@mutagent/cli 0.1.265 → 0.1.267

package/dist/bin/cli.js

@@ -886,7 +886,7 @@ var init_sdk_client = __esm(() => {
 import { Command as Command14 } from "commander";
 import chalk25 from "chalk";
 import { readFileSync as readFileSync12 } from "fs";
-import { join as join15, dirname as dirname4 } from "path";
+import { join as join14, dirname as dirname4 } from "path";
 import { fileURLToPath as fileURLToPath2 } from "url";
 
 // src/commands/auth.ts
@@ -895,7 +895,7 @@ init_sdk_client();
 import { Command } from "commander";
 import chalk4 from "chalk";
 import { existsSync as existsSync5 } from "fs";
-import { join as join7 } from "path";
+import { join as join6 } from "path";
 
 // src/lib/output.ts
 import chalk from "chalk";
@@ -1133,10 +1133,6 @@ function scaffoldRcConfig(cwd = process.cwd(), deps = {}) {
 // src/lib/installer.ts
 init_errors();
 init_config();
-import { spawn as spawn2 } from "child_process";
-import { mkdirSync as mkdirSync3, readdirSync } from "fs";
-import { homedir as homedir3 } from "os";
-import { join as join6 } from "path";
 
 // src/lib/installer-helix.ts
 init_errors();
@@ -1363,61 +1359,15 @@ function safeRm(path) {
 }
 
