@askexenow/exe-os 0.9.48 → 0.9.51

package/dist/bin/cli.js

@@ -1886,8 +1886,8 @@ function deriveMachineKey() {
 }
 function readMachineId() {
   try {
-    const { readFileSync: readFileSync30 } = __require("fs");
-    return readFileSync30("/etc/machine-id", "utf-8").trim();
+    const { readFileSync: readFileSync31 } = __require("fs");
+    return readFileSync31("/etc/machine-id", "utf-8").trim();
   } catch {
     return "";
   }
@@ -9140,9 +9140,9 @@ Unclassified: ${unclassified}
 }
 async function exportBatches(options) {
   const fs8 = await import("fs");
-  const path49 = await import("path");
+  const path50 = await import("path");
   const client = getClient();
-  const outDir = path49.join(process.cwd(), "exe/output/classifications/input");
+  const outDir = path50.join(process.cwd(), "exe/output/classifications/input");
   fs8.mkdirSync(outDir, { recursive: true });
   const countResult = await client.execute({
     sql: "SELECT COUNT(*) as cnt FROM memories WHERE intent IS NULL AND outcome IS NULL AND domain IS NULL",
@@ -9166,7 +9166,7 @@ async function exportBatches(options) {
       const text = String(row.text || "").replace(/\n/g, " ");
       return JSON.stringify({ id: row.id, text });
     });
-    const batchFile = path49.join(outDir, `batch-${String(batchNum).padStart(4, "0")}.jsonl`);
+    const batchFile = path50.join(outDir, `batch-${String(batchNum).padStart(4, "0")}.jsonl`);
     fs8.writeFileSync(batchFile, lines.join("\n") + "\n");
     exported += batch.rows.length;
     offset += options.batchSize;
@@ -9182,7 +9182,7 @@ async function exportBatches(options) {
 }
 async function importClassifications(importDir) {
   const fs8 = await import("fs");
-  const path49 = await import("path");
+  const path50 = await import("path");
   const client = getClient();
   const files = fs8.readdirSync(importDir).filter((f) => f.endsWith(".jsonl")).sort();
   process.stderr.write(`[backfill-metadata] Found ${files.length} JSONL files to import from ${importDir}
@@ -9190,7 +9190,7 @@ async function importClassifications(importDir) {
   let imported = 0;
   let invalid = 0;
   for (const file of files) {
-    const lines = fs8.readFileSync(path49.join(importDir, file), "utf-8").split("\n").filter(Boolean);
+    const lines = fs8.readFileSync(path50.join(importDir, file), "utf-8").split("\n").filter(Boolean);
     for (const line of lines) {
       try {
         const rec = JSON.parse(line);
@@ -11828,10 +11828,10 @@ async function disposeEmbedder() {
 async function embedDirect(text) {
   const llamaCpp = await import("node-llama-cpp");
   const { MODELS_DIR: MODELS_DIR2 } = await Promise.resolve().then(() => (init_config(), config_exports));
-  const { existsSync: existsSync35 } = await import("fs");
-  const path49 = await import("path");
-  const modelPath = path49.join(MODELS_DIR2, "jina-embeddings-v5-small-q4_k_m.gguf");
-  if (!existsSync35(modelPath)) {
+  const { existsSync: existsSync36 } = await import("fs");
+  const path50 = await import("path");
+  const modelPath = path50.join(MODELS_DIR2, "jina-embeddings-v5-small-q4_k_m.gguf");
+  if (!existsSync36(modelPath)) {
     throw new Error(`Embedding model not found at ${modelPath}. Run '/exe-setup' to download it.`);
   }
   const llama = await llamaCpp.getLlama();
@@ -16607,7 +16607,20 @@ async function runUpdate(cliArgs) {
     } catch {
     }
   }
-  console.log("   Hooks re-wired, daemon restarted automatically.");
+  console.log("\u{1F527} Re-registering MCP, hooks, wrappers, and daemon...");
+  try {
+    execSync13("exe-os-install --global", {
+      stdio: ["pipe", "inherit", "inherit"],
+      timeout: 3e5
+    });
+  } catch (err) {
+    console.error("\n\u26A0\uFE0F  Package updated, but post-update install failed.");
+    console.error("   Run manually: exe-os-install --global");
+    if (err instanceof Error && err.message) {
+      console.error(`   Error: ${err.message.split("\n")[0]}`);
+    }
+  }
+  console.log("   MCP, hooks, and daemon refreshed.");
   console.log("");
   console.log("   \x1B[33m\u26A1 Run /mcp in each active Claude Code session to pick up new tools.\x1B[0m");
   console.log("   \x1B[2m(MCP servers can't hot-reload \u2014 Claude Code needs to reconnect them.)\x1B[0m");
@@ -21308,8 +21321,8 @@ var init_ErrorOverview = __esm({
     "use strict";
     init_Box();
     init_Text();
-    cleanupPath = (path49) => {
-      return path49?.replace(`file://${cwd()}/`, "");
+    cleanupPath = (path50) => {
+      return path50?.replace(`file://${cwd()}/`, "");
     };
     stackUtils = new StackUtils({
       cwd: cwd(),
@@ -23717,11 +23730,11 @@ function Footer() {
       } catch {
       }
       try {
-        const { existsSync: existsSync35 } = await import("fs");
+        const { existsSync: existsSync36 } = await import("fs");
         const { join } = await import("path");
         const home = process.env.HOME ?? "";
         const pidPath = join(home, ".exe-os", "exed.pid");
-        setDaemon(existsSync35(pidPath) ? "running" : "stopped");
+        setDaemon(existsSync36(pidPath) ? "running" : "stopped");
       } catch {
         setDaemon("unknown");
       }
@@ -26505,15 +26518,15 @@ function CommandCenterView({
         const { createPermissionsFromPreset: createPermissionsFromPreset2, EMPLOYEE_PERMISSIONS: EMPLOYEE_PERMISSIONS2 } = await Promise.resolve().then(() => (init_permissions(), permissions_exports));
