secret.slice(-visibleChars)}`;
+}
 var ManualProvider = () => ({
   name: () => "Manual Configuration",
   id: () => "manual",
   supportsLocal: () => false,
-  install(cfg) {
+  install(cfg, _global, opts = {}) {
     const url = mcpEndpoint3(cfg);
+    const apiKey = mcpHeaders(cfg.api_key)["X-Dosu-API-Key"];
+    const headerValue = opts.showSecret ? apiKey : maskSecret(apiKey);
     console.log("Use these details to configure the Dosu MCP server in your client:");
     console.log();
     console.log(`  Transport:      HTTP`);
     console.log(`  Endpoint:       ${url}`);
-    console.log(`  Header:         X-Dosu-API-Key: ${cfg.api_key}`);
+    console.log(`  Header:         X-Dosu-API-Key: ${headerValue}`);
+    if (!opts.showSecret) {
+      console.log();
+      console.log("  Secret hidden. Re-run with --show-secret to print the full API key.");
+    }
     console.log();
   },
   remove() {
@@ -9686,7 +9727,7 @@ async function startCallbackServer() {
     const url = new URL(req.url ?? "/", `http://localhost`);
     const cookieLen = (req.headers.cookie ?? "").length;
     const ua = req.headers["user-agent"] ?? "none";
-    logger.debug("auth.server", `Request: ${req.method} ${req.url} cookie-len=${cookieLen} ua=${ua} has-token=${url.searchParams.has("access_token")}`);
+    logger.debug("auth.server", `Request: ${req.method} ${url.pathname} cookie-len=${cookieLen} ua=${ua} has-token=${url.searchParams.has("access_token")}`);
     if (url.pathname !== "/callback") {
       logger.debug("auth.server", `404: ${url.pathname}`);
       res.writeHead(404, { "Content-Type": "text/plain" });
@@ -9824,7 +9865,7 @@ var exports_flow = {};
 __export(exports_flow, {
   startOAuthFlow: () => startOAuthFlow
 });
-async function startOAuthFlow(signal, path2 = "/cli/auth", params = {}) {
+async function startOAuthFlow(signal, path2 = "/cli/auth", params = {}, opts = {}) {
   const { server, tokenPromise } = await startCallbackServer();
   let timeoutId;
   try {
@@ -9832,9 +9873,12 @@ async function startOAuthFlow(signal, path2 = "/cli/auth", params = {}) {
     logger.debug("auth.flow", `Callback URL: ${callbackURL}`);
     const authURL = buildAuthURL(callbackURL, path2, params);
     logger.info("auth.flow", `Auth URL: ${authURL}`);
-    const open2 = await Promise.resolve().then(() => (init_open(), exports_open));
-    await open2.default(authURL);
-    logger.info("auth.flow", "Browser open command executed");
+    opts.onAuthURL?.(authURL);
+    if (opts.openBrowser !== false) {
+      const open2 = await Promise.resolve().then(() => (init_open(), exports_open));
+      await open2.default(authURL);
+      logger.info("auth.flow", "Browser open command executed");
+    }
     const timeout = new Promise((_3, reject) => {
       timeoutId = setTimeout(() => {
         logger.warn("auth.flow", "Authentication timed out (8min)");
@@ -9894,7 +9938,7 @@ async function runSetup(opts = {}) {
     cfg.mode = undefined;
     saveConfig(cfg);
   }
-  const authedCfg = await stepAuthenticate(cfg, onboardingRunID);
+  const authedCfg = await stepAuthenticate(cfg, onboardingRunID, opts);
   if (!authedCfg)
     return;
   cfg = authedCfg;
@@ -9944,7 +9988,8 @@ async function runSetup(opts = {}) {
   cfg.api_key = apiKey;
   saveConfig(cfg);
   const choices = await stepOneShotConfirm({
-    includeGitHub: cloudSetupContext?.kind === "onboarding"
+    includeGitHub: cloudSetupContext?.kind === "onboarding",
+    setupOptions: opts
   });
   if (!choices) {
     await trackCliOnboardingEvent(cfg, onboardingRunID, "cli_onboarding_cancelled", {
@@ -9962,7 +10007,7 @@ async function runSetup(opts = {}) {
   let skillCompleted = false;
   let docsImported = false;
   if (choices.configureMcp) {
-    const configured = await stepConfigureMcpTools(cfg);