 // src/lib/installer.ts
-var VALID_PACKAGES = ["helix", "diagnostics", "evaluator"];
-var VALID_HARNESSES = ["claude-code", "codex", "omp"];
-var VERSION_MATRIX = {
-  helix: "latest",
-  diagnostics: "latest",
-  evaluator: "latest"
-};
-var NPM_PACKAGES = {
+var VALID_PACKAGES = ["helix"];
+var RETIRED_PACKAGES = {
   diagnostics: "@mutagent/diagnostics",
   evaluator: "@mutagent/evaluator"
 };
-var INIT_BINS = {
-  diagnostics: "mutagent-diagnostics",
-  evaluator: "mutagent-evaluator"
+var VALID_HARNESSES = ["claude-code", "codex", "omp"];
+var VERSION_MATRIX = {
+  helix: "latest"
 };
-var defaultRunner = (cmd, args) => new Promise((resolve, reject) => {
-  const child = spawn2(cmd, args, { stdio: ["ignore", "pipe", "pipe"] });
-  let stdout = "";
-  let stderr = "";
-  child.stdout.on("data", (chunk) => {
-    stdout += chunk.toString("utf-8");
-  });
-  child.stderr.on("data", (chunk) => {
-    stderr += chunk.toString("utf-8");
-  });
-  child.on("error", (err) => {
-    reject(new MutagentError("INSTALL_FAILED", `Failed to run ${cmd}: ${err.message}`, `Ensure "${cmd}" is installed and available on your PATH.`));
-  });
-  child.on("close", (code) => {
-    resolve({ code: code ?? 1, stdout, stderr });
-  });
-});
-function countProjectFiles(root) {
-  const roots = [".claude", ".codex", ".agents"];
-  let n = 0;
-  const walk = (dir, depth) => {
-    if (depth > 6)
-      return;
-    let entries;
-    try {
-      entries = readdirSync(dir, { withFileTypes: true });
-    } catch {
-      return;
-    }
-    for (const e of entries) {
-      if (e.isDirectory())
-        walk(join6(dir, e.name), depth + 1);
-      else
-        n++;
-    }
-  };
-  for (const r of roots)
-    walk(join6(root, r), 0);
-  return n;
-}
 function isValidPackage(pkg) {
   return VALID_PACKAGES.includes(pkg);
 }
@@ -1425,6 +1375,10 @@ function isValidHarness(harness) {
   return VALID_HARNESSES.includes(harness);
 }
 async function installPackage(pkg, opts, deps = {}) {
+  const retiredNpmName = RETIRED_PACKAGES[pkg];
+  if (retiredNpmName !== undefined) {
+    throw new MutagentError("INVALID_ARGUMENTS", `"${pkg}" is no longer an install target — ${retiredNpmName} is no longer published.`, `The ${pkg} skill now ships inside helix. Run: mutagent install helix`);
+  }
   const isAuthed = deps.isAuthed ?? hasCredentials;
   if (!isAuthed()) {
     throw new MutagentError("AUTH_REQUIRED", `Authentication required to install ${pkg}.`, "Run: mutagent login");
@@ -1446,44 +1400,24 @@ async function installPackage(pkg, opts, deps = {}) {
     throw new MutagentError("INVALID_ARGUMENTS", `Unknown harness "${opts.harness}". Valid: ${VALID_HARNESSES.join(", ")}`, "Run: mutagent install --help");
   }
   const version = opts.version ?? VERSION_MATRIX[pkg];
-  if (pkg === "helix") {
-    const { version: resolved } = await installHelix({ harness: opts.harness, version }, deps.helix ?? {});
-    return finish({
-      package: pkg,
-      version: resolved,
-      harness: opts.harness,
-      scope: "project",
-      projectPath,
-      skillInstalled: true
-    }, deps);
-  }
-  const npmPackage = NPM_PACKAGES[pkg];
-  const installRoot = join6(deps.homeDir ?? join6(homedir3(), ".mutagent", pkg), version);
-  mkdirSync3(installRoot, { recursive: true });
-  const args = ["install", "--prefix", installRoot, "--no-save", `${npmPackage}@${version}`];
-  const runner = deps.runner ?? defaultRunner;
-  const result = await runner("npm", args);
-  if (result.code !== 0) {
-    const detail = result.stderr.trim();
-    throw new MutagentError("INSTALL_FAILED", `npm failed to install ${npmPackage}@${version} (exit ${String(result.code)}).${detail ? ` ${detail.slice(0, 200)}` : ""}`, `Verify the package and version exist, and that ${installRoot} is writable.`);
-  }
-  const pkgDir = join6(installRoot, "node_modules", npmPackage);
-  const initBin = await (deps.locateInitBin ?? defaultLocateInitBin)(pkgDir);
-  const countFiles = deps.countProjectFiles ?? countProjectFiles;
-  const before = countFiles(projectPath);
-  const initCode = await (deps.runInit ?? defaultRunInit)(initBin, ["init", "--yes"], projectPath);
-  const landed = countFiles(projectPath) > before;
-  return finish({
-    package: pkg,
-    version,
-    harness: opts.harness,
-    scope: "project",
-    projectPath,
-    installRoot,
-    skillInstalled: initCode === 0 && landed,
-    ...initCode === 0 && landed ? {} : { nextStep: `${INIT_BINS[pkg]} init` },
-    command: `npm ${args.join(" ")}`
-  }, deps);
+  switch (pkg) {
+    case "helix": {
+      const { version: resolved } = await installHelix({ harness: opts.harness, version }, deps.helix ?? {});
+      return finish({
+        package: pkg,
+        version: resolved,
+        harness: opts.harness,
+        scope: "project",
+        projectPath,
+        skillInstalled: true
+      }, deps);
+    }
+    default:
+      return assertNoInstallPath(pkg);
+  }
+}
+function assertNoInstallPath(pkg) {
+  throw new MutagentError("INVALID_ARGUMENTS", `No install path is implemented for "${String(pkg)}".`, "Run: mutagent install --help");
 }
 async function finish(result, deps) {
   await reportInstall({ pkg: result.package, version: result.version, harness: result.harness }, deps.telemetry ?? {});
@@ -1981,7 +1915,7 @@ Examples:
     }
     const isValid = await validateApiKey(apiKey, endpoint);
     const cwd = process.cwd();
-    const hasOnboarding = existsSync5(join7(cwd, ".mutagentrc.json"));
+    const hasOnboarding = existsSync5(join6(cwd, ".mutagentrc.json"));
     if (isJson) {
       const statusResult = {
         authenticated: isValid,
@@ -3370,14 +3304,14 @@ init_config();
 import { Command as Command7 } from "commander";
 import chalk13 from "chalk";
 import { readFileSync as readFileSync5 } from "fs";
-import { join as join9 } from "path";
+import { join as join8 } from "path";
 init_errors();
 
 // src/commands/skills.ts
 import { Command as Command6 } from "commander";
 import chalk12 from "chalk";
-import { existsSync as existsSync6, mkdirSync as mkdirSync4, writeFileSync as writeFileSync4 } from "fs";
-import { dirname, join as join8 } from "path";
+import { existsSync as existsSync6, mkdirSync as mkdirSync3, writeFileSync as writeFileSync4 } from "fs";
+import { dirname, join as join7 } from "path";
 import { execSync } from "child_process";
 