         const { getPresetByRole: getPresetByRole2 } = await Promise.resolve().then(() => (init_permission_presets(), permission_presets_exports));
         const { createDefaultHooks: createDefaultHooks2 } = await Promise.resolve().then(() => (init_hooks(), hooks_exports));
-        const { readFileSync: readFileSync30, existsSync: existsSync35 } = await import("fs");
+        const { readFileSync: readFileSync31, existsSync: existsSync36 } = await import("fs");
         const { join } = await import("path");
         const { homedir: homedir8 } = await import("os");
         const configPath = join(homedir8(), ".exe-os", "config.json");
         let failoverChain = ["anthropic", "opencode", "gemini", "openai"];
         let providerConfigs = {};
-        if (existsSync35(configPath)) {
+        if (existsSync36(configPath)) {
           try {
-            const raw = JSON.parse(readFileSync30(configPath, "utf8"));
+            const raw = JSON.parse(readFileSync31(configPath, "utf8"));
             if (Array.isArray(raw.failoverChain)) failoverChain = raw.failoverChain;
             if (raw.providers && typeof raw.providers === "object") {
               providerConfigs = raw.providers;
@@ -26574,7 +26587,7 @@ function CommandCenterView({
           const markerDir = join(homedir8(), ".exe-os", "session-cache");
           const agentFiles = (await import("fs")).readdirSync(markerDir).filter((f) => f.startsWith("active-agent-"));
           for (const f of agentFiles) {
-            const data = JSON.parse(readFileSync30(join(markerDir, f), "utf8"));
+            const data = JSON.parse(readFileSync31(join(markerDir, f), "utf8"));
             if (data.agentRole) {
               agentRole = data.agentRole;
               break;
@@ -26757,7 +26770,7 @@ function CommandCenterView({
         const { listSessions: listSessions2 } = await Promise.resolve().then(() => (init_session_registry(), session_registry_exports));
         const { listTmuxSessions: listTmuxSessions2, inTmux: inTmux2 } = await Promise.resolve().then(() => (init_tmux_status(), tmux_status_exports));
         const { loadEmployees: loadEmployees2 } = await Promise.resolve().then(() => (init_employees(), employees_exports));
-        const { existsSync: existsSync35 } = await import("fs");
+        const { existsSync: existsSync36 } = await import("fs");
         const { join } = await import("path");
         const client = getClient2();
         if (!client) {
@@ -26828,7 +26841,7 @@ function CommandCenterView({
           }
           const memoryCount = memoryCounts.get(name) ?? 0;
           const openTaskCount = openTaskCounts.get(name) ?? 0;
-          const hasGit = projectDir ? existsSync35(join(projectDir, ".git")) : false;
+          const hasGit = projectDir ? existsSync36(join(projectDir, ".git")) : false;
           const type = hasGit ? "code" : memoryCount > 0 ? "code" : "automation";
           projectList.push({
             projectName: name,
@@ -26853,7 +26866,7 @@ function CommandCenterView({
         setHealth((h) => ({ ...h, memories: Number(totalResult.rows[0]?.cnt ?? 0) }));
         try {
           const pidPath = join(process.env.HOME ?? "", ".exe-os", "exed.pid");
-          setHealth((h) => ({ ...h, daemon: existsSync35(pidPath) ? "running" : "stopped" }));
+          setHealth((h) => ({ ...h, daemon: existsSync36(pidPath) ? "running" : "stopped" }));
         } catch {
         }
         const activityResult = await client.execute(
@@ -28976,12 +28989,12 @@ async function loadGatewayConfig() {
     state.running = false;
   }
   try {
-    const { existsSync: existsSync35, readFileSync: readFileSync30 } = await import("fs");
+    const { existsSync: existsSync36, readFileSync: readFileSync31 } = await import("fs");
     const { join } = await import("path");
     const home = process.env.HOME ?? "";
     const configPath = join(home, ".exe-os", "gateway.json");
-    if (existsSync35(configPath)) {
-      const raw = JSON.parse(readFileSync30(configPath, "utf8"));
+    if (existsSync36(configPath)) {
+      const raw = JSON.parse(readFileSync31(configPath, "utf8"));
       state.port = raw.port ?? 3100;
       state.gatewayUrl = raw.gatewayUrl ?? "";
       if (raw.adapters) {
@@ -29579,12 +29592,12 @@ function TeamView({ onBack, onViewSessions }) {
         setMembers(teamData);
         setDbError(null);
         try {
-          const { existsSync: existsSync35, readFileSync: readFileSync30 } = await import("fs");
+          const { existsSync: existsSync36, readFileSync: readFileSync31 } = await import("fs");
           const { join } = await import("path");
           const home = process.env.HOME ?? "";
           const gatewayConfig = join(home, ".exe-os", "gateway.json");
-          if (existsSync35(gatewayConfig)) {
-            const raw = JSON.parse(readFileSync30(gatewayConfig, "utf8"));
+          if (existsSync36(gatewayConfig)) {
+            const raw = JSON.parse(readFileSync31(gatewayConfig, "utf8"));
             if (raw.agents && raw.agents.length > 0) {
               setExternals(raw.agents.map((a) => ({
                 name: a.name,
@@ -29764,8 +29777,8 @@ __export(wiki_client_exports, {
   listDocuments: () => listDocuments,
   listWorkspaces: () => listWorkspaces