+    const configured = await stepConfigureMcpTools(cfg, opts.toolIDs);
     if (configured === null) {
       await trackCliOnboardingEvent(cfg, onboardingRunID, "cli_onboarding_cancelled", {
         reason: "mcp_selection_cancelled"
@@ -10085,6 +10130,13 @@ function applyModeOverride(cfg, opts) {
   saveConfig(cfg);
 }
 async function stepOneShotConfirm(opts) {
+  if (opts.setupOptions?.yes) {
+    return {
+      configureMcp: !opts.setupOptions.skipMcp,
+      installSkill: !opts.setupOptions.skipSkill,
+      connectGitHub: opts.includeGitHub && !opts.setupOptions.skipGitHub
+    };
+  }
   const items = [
     { value: "configureMcp", label: "Install Dosu MCP" },
     { value: "installSkill", label: "Install Dosu skill" }
@@ -10112,7 +10164,15 @@ async function stepOneShotConfirm(opts) {
     connectGitHub: chosen.has("connectGitHub")
   };
 }
-async function stepConfigureMcpTools(cfg) {
+async function stepConfigureMcpTools(cfg, requestedToolIDs) {
+  if (requestedToolIDs && requestedToolIDs.length > 0) {
+    const selection2 = selectRequestedTools(requestedToolIDs);
+    if (!selection2)
+      return null;
+    const results2 = stepConfigureTools(cfg, selection2);
+    stepShowSummary(results2);
+    return results2;
+  }
   const detected = stepDetectTools();
   if (detected.length === 0) {
     M2.warn(`No supported AI agents detected on your system.
@@ -10144,7 +10204,7 @@ async function runInstallSkill() {
     return false;
   }
 }
-async function stepAuthenticate(existingCfg, onboardingRunID) {
+async function stepAuthenticate(existingCfg, onboardingRunID, opts = {}) {
   logger.info("setup", "Step: authenticate");
   const cfg = existingCfg ?? loadConfig();
   if (cfg.access_token) {
@@ -10174,26 +10234,36 @@ async function stepAuthenticate(existingCfg, onboardingRunID) {
       s.stop("Session verification failed");
     }
   }
-  const shouldLogin = await ye({ message: "Open browser to log in?" });
-  if (pD(shouldLogin) || !shouldLogin) {
-    if (onboardingRunID) {
-      await trackCliOnboardingPreAuthEvent(onboardingRunID, "cli_onboarding_auth_cancelled", {
-        reason: pD(shouldLogin) ? "prompt_cancelled" : "login_declined"
-      });
+  if (!opts.yes && opts.openBrowser !== false) {
+    const shouldLogin = await ye({ message: "Open browser to log in?" });
+    if (pD(shouldLogin) || !shouldLogin) {
+      if (onboardingRunID) {
+        await trackCliOnboardingPreAuthEvent(onboardingRunID, "cli_onboarding_auth_cancelled", {
+          reason: pD(shouldLogin) ? "prompt_cancelled" : "login_declined"
+        });
+      }
+      return null;
     }
-    return null;
   }
   if (onboardingRunID) {
     await trackCliOnboardingPreAuthEvent(onboardingRunID, "cli_onboarding_auth_started");
   }
-  return await openBrowserForSetup(cfg, onboardingRunID);
+  return await openBrowserForSetup(cfg, onboardingRunID, opts);
 }
-async function openBrowserForSetup(cfg, onboardingRunID) {
+async function openBrowserForSetup(cfg, onboardingRunID, opts = {}) {
   try {
     const { startOAuthFlow: startOAuthFlow2 } = await Promise.resolve().then(() => (init_flow(), exports_flow));
     const s = Y2();
     s.start("Waiting for authentication...");
-    const token = await startOAuthFlow2(undefined, "/cli/auth", onboardingRunID ? { onboarding_run_id: onboardingRunID } : {});
+    const token = await startOAuthFlow2(undefined, "/cli/auth", onboardingRunID ? { onboarding_run_id: onboardingRunID } : {}, {
+      openBrowser: opts.openBrowser !== false,
+      onAuthURL: opts.openBrowser === false ? (url) => {
+        M2.info(`Open this URL to authenticate:
+${url}
+
+Waiting for login to complete...`);
+      } : undefined
+    });
     s.stop("Authenticated");
     logger.info("setup", "Browser auth completed");