 // src/generated/skill-content.ts
@@ -3387,7 +3321,7 @@ name: mutagent-cli
 description: |
   Mutagent CLI - the command-line client for the Mutagent platform.
   Guides coding agents through setup (login, init, providers, workspaces),
-  installing Mutagent packages (helix, diagnostics, evaluator), and sending
+  installing Mutagent packages (helix), and sending
   product feedback.
   Triggers: "mutagent", "mutagent cli", "mutagent login", "set up mutagent",
   "install diagnostics", "install evaluator", "install helix", "mutagent install",
@@ -3520,7 +3454,7 @@ skill never inlines flags. The active surface:
 | \`usage\` | Show usage + quota | [workflows/setup.md](./workflows/setup.md) |
 | \`skills install\` | Install this skill into a project | [workflows/setup.md](./workflows/setup.md) |
 | \`hooks install\` | Install Claude Code telemetry hooks | [workflows/setup.md](./workflows/setup.md) |
-| \`install <pkg>\` | Install helix / diagnostics / evaluator | [workflows/install.md](./workflows/install.md) |
+| \`install <pkg>\` | Install helix (diagnostics / evaluator are retired) | [workflows/install.md](./workflows/install.md) |
 | \`feedback send\` | Send product feedback | [workflows/feedback.md](./workflows/feedback.md) |
 
 ---
@@ -3542,7 +3476,7 @@ Match the user's first request. Load ONLY the matching subfile per the table. Do
 | User said / signal detected | Load subfile | Why |
 |---|---|---|
 | "log in", "authenticate", "set up mutagent", "init", "which workspace", "what models", "usage", "quota", "install the skill", "install hooks" | [workflows/setup.md](./workflows/setup.md) | Auth + project setup + discovery commands |
-| "install helix", "install diagnostics", "install evaluator", "add mutagent package" | [workflows/install.md](./workflows/install.md) | Login-gated meta-installer |
+| "install helix", "install diagnostics", "install evaluator", "add mutagent package" | [workflows/install.md](./workflows/install.md) | Login-gated meta-installer (diagnostics/evaluator are retired → helix) |
 | "send feedback", "report a bug", "file feedback", "the CLI crashed" | [workflows/feedback.md](./workflows/feedback.md) | Product feedback (+ optional transcript) |
 | Unclear / first time | run \`mutagent --help --json\` then reroute | Discover the surface before acting |
 
@@ -3553,7 +3487,7 @@ Match the user's first request. Load ONLY the matching subfile per the table. Do
 | File | WHEN to load | WHY |
 |---|---|---|
 | [workflows/setup.md](./workflows/setup.md) | User is onboarding: login, init, config, workspaces, providers, usage, skill/hooks install | Auth + configuration + discovery |
-| [workflows/install.md](./workflows/install.md) | User wants to install a Mutagent package | \`install <helix\\|diagnostics\\|evaluator>\` meta-command |
+| [workflows/install.md](./workflows/install.md) | User wants to install a Mutagent package | \`install helix\` meta-command |
 | [workflows/feedback.md](./workflows/feedback.md) | User wants to send feedback or report a bug | \`feedback send\` + \`--attach-transcript\` |
 
 ---
@@ -3775,33 +3709,33 @@ how they learn something sensitive was in the file at all.
   "workflows/install.md": `---
 name: mutagent-cli-workflows-install
 description: |
-  Meta-installer workflow. Installs a Mutagent package (helix, diagnostics, or
-  evaluator) into the user's environment via \`mutagent install <package>\`.
-  Login-gated. diagnostics/evaluator come from public npm; helix is fetched
-  from a private registry via a login-brokered signed URL (no static secret).
+  Meta-installer workflow. Installs helix into the user's environment via
+  \`mutagent install helix\`. Login-gated. helix is fetched from a private
+  registry via a login-brokered signed URL (no static secret ships in the CLI).
+  \`diagnostics\` and \`evaluator\` are RETIRED as install targets — both skills
+  now ship inside helix.
 triggers:
-  - "install diagnostics"
-  - "install evaluator"
   - "install helix"
   - "mutagent install"
   - "add mutagent package"
+  - "install diagnostics"
+  - "install evaluator"
   - "set up diagnostics"
   - "set up evaluator"
 ---
 
 # Workflow — Install (Meta-Installer)
 
-> **Scope differs by package** — read \`scope\` in the response, never assume:
-> - \`helix\` → installed into the CURRENT project directory (\`scope: "project"\`).
-> - \`diagnostics\` / \`evaluator\` → **npm installs the package GLOBALLY**
->   (\`scope: "global"\`, literally \`npm install -g\`). It does NOT go in the
->   user's project. Its skill init is the part you later run in the project.
+> **\`helix\` is the only install target.** It installs into the CURRENT project
+> directory (\`scope: "project"\`).
 >
-> This WRITES to the user's machine — confirm before running (Core Rule 5).
+> \`diagnostics\` and \`evaluator\` are **retired** — their npm packages are no
+> longer published. Both skills ship *inside* the helix payload, so a user
+> asking for either one needs \`mutagent install helix\`. The CLI says so itself:
+> \`mutagent install diagnostics\` fails with \`INVALID_ARGUMENTS\` and names helix
+> as the route. Do not work around that error — follow it.
 >
-> **\`success: true\` does NOT mean the user is ready to go.** For \`diagnostics\`
-> and \`evaluator\` it means the npm package landed; the skill still needs the
-> package's own init. Branch on \`skillInstalled\` — see *Output handling* below.
+> This WRITES to the user's machine — confirm before running (Core Rule 5).
 