 });
-async function wikiFetch(config, path49, method = "GET", body) {
-  const url = `${config.baseUrl}/api/v1${path49}`;
+async function wikiFetch(config, path50, method = "GET", body) {
+  const url = `${config.baseUrl}/api/v1${path50}`;
   const headers = {
     Authorization: `Bearer ${config.apiKey}`,
     "Content-Type": "application/json"
@@ -29798,7 +29811,7 @@ async function wikiFetch(config, path49, method = "GET", body) {
       }
     }
     if (!response.ok) {
-      throw new Error(`Wiki API ${method} ${path49}: ${response.status} ${response.statusText}`);
+      throw new Error(`Wiki API ${method} ${path50}: ${response.status} ${response.statusText}`);
     }
     return response.json();
   } finally {
@@ -30392,12 +30405,12 @@ function SettingsView({ onBack }) {
     }
     setProviders(providerList);
     try {
-      const { existsSync: existsSync35 } = await import("fs");
+      const { existsSync: existsSync36 } = await import("fs");
       const { join } = await import("path");
       const { loadConfig: loadConfig2 } = await Promise.resolve().then(() => (init_config(), config_exports));
       const cfg = await loadConfig2();
       const home = process.env.HOME ?? "";
-      const hasKey = existsSync35(join(home, ".exe-os", "master.key"));
+      const hasKey = existsSync36(join(home, ".exe-os", "master.key"));
       if (cfg.cloud) {
         setCloud({
           configured: true,
@@ -30410,22 +30423,22 @@ function SettingsView({ onBack }) {
       const pidPath = join(home, ".exe-os", "exed.pid");
       let daemon = "unknown";
       try {
-        daemon = existsSync35(pidPath) ? "running" : "stopped";
+        daemon = existsSync36(pidPath) ? "running" : "stopped";
       } catch {
       }
       let version = "unknown";
       try {
-        const { readFileSync: readFileSync30 } = await import("fs");
+        const { readFileSync: readFileSync31 } = await import("fs");
         const { createRequire: createRequire3 } = await import("module");
         const require2 = createRequire3(import.meta.url);
         const pkgPath = require2.resolve("@askexenow/exe-os/package.json");
-        const pkg = JSON.parse(readFileSync30(pkgPath, "utf8"));
+        const pkg = JSON.parse(readFileSync31(pkgPath, "utf8"));
         version = pkg.version;
       } catch {
         try {
-          const { readFileSync: readFileSync30 } = await import("fs");
+          const { readFileSync: readFileSync31 } = await import("fs");
           const { join: joinPath } = await import("path");
-          const pkg = JSON.parse(readFileSync30(joinPath(process.cwd(), "package.json"), "utf8"));
+          const pkg = JSON.parse(readFileSync31(joinPath(process.cwd(), "package.json"), "utf8"));
           version = pkg.version;
         } catch {
         }
@@ -31624,15 +31637,199 @@ var init_installer3 = __esm({
   }
 });
 
-// src/bin/cli.ts
-import { existsSync as existsSync34, readFileSync as readFileSync29, writeFileSync as writeFileSync21, readdirSync as readdirSync10, rmSync } from "fs";
+// src/adapters/claude/mcp-diagnostics.ts
+var mcp_diagnostics_exports = {};
+__export(mcp_diagnostics_exports, {
+  diagnoseClaudeMcpConfig: () => diagnoseClaudeMcpConfig,
+  formatMcpDiagnosticReport: () => formatMcpDiagnosticReport
+});
+import { existsSync as existsSync34, readFileSync as readFileSync29 } from "fs";
 import path48 from "path";
 import os21 from "os";
+function readJson(filePath) {
+  if (!existsSync34(filePath)) return null;
+  try {
+    return JSON.parse(readFileSync29(filePath, "utf8"));
+  } catch {
+    return null;
+  }
+}
+function pathApplies2(projectPath, cwd2) {
+  const project = path48.resolve(projectPath);
+  const current = path48.resolve(cwd2);
+  return current === project || current.startsWith(project + path48.sep);
+}
+function findAncestorMcpJsons2(cwd2, homeDir) {
+  const files = [];
+  let dir = path48.resolve(cwd2);
+  const root = path48.parse(dir).root;
+  const stop = path48.resolve(homeDir);
+  while (dir !== root) {
+    const candidate = path48.join(dir, ".mcp.json");
+    if (existsSync34(candidate)) files.push(candidate);
+    if (dir === stop) break;
+    dir = path48.dirname(dir);
+  }
+  return files;
+}
+function extractPermissionPrefixes(settings) {
+  const allow = settings?.permissions?.allow ?? [];
+  const prefixes = /* @__PURE__ */ new Set();
+  for (const entry of allow) {
+    const match = entry.match(/^mcp__(.+?)__/);
+    if (match?.[1]) prefixes.add(match[1]);
+  }
+  return [...prefixes].sort();
+}
+function serverAllowedByPermissions(serverName, prefixes) {
+  return prefixes.has(serverName) || prefixes.has(serverName.replace(/-/g, "_"));
+}
+function diagnoseClaudeMcpConfig(homeDir = os21.homedir(), cwd2 = process.cwd(), env = process.env) {
+  const claudeJsonPath = path48.join(homeDir, ".claude.json");
+  const settingsPath = path48.join(homeDir, ".claude", "settings.json");
+  const claudeJson = readJson(claudeJsonPath);
+  const settings = readJson(settingsPath);
+  const issues = [];
+  if (!claudeJson) {
+    issues.push({
+      severity: "error",
+      code: "claude-json-missing-or-invalid",
+      message: "~/.claude.json is missing or invalid, so Claude MCP server config cannot be audited.",
+      fix: "Run exe-os claude install, then re-open Claude Code."