     cfg.access_token = token.access_token;
@@ -10302,10 +10372,10 @@ async function resolveDeployment(apiClient, cfg, opts) {
     }
     return true;
   }
-  const org = await stepSelectOrg(apiClient);
+  const org = await stepSelectOrg(apiClient, opts.yes === true);
   if (!org)
     return false;
-  const d3 = await stepSelectDeployment(apiClient, org);
+  const d3 = await stepSelectDeployment(apiClient, org, opts.yes === true);
   if (!d3)
     return false;
   cfg.mode = undefined;
@@ -10319,7 +10389,7 @@ async function fetchDeployments(apiClient) {
     return [];
   }
 }
-async function stepSelectOrg(apiClient) {
+async function stepSelectOrg(apiClient, noPrompt = false) {
   try {
     const orgs = await apiClient.getOrgs();
     if (orgs.length === 0) {
@@ -10332,6 +10402,10 @@ async function stepSelectOrg(apiClient) {
 ${dim(orgs[0].name)}`);
       return orgs[0];
     }
+    if (noPrompt) {
+      M2.error("Multiple organizations found. Run `dosu deployments list --json`, choose a deployment, then re-run setup with `--deployment <id>`.");
+      return null;
+    }
     const selected = await ve({
       message: "Select an organization",
       options: orgs.map((o2) => ({ label: o2.name, value: o2.org_id }))
@@ -10369,7 +10443,7 @@ ${dim(d3.name)}`);
     return null;
   }
 }
-async function stepSelectDeployment(apiClient, org) {
+async function stepSelectDeployment(apiClient, org, noPrompt = false) {
   try {
     const allDeployments = await apiClient.getDeployments();
     const deployments = allDeployments.filter((d4) => d4.org_id === org.org_id);
@@ -10383,6 +10457,10 @@ async function stepSelectDeployment(apiClient, org) {
 ${dim(deployments[0].name)}`);
       return deployments[0];
     }
+    if (noPrompt) {
+      M2.error("Multiple MCPs found. Run `dosu deployments list --json`, choose one, then re-run setup with `--deployment <id>`.");
+      return null;
+    }
     const selected = await ve({
       message: "Select an MCP",
       options: deployments.map((d4) => ({ label: d4.name, value: d4.deployment_id }))
@@ -10430,6 +10508,24 @@ function isStdioOnly(p2) {
 function stepDetectTools() {
   return allSetupProviders().filter((p2) => p2.isInstalled() && !isStdioOnly(p2));
 }
+function selectRequestedTools(requestedToolIDs) {
+  const normalized = [...new Set(requestedToolIDs.map((id) => id.toLowerCase()))];
+  const providers = allSetupProviders();
+  const selected = [];
+  for (const id of normalized) {
+    const provider = providers.find((p2) => p2.id() === id);
+    if (!provider) {
+      M2.error(`Unknown AI tool '${id}'. Run 'dosu mcp list' to see available tools.`);
+      return null;
+    }
+    if (isStdioOnly(provider)) {
+      M2.error(`${provider.name()} is not supported by setup. Use 'dosu mcp add ${id}'.`);
+      return null;
+    }
+    selected.push(provider);
+  }
+  return { toInstall: selected, toRemove: [], skipped: [] };
+}
 async function stepSelectTools(detected) {
   const configuredMap = new Map;
   for (const p2 of detected) {
@@ -10545,8 +10641,8 @@ var init_flow2 = __esm(() => {
 });
 
 // src/commands/insights.ts
-import { existsSync as existsSync9, mkdirSync as mkdirSync6, readdirSync, unlinkSync, writeFileSync as writeFileSync6 } from "node:fs";
-import { dirname as dirname3, join as join19 } from "node:path";
+import { existsSync as existsSync9, mkdirSync as mkdirSync5, readdirSync, unlinkSync, writeFileSync as writeFileSync4 } from "node:fs";
+import { dirname as dirname2, join as join19 } from "node:path";
 function shuffled(arr) {
   const copy2 = [...arr];
   for (let i = copy2.length - 1;i > 0; i--) {
@@ -10744,10 +10840,10 @@ function defaultRunner(cfg) {
     build: buildInsights,
     render: renderHTML,
     writeFile: (path2, content) => {
-      const dir = dirname3(path2);