+    });
+  }
+  if (!settings) {
+    issues.push({
+      severity: "warn",
+      code: "settings-json-missing-or-invalid",
+      message: "~/.claude/settings.json is missing or invalid; MCP permissions cannot be audited.",
+      fix: "Run exe-os claude install, then re-open Claude Code."
+    });
+  }
+  const globalServers = Object.keys(claudeJson?.mcpServers ?? {}).sort();
+  const projectServers = [];
+  const applicableProjects = [];
+  for (const [projectPath, projectConfig] of Object.entries(claudeJson?.projects ?? {})) {
+    if (!pathApplies2(projectPath, cwd2)) continue;
+    applicableProjects.push([projectPath, projectConfig]);
+    for (const name of Object.keys(projectConfig.mcpServers ?? {})) {
+      projectServers.push({ name, source: "project", path: projectPath });
+    }
+    if (Array.isArray(projectConfig.enabledMcpServers)) {
+      issues.push({
+        severity: projectConfig.enabledMcpServers.length === 0 ? "warn" : "info",
+        code: "enabled-mcp-servers-present",
+        message: `Project ${projectPath} contains enabledMcpServers=${JSON.stringify(projectConfig.enabledMcpServers)}. This key is not the same as enabledMcpjsonServers and has caused confusing /mcp debugging reports.`,
+        fix: "If MCP tools are hidden, back up ~/.claude.json, remove only this key, restart Claude Code, and compare /mcp + ToolSearch."
+      });
+    }
+  }
+  const mcpJsonServers = [];
+  for (const mcpJsonPath of findAncestorMcpJsons2(cwd2, homeDir)) {
+    const mcpJson = readJson(mcpJsonPath);
+    for (const name of Object.keys(mcpJson?.mcpServers ?? {})) {
+      mcpJsonServers.push({ name, source: "mcp.json", path: mcpJsonPath });
+    }
+  }
+  const permissionPrefixes = extractPermissionPrefixes(settings);
+  const permissionPrefixSet = new Set(permissionPrefixes);
+  const allConfiguredServerNames = [...globalServers, ...projectServers.map((s) => s.name), ...mcpJsonServers.map((s) => s.name)];
+  const configuredServers = [...new Set(allConfiguredServerNames)].sort();
+  const nonExeServers = configuredServers.filter((s) => s !== "exe-os" && s !== "exe-mem");
+  const nonExeWithoutPermissions = nonExeServers.filter((s) => !serverAllowedByPermissions(s, permissionPrefixSet));
+  if (nonExeWithoutPermissions.length > 0 && permissionPrefixes.some((p) => p === "exe-os" || p === "exe-mem")) {
+    issues.push({
+      severity: "warn",
+      code: "non-exe-mcp-not-permission-allowlisted",
+      message: `Interactive Claude Code may only surface/auto-run permission-allowed MCP tools. exe-os is allowlisted, but these configured servers are not: ${nonExeWithoutPermissions.join(", ")}.`,
+      fix: "In Claude Code, run /permissions and allow the needed MCP server tools (for example mcp__figma__*), then restart. As a diagnostic only, test ENABLE_TOOL_SEARCH=false claude to compare tool injection."
+    });
+  }
+  const duplicateNames = allConfiguredServerNames.filter((name, index, arr) => arr.indexOf(name) !== index);
+  if (duplicateNames.length > 0) {
+    issues.push({
+      severity: "warn",
+      code: "duplicate-mcp-server-names",
+      message: `Duplicate MCP server names exist across global/project/.mcp.json scopes: ${[...new Set(duplicateNames)].join(", ")}. Claude Code can show Connected while dropping tools when scopes collide.`,
+      fix: "Use one source of truth per MCP server name; remove or rename duplicates."
+    });
+  }
+  for (const server of mcpJsonServers) {
+    for (const [projectPath, projectConfig] of applicableProjects) {
+      if (!projectConfig.mcpServers?.[server.name]) continue;
+      const enabled = new Set(projectConfig.enabledMcpjsonServers ?? []);
+      if (!enabled.has(server.name)) {
+        issues.push({
+          severity: "error",
+          code: "disabled-mcp-json-shadows-project-server",
+          message: `${server.name} appears in ${server.path} and project ${projectPath}, but is not enabled in enabledMcpjsonServers. This can shadow the project server and yield Connected/0 tools.`,
+          fix: "Remove/rename the duplicate .mcp.json entry or enable that .mcp.json server explicitly."
+        });
+      }
+    }
+  }
+  if (env.ENABLE_TOOL_SEARCH && env.ENABLE_TOOL_SEARCH !== "auto") {
+    issues.push({
+      severity: "info",
+      code: "enable-tool-search-env-set",
+      message: `ENABLE_TOOL_SEARCH is set to ${env.ENABLE_TOOL_SEARCH}. This changes Claude Code's deferred tool injection path.`,
+      fix: "For debugging, compare interactive launches with ENABLE_TOOL_SEARCH=false, ENABLE_TOOL_SEARCH=auto, and unset."
+    });
+  }
+  if (configuredServers.length > 8) {
+    issues.push({
+      severity: "info",
+      code: "large-mcp-surface",
+      message: `${configuredServers.length} MCP servers are configured for this project. If pipe mode sees tools but interactive mode does not, reduce scope temporarily or enable only needed servers while debugging Claude Code tool injection.`,
+      fix: "Keep exe-os global, move project/design tools into the active project only, and use /permissions for the servers needed in that session."
+    });
+  }
+  return {
+    cwd: path48.resolve(cwd2),
+    globalServers,
+    projectServers: projectServers.sort((a, b) => a.name.localeCompare(b.name)),
+    mcpJsonServers: mcpJsonServers.sort((a, b) => a.name.localeCompare(b.name)),
+    permissionPrefixes,
+    issues
+  };
+}
+function formatMcpDiagnosticReport(report) {
+  const lines = [];
+  lines.push("Claude MCP Diagnostic");
+  lines.push(`cwd: ${report.cwd}`);
+  lines.push("");
+  lines.push(`global servers: ${report.globalServers.length ? report.globalServers.join(", ") : "none"}`);
+  lines.push(`project servers: ${report.projectServers.length ? report.projectServers.map((s) => `${s.name} (${s.path})`).join(", ") : "none"}`);
+  lines.push(`.mcp.json servers: ${report.mcpJsonServers.length ? report.mcpJsonServers.map((s) => `${s.name} (${s.path})`).join(", ") : "none"}`);
+  lines.push(`permission MCP prefixes: ${report.permissionPrefixes.length ? report.permissionPrefixes.join(", ") : "none"}`);
+  lines.push("");
+  if (report.issues.length === 0) {
+    lines.push("\u2713 No obvious MCP config hazards detected.");
+    return lines.join("\n");
+  }
+  lines.push("Issues / clues:");
+  for (const issue of report.issues) {
+    const icon = issue.severity === "error" ? "\u2717" : issue.severity === "warn" ? "!" : "i";
+    lines.push(`${icon} [${issue.code}] ${issue.message}`);
+    if (issue.fix) lines.push(`  Fix/test: ${issue.fix}`);
+  }
+  return lines.join("\n");
+}
+var init_mcp_diagnostics = __esm({
+  "src/adapters/claude/mcp-diagnostics.ts"() {
+    "use strict";
+  }
+});
+
+// src/bin/cli.ts
+import { existsSync as existsSync35, readFileSync as readFileSync30, writeFileSync as writeFileSync21, readdirSync as readdirSync10, rmSync } from "fs";
+import path49 from "path";
+import os22 from "os";
 var args = process.argv.slice(2);
 if (args.includes("--version") || args.includes("-v")) {
   try {
-    const pkgPath = path48.join(path48.dirname(new URL(import.meta.url).pathname), "..", "..", "package.json");
-    const pkg = JSON.parse(readFileSync29(pkgPath, "utf8"));
+    const pkgPath = path49.join(path49.dirname(new URL(import.meta.url).pathname), "..", "..", "package.json");
+    const pkg = JSON.parse(readFileSync30(pkgPath, "utf8"));
     console.log(pkg.version);
   } catch {
     console.log("unknown");
@@ -31666,6 +31863,17 @@ if (args.includes("--global")) {
     case "check":
       await runClaudeCheck();
       break;
+    case "mcp-doctor":
+      await runClaudeMcpDoctor();
+      break;
+    case "mcp":
+      if (args[2] === "doctor") {
+        await runClaudeMcpDoctor();
+      } else {
+        console.error("Usage: exe-os claude mcp-doctor");
+        process.exit(1);
+      }
+      break;
     case "uninstall":
       await runClaudeUninstall(args.slice(2));
       break;
@@ -31799,11 +32007,11 @@ ID: ${result.id}`);
   });
   await init_App2().then(() => App_exports);
 } else {
-  const claudeDir = path48.join(os21.homedir(), ".claude");
-  const settingsPath = path48.join(claudeDir, "settings.json");
-  const hasClaudeCode = existsSync34(settingsPath) && (() => {
+  const claudeDir = path49.join(os22.homedir(), ".claude");
+  const settingsPath = path49.join(claudeDir, "settings.json");
+  const hasClaudeCode = existsSync35(settingsPath) && (() => {
     try {
-      const raw = readFileSync29(settingsPath, "utf8");
+      const raw = readFileSync30(settingsPath, "utf8");
       return raw.includes("exe-os") || raw.includes("exe-mem");
     } catch {
       return false;
@@ -31813,9 +32021,9 @@ ID: ${result.id}`);
     const { DEFAULT_COORDINATOR_TEMPLATE_NAME: DEFAULT_COORDINATOR_TEMPLATE_NAME2 } = await Promise.resolve().then(() => (init_employees(), employees_exports));
     let cooName = DEFAULT_COORDINATOR_TEMPLATE_NAME2;
     try {
-      const rosterPath = path48.join(os21.homedir(), ".exe-os", "exe-employees.json");
-      if (existsSync34(rosterPath)) {
-        const roster = JSON.parse(readFileSync29(rosterPath, "utf8"));
+      const rosterPath = path49.join(os22.homedir(), ".exe-os", "exe-employees.json");
+      if (existsSync35(rosterPath)) {
+        const roster = JSON.parse(readFileSync30(rosterPath, "utf8"));
         const coo = roster.find((e) => e.role === "COO");
         if (coo) cooName = coo.name;
       }
@@ -31833,6 +32041,7 @@ cd into a project folder and run \x1B[1m${cooName}1\x1B[0m to boot your COO.