+      const dir = dirname2(path2);
       if (!existsSync9(dir))
-        mkdirSync6(dir, { recursive: true, mode: 448 });
-      writeFileSync6(path2, content, { mode: 384 });
+        mkdirSync5(dir, { recursive: true, mode: 448 });
+      writeFileSync4(path2, content, { mode: 384 });
     },
     prune: pruneOldReports,
     openInBrowser: async (path2) => {
@@ -12378,7 +12474,7 @@ init_skill_update_check();
 init_config();
 init_logger();
 var import_picocolors24 = __toESM(require_picocolors(), 1);
-import { existsSync as existsSync10, mkdirSync as mkdirSync7, readFileSync as readFileSync7, writeFileSync as writeFileSync7 } from "node:fs";
+import { existsSync as existsSync10, mkdirSync as mkdirSync6, readFileSync as readFileSync7, writeFileSync as writeFileSync5 } from "node:fs";
 import { join as join20 } from "node:path";
 var CACHE_FILENAME2 = "update-check.json";
 var CHECK_INTERVAL_MS2 = 24 * 60 * 60 * 1000;
@@ -12422,9 +12518,9 @@ function writeCache(cache) {
   try {
     const dir = getConfigDir();
     if (!existsSync10(dir)) {
-      mkdirSync7(dir, { recursive: true, mode: 448 });
+      mkdirSync6(dir, { recursive: true, mode: 448 });
     }
-    writeFileSync7(getCachePath2(), JSON.stringify(cache), { mode: 384 });
+    writeFileSync5(getCachePath2(), JSON.stringify(cache), { mode: 384 });
   } catch {}
 }
 async function fetchLatestVersion() {
@@ -12487,19 +12583,27 @@ function createProgram() {
     const { runTUI: runTUI2 } = await Promise.resolve().then(() => (init_tui(), exports_tui));
     await runTUI2();
   });
-  program2.command("login").description("Authenticate with Dosu via OAuth").action(async () => {
+  program2.command("login").description("Authenticate with Dosu via OAuth").option("--no-open", "Print the login URL instead of opening a browser").action(async (opts) => {
     const cfg = loadConfig();
     if (isAuthenticated(cfg) && !isTokenExpired(cfg)) {
       console.log("You are already logged in.");
       console.log("Run 'dosu logout' first to re-authenticate.");
       return;
     }
-    console.log("Opening browser for authentication...");
+    console.log(opts.open === false ? "Starting authentication..." : "Opening browser for authentication...");
     const { startOAuthFlow: startOAuthFlow2 } = await Promise.resolve().then(() => (init_flow(), exports_flow));
     const { OAuthCallbackError: OAuthCallbackError2 } = await Promise.resolve().then(() => (init_errors(), exports_errors));
     let token;
     try {
-      token = await startOAuthFlow2();
+      token = await startOAuthFlow2(undefined, "/cli/auth", {}, {
+        openBrowser: opts.open !== false,
+        onAuthURL: opts.open === false ? (url) => {
+          console.log("Open this URL to authenticate:");
+          console.log(url);
+          console.log(`
+Waiting for login to complete...`);
+        } : undefined
+      });
     } catch (err) {
       if (err instanceof OAuthCallbackError2) {
         console.error(err.userMessage);
@@ -12557,7 +12661,7 @@ function createProgram() {
     }
   });
   const mcp = program2.command("mcp").description("Manage MCP server integrations");
-  mcp.command("add <agent>").description("Add Dosu MCP to an AI tool").option("-g, --global", "Add globally (all projects) instead of project-local", false).action((toolId, opts) => {
+  mcp.command("add <agent>").description("Add Dosu MCP to an AI tool").option("-g, --global", "Add globally (all projects) instead of project-local", false).option("--show-secret", "Print full manual configuration secrets", false).action((toolId, opts) => {
     let provider;
     try {
       provider = getProvider(toolId.toLowerCase());
@@ -12574,8 +12678,11 @@ function createProgram() {
     if (cfg.mode !== MODE_OSS && !cfg.deployment_id) {