   exe-os setup           Re-run setup wizard
   exe-os cloud sync      Sync all data with Exe Cloud
   exe-os claude check    Verify Claude Code integration
+  exe-os claude mcp-doctor  Diagnose Claude MCP tool visibility
   exe-os tui             Launch TUI dashboard (Mode 2)
   exe-os --help          Show all commands
 `);
@@ -31880,14 +32089,14 @@ async function runCodexInstall() {
 }
 async function runClaudeCheck() {
   const { detectMcpNameCollisions: detectMcpNameCollisions2 } = await Promise.resolve().then(() => (init_installer(), installer_exports));
-  const claudeDir = path48.join(os21.homedir(), ".claude");
-  const settingsPath = path48.join(claudeDir, "settings.json");
-  const claudeJsonPath = path48.join(os21.homedir(), ".claude.json");
+  const claudeDir = path49.join(os22.homedir(), ".claude");
+  const settingsPath = path49.join(claudeDir, "settings.json");
+  const claudeJsonPath = path49.join(os22.homedir(), ".claude.json");
   let ok = true;
-  if (existsSync34(settingsPath)) {
+  if (existsSync35(settingsPath)) {
     let settings;
     try {
-      settings = JSON.parse(readFileSync29(settingsPath, "utf8"));
+      settings = JSON.parse(readFileSync30(settingsPath, "utf8"));
     } catch {
       console.log("\x1B[31m\u2717\x1B[0m settings.json is malformed (invalid JSON)");
       ok = false;
@@ -31913,10 +32122,10 @@ async function runClaudeCheck() {
     console.log("\x1B[31m\u2717\x1B[0m settings.json not found");
     ok = false;
   }
-  if (existsSync34(claudeJsonPath)) {
+  if (existsSync35(claudeJsonPath)) {
     let claudeJson;
     try {
-      claudeJson = JSON.parse(readFileSync29(claudeJsonPath, "utf8"));
+      claudeJson = JSON.parse(readFileSync30(claudeJsonPath, "utf8"));
     } catch {
       console.log("\x1B[31m\u2717\x1B[0m claude.json is malformed (invalid JSON)");
       ok = false;
@@ -31935,7 +32144,7 @@ async function runClaudeCheck() {
     console.log("\x1B[31m\u2717\x1B[0m claude.json not found");
     ok = false;
   }
-  const collisions = detectMcpNameCollisions2(os21.homedir(), process.cwd());
+  const collisions = detectMcpNameCollisions2(os22.homedir(), process.cwd());
   const disabledCollisions = collisions.filter((c) => c.disabledInMcpJson);
   if (disabledCollisions.length > 0) {
     console.log("\x1B[31m\u2717\x1B[0m MCP name collision: disabled .mcp.json entries shadow project MCP servers");
@@ -31949,8 +32158,8 @@ async function runClaudeCheck() {
   } else {
     console.log("\x1B[32m\u2713\x1B[0m No .mcp.json/project MCP name collisions detected");
   }
-  const skillsDir = path48.join(claudeDir, "skills");
-  if (existsSync34(skillsDir)) {
+  const skillsDir = path49.join(claudeDir, "skills");
+  if (existsSync35(skillsDir)) {
     console.log("\x1B[32m\u2713\x1B[0m Slash skills directory exists");
   } else {
     console.log("\x1B[31m\u2717\x1B[0m Slash skills directory missing");
@@ -31963,20 +32172,27 @@ async function runClaudeCheck() {
     console.log("\nAll checks passed.");
   }
 }
+async function runClaudeMcpDoctor() {
+  const { diagnoseClaudeMcpConfig: diagnoseClaudeMcpConfig2, formatMcpDiagnosticReport: formatMcpDiagnosticReport2 } = await Promise.resolve().then(() => (init_mcp_diagnostics(), mcp_diagnostics_exports));
+  const report = diagnoseClaudeMcpConfig2(os22.homedir(), process.cwd(), process.env);
+  console.log(formatMcpDiagnosticReport2(report));
+  const hasError = report.issues.some((issue) => issue.severity === "error");
+  process.exit(hasError ? 1 : 0);
+}
 async function runClaudeUninstall(flags = []) {
   const dryRun = flags.includes("--dry-run");
   const purge = flags.includes("--purge");
-  const homeDir = os21.homedir();
-  const claudeDir = path48.join(homeDir, ".claude");
-  const settingsPath = path48.join(claudeDir, "settings.json");
-  const claudeJsonPath = path48.join(homeDir, ".claude.json");
-  const exeOsDir = path48.join(homeDir, ".exe-os");
+  const homeDir = os22.homedir();
+  const claudeDir = path49.join(homeDir, ".claude");
+  const settingsPath = path49.join(claudeDir, "settings.json");
+  const claudeJsonPath = path49.join(homeDir, ".claude.json");
+  const exeOsDir = path49.join(homeDir, ".exe-os");
   let removed = 0;
   const log = (msg) => console.log(dryRun ? `[dry-run] ${msg}` : msg);
   let settings = {};
-  if (existsSync34(settingsPath)) {
+  if (existsSync35(settingsPath)) {
     try {
-      settings = JSON.parse(readFileSync29(settingsPath, "utf8"));
+      settings = JSON.parse(readFileSync30(settingsPath, "utf8"));
     } catch {
       console.error("Your ~/.claude/settings.json appears malformed.");
       if (purge) {
@@ -32021,8 +32237,8 @@ async function runClaudeUninstall(flags = []) {
       removed++;
     }
   }
-  if (existsSync34(claudeJsonPath)) {
-    const raw = readFileSync29(claudeJsonPath, "utf8");
+  if (existsSync35(claudeJsonPath)) {
+    const raw = readFileSync30(claudeJsonPath, "utf8");
     if (raw.length > 1e6) {
       console.error("claude.json exceeds 1 MB \u2014 skipping parse.");
     } else {
@@ -32051,14 +32267,14 @@ async function runClaudeUninstall(flags = []) {
       }
     }
   }
-  const skillsDir = path48.join(claudeDir, "skills");
-  if (existsSync34(skillsDir)) {
+  const skillsDir = path49.join(claudeDir, "skills");
+  if (existsSync35(skillsDir)) {
     let skillCount = 0;
     try {
       const entries = readdirSync10(skillsDir);
       for (const entry of entries) {
         if (entry.startsWith("exe")) {
-          const fullPath = path48.join(skillsDir, entry);
+          const fullPath = path49.join(skillsDir, entry);
           if (!dryRun) rmSync(fullPath, { recursive: true, force: true });
           skillCount++;
         }
@@ -32070,9 +32286,9 @@ async function runClaudeUninstall(flags = []) {
       removed++;
     }
   }
-  const claudeMdPath = path48.join(claudeDir, "CLAUDE.md");
-  if (existsSync34(claudeMdPath)) {
-    const content = readFileSync29(claudeMdPath, "utf8");
+  const claudeMdPath = path49.join(claudeDir, "CLAUDE.md");
+  if (existsSync35(claudeMdPath)) {
+    const content = readFileSync30(claudeMdPath, "utf8");
     const startMarker = "<!-- exe-os:orchestration-start -->";
     const endMarker = "<!-- exe-os:orchestration-end -->";
     const startIdx = content.indexOf(startMarker);
@@ -32084,16 +32300,16 @@ async function runClaudeUninstall(flags = []) {
       removed++;
     }
   }
-  const agentsDir = path48.join(claudeDir, "agents");
-  if (existsSync34(agentsDir)) {
+  const agentsDir = path49.join(claudeDir, "agents");
+  if (existsSync35(agentsDir)) {
     let agentCount = 0;
     try {
       const entries = readdirSync10(agentsDir).filter((f) => f.endsWith(".md"));
       let knownNames = /* @__PURE__ */ new Set();
-      const rosterPath = path48.join(exeOsDir, "exe-employees.json");
-      if (existsSync34(rosterPath)) {
+      const rosterPath = path49.join(exeOsDir, "exe-employees.json");
+      if (existsSync35(rosterPath)) {
         try {
-          const roster = JSON.parse(readFileSync29(rosterPath, "utf8"));
+          const roster = JSON.parse(readFileSync30(rosterPath, "utf8"));
           knownNames = new Set(roster.map((e) => e.name));
         } catch {
         }
@@ -32101,7 +32317,7 @@ async function runClaudeUninstall(flags = []) {
       for (const entry of entries) {
         const name = entry.replace(/\.md$/, "");
         if (knownNames.has(name)) {
-          if (!dryRun) rmSync(path48.join(agentsDir, entry), { force: true });
+          if (!dryRun) rmSync(path49.join(agentsDir, entry), { force: true });
           agentCount++;
         }
       }
@@ -32112,16 +32328,16 @@ async function runClaudeUninstall(flags = []) {
       removed++;
     }
   }
-  const projectsDir = path48.join(claudeDir, "projects");
-  if (existsSync34(projectsDir)) {
+  const projectsDir = path49.join(claudeDir, "projects");
+  if (existsSync35(projectsDir)) {
     let projectCount = 0;
     try {
       const projects = readdirSync10(projectsDir);
       for (const proj of projects) {
-        const projSettings = path48.join(projectsDir, proj, "settings.json");
-        if (!existsSync34(projSettings)) continue;
+        const projSettings = path49.join(projectsDir, proj, "settings.json");
+        if (!existsSync35(projSettings)) continue;
         try {
-          const pSettings = JSON.parse(readFileSync29(projSettings, "utf8"));
+          const pSettings = JSON.parse(readFileSync30(projSettings, "utf8"));
           let changed = false;
           if (Array.isArray(pSettings.permissions?.allow)) {
             const before = pSettings.permissions.allow.length;
@@ -32155,18 +32371,18 @@ async function runClaudeUninstall(flags = []) {
     };