       throw new Error("no MCP selected. Run 'dosu' to open the TUI and select an MCP");
     }
+    if (!cfg.api_key) {
+      throw new Error("no API key available. Run 'dosu setup' to create one");
+    }
     if (provider.id() === "manual") {
-      provider.install(cfg, false);
+      provider.install(cfg, false, { showSecret: opts.showSecret });
       return;
     }
     let global = opts.global;
@@ -12586,7 +12693,7 @@ function createProgram() {
     }
     const scope = global ? "global (all projects)" : "project-local";
     console.log(`Adding Dosu MCP to ${provider.name()} (${scope})...`);
-    provider.install(cfg, global);
+    provider.install(cfg, global, { showSecret: opts.showSecret });
     console.log(`
 ✓ Successfully added Dosu MCP to ${provider.name()}!`);
     if (global) {
@@ -12626,7 +12733,7 @@ Use 'dosu mcp add <agent>' to add Dosu MCP to a tool.`);
   program2.addCommand(tagsCommand());
   program2.addCommand(threadsCommand());
   program2.addCommand(skillCommand());
-  program2.command("setup").description("Set up Dosu MCP for your AI tools").option("--deployment <id>", "Skip to tool configuration for a specific MCP").option("--mode <mode>", "Force OSS or Cloud mode, skipping the interactive prompt (oss|cloud)").action(async (opts) => {
+  program2.command("setup").description("Set up Dosu MCP for your AI tools").option("--deployment <id>", "Skip to tool configuration for a specific MCP").option("--mode <mode>", "Force OSS or Cloud mode, skipping the interactive prompt (oss|cloud)").option("--agent", "Run an agent-assisted setup with safe defaults", false).option("-y, --yes", "Accept setup defaults and skip confirmation prompts", false).option("--no-open", "Print browser login URLs instead of opening them").option("--tool <agent>", "Configure a specific AI tool; may be repeated", collectValues, []).option("--skip-mcp", "Do not configure AI tool MCP entries", false).option("--skip-skill", "Do not install the Dosu agent skill", false).option("--skip-github", "Do not run GitHub repository/doc onboarding", false).action(async (opts) => {
     const { runSetup: runSetup2 } = await Promise.resolve().then(() => (init_flow2(), exports_flow2));
     let mode;
     if (opts.mode !== undefined) {
@@ -12636,7 +12743,16 @@ Use 'dosu mcp add <agent>' to add Dosu MCP to a tool.`);
       }
       mode = normalized;
     }
-    await runSetup2({ deploymentID: opts.deployment, mode });
+    await runSetup2({
+      deploymentID: opts.deployment,
+      mode,
+      yes: opts.agent === true || opts.yes === true,
+      openBrowser: opts.agent === true ? false : opts.open !== false,
+      toolIDs: opts.tool ?? [],
+      skipMcp: opts.skipMcp === true,
+      skipSkill: opts.skipSkill === true,
+      skipGitHub: opts.agent === true || opts.skipGithub === true
+    });
   });
   program2.command("logs").description("View or manage debug logs").option("-t, --tail [n]", "Show last N lines (default: 50)").option("--clear", "Delete the log file").action((opts) => {
     const logPath = logger.getLogPath();
@@ -12666,6 +12782,10 @@ Use 'dosu mcp add <agent>' to add Dosu MCP to a tool.`);
   });
   return program2;
 }
+function collectValues(value, previous) {
+  previous.push(value);
+  return previous;
+}
 async function execute() {
   const program2 = createProgram();
   await program2.parseAsync(process.argv);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@dosu/cli",
-  "version": "0.13.2",
+  "version": "0.14.0",
   "type": "module",
   "description": "Dosu CLI - Manage MCP servers for AI tools",
   "license": "MIT",
@@ -52,6 +52,7 @@
     "commander": "^13.1.0",
     "open": "^10.1.0",
     "picocolors": "^1.1.1",
-    "superjson": "^2.2.6"
+    "superjson": "^2.2.6",
+    "write-file-atomic": "^5.0.1"
   }
 }