     const exeBinPath = findExeBin3();
     if (!exeBinPath) throw new Error("exe-os not found in PATH");
-    const binDir = path48.dirname(exeBinPath);
+    const binDir = path49.dirname(exeBinPath);
     let symlinkCount = 0;
-    const rosterPath = path48.join(exeOsDir, "exe-employees.json");
-    if (existsSync34(rosterPath)) {
-      const roster = JSON.parse(readFileSync29(rosterPath, "utf8"));
+    const rosterPath = path49.join(exeOsDir, "exe-employees.json");
+    if (existsSync35(rosterPath)) {
+      const roster = JSON.parse(readFileSync30(rosterPath, "utf8"));
       const { DEFAULT_COORDINATOR_TEMPLATE_NAME: DEFAULT_COORDINATOR_TEMPLATE_NAME2 } = await Promise.resolve().then(() => (init_employees(), employees_exports));
       const coordinatorName = roster.find((e) => e.role?.toLowerCase() === "coo")?.name ?? DEFAULT_COORDINATOR_TEMPLATE_NAME2;
       for (const emp of roster) {
         if (emp.name === coordinatorName) continue;
         for (const suffix of ["", "-opencode"]) {
-          const linkPath = path48.join(binDir, `${emp.name}${suffix}`);
-          if (existsSync34(linkPath)) {
+          const linkPath = path49.join(binDir, `${emp.name}${suffix}`);
+          if (existsSync35(linkPath)) {
             if (!dryRun) rmSync(linkPath, { force: true });
             symlinkCount++;
           }
@@ -32179,7 +32395,7 @@ async function runClaudeUninstall(flags = []) {
     }
   } catch {
   }
-  if (purge && existsSync34(exeOsDir)) {
+  if (purge && existsSync35(exeOsDir)) {
     if (!dryRun) {
       process.stdout.write("\x1B[33m\u26A0 This will delete all memories, identities, and agent data.\x1B[0m\n");
       process.stdout.write("  Removing ~/.exe-os...\n");
@@ -32204,13 +32420,13 @@ async function checkForUpdateOnBoot() {
     const config = await loadConfig2();
     if (!config.autoUpdate.checkOnBoot) return;
     const { checkForUpdate: checkForUpdate2 } = await Promise.resolve().then(() => (init_update(), update_exports));
-    const packageRoot = path48.resolve(
+    const packageRoot = path49.resolve(
       new URL("../..", import.meta.url).pathname
     );
     const result = checkForUpdate2(packageRoot);
     if (result.updateAvailable) {
       process.stderr.write(
-        `\x1B[33m[update]\x1B[0m exe-os v${result.remoteVersion} available (current: v${result.localVersion}). Run \x1B[36mnpm update -g @askexenow/exe-os\x1B[0m to upgrade.
+        `\x1B[33m[update]\x1B[0m exe-os v${result.remoteVersion} available (current: v${result.localVersion}). Run \x1B[36mexe-os update\x1B[0m to upgrade.
 `
       );
     }
@@ -32265,7 +32481,7 @@ async function runActivate(key) {
       const idTemplate = getIdentityTemplate(identityKey);
       if (idTemplate) {
         const idPath = identityPath2(name);
-        const dir = path48.dirname(idPath);
+        const dir = path49.dirname(idPath);
         if (!fs8.existsSync(dir)) fs8.mkdirSync(dir, { recursive: true });
         fs8.writeFileSync(idPath, idTemplate.replace(/^agent_id: \w+/m, `agent_id: ${name}`), "utf-8");
       }

package/dist/bin/update.js

@@ -901,7 +901,20 @@ async function runUpdate(cliArgs) {
     } catch {
     }
   }
-  console.log("   Hooks re-wired, daemon restarted automatically.");
+  console.log("\u{1F527} Re-registering MCP, hooks, wrappers, and daemon...");
+  try {
+    execSync2("exe-os-install --global", {
+      stdio: ["pipe", "inherit", "inherit"],
+      timeout: 3e5
+    });
+  } catch (err) {
+    console.error("\n\u26A0\uFE0F  Package updated, but post-update install failed.");
+    console.error("   Run manually: exe-os-install --global");
+    if (err instanceof Error && err.message) {
+      console.error(`   Error: ${err.message.split("\n")[0]}`);
+    }
+  }
+  console.log("   MCP, hooks, and daemon refreshed.");
   console.log("");
   console.log("   \x1B[33m\u26A1 Run /mcp in each active Claude Code session to pick up new tools.\x1B[0m");
   console.log("   \x1B[2m(MCP servers can't hot-reload \u2014 Claude Code needs to reconnect them.)\x1B[0m");

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@askexenow/exe-os",
-  "version": "0.9.48",
+  "version": "0.9.51",
   "description": "AI employee operating system — persistent memory, task management, and multi-agent coordination for Claude Code.",
   "license": "SEE LICENSE IN LICENSE",
   "type": "module",