 Read the **Core Rules** in [SKILL.md](../SKILL.md) first. Key reminders:
 - \`--json\` on every command
@@ -3816,23 +3750,28 @@ Read the **Core Rules** in [SKILL.md](../SKILL.md) first. Key reminders:
 \`\`\`bash
 mutagent install --help    # authoritative flags — read before first use
 
-mutagent install <package> [--harness <claude-code|codex|omp>] \\
-                           [--version <v>] [--json]
+mutagent install helix [--harness <claude-code|codex|omp>] \\
+                       [--version <v>] [--json]
 \`\`\`
 
-Where \`<package>\` is one of:
+Where \`<package>\` is:
 
 | Package | Source | Notes |
 |---|---|---|
-| \`diagnostics\` | public npm \`@mutagent/diagnostics\` | Ready to install |
-| \`evaluator\` | public npm \`@mutagent/evaluator\` | Ready to install |
-| \`helix\` | private registry via login-brokered signed URL | Ready to install — login-gated download, sha256-verified, then initialized into your project |
+| \`helix\` | private registry via login-brokered signed URL | Ready to install — login-gated download, sha256-verified, then initialized into your project. Carries the diagnostics + evaluator skills and the \`mutagent-cli\` binary. |
+
+Retired — these are rejected by name, they do not fall through to a generic error:
+
+| Retired target | Was | Use instead |
+|---|---|---|
+| \`diagnostics\` | public npm \`@mutagent/diagnostics\` | \`mutagent install helix\` |
+| \`evaluator\` | public npm \`@mutagent/evaluator\` | \`mutagent install helix\` |
 
 **Flags** (verify against \`--help\`):
-- \`--harness <claude-code|codex|omp>\` -- target coding-agent harness (default \`claude-code\`).
-- Install scope is FIXED PER PACKAGE and is not selectable: \`helix\` installs into the current directory; \`diagnostics\`/\`evaluator\` are installed GLOBALLY by npm. \`--global\` is retired: passing it fails and explains both paths.
+- \`--harness <claude-code|codex|omp>\` -- target coding-agent harness (default \`claude-code\`). helix installs every harness itself, so this does not change what lands.
 - \`--version <v>\` -- pin a specific version (default: latest).
 - \`--json\` -- structured output (Rule 1).
+- Install scope is NOT selectable: helix installs into the current directory. \`--global\` is retired — passing it fails and explains what happens instead.
 
 ---
 
@@ -3847,23 +3786,17 @@ Where \`<package>\` is one of:
    → read the current packages + flags (Rule 2)
 
 3. Confirm with the user WHAT will be installed and WHERE
-   → state the REAL destination for the package being installed, e.g.
-      helix:        "I'll install helix into <current directory>. Proceed?"
-      diagnostics:  "I'll install @mutagent/diagnostics GLOBALLY via npm, then
-                     you'll run its init inside your project. Proceed?"
+   → "I'll install helix into <current directory>. Proceed?"
 
-4. mutagent install <package> [--harness <h>] [--version <v>] --json
+4. mutagent install helix [--harness <h>] [--version <v>] --json
    → run the install
-   → show the command output to the user: package, version, harness, and
-      \`scope\`. Surface \`projectPath\` ONLY when \`scope\` is \`"project"\` — it is
-      ABSENT from the response on the global npm path.
+   → show the output: package, version, harness, scope, and projectPath
 
 5. CHECK \`skillInstalled\` in the JSON response — do NOT stop at \`success: true\`
    → skillInstalled === true  → done; the skill is installed and usable
-   → skillInstalled === false → NOT done. Tell the user plainly that the npm
-      package is installed but the skill is not, then surface \`nextStep\`
-      (e.g. \`mutagent-diagnostics init\`) as the command to run next.
-      Confirm before running it — it writes to their project (Core Rule 5).
+   → skillInstalled === false → NOT done. Say so plainly and surface \`nextStep\`
+      as the command to run next. Confirm before running it — it writes to
+      their project (Core Rule 5).
 \`\`\`
 
 ---
@@ -3873,9 +3806,7 @@ Where \`<package>\` is one of:
 \`\`\`bash
 mutagent install helix --json
 mutagent install helix --harness codex --json
-mutagent install diagnostics --json
-mutagent install evaluator --version 1.2.3 --json
-mutagent install diagnostics --harness codex --json
+mutagent install helix --version 1.2.3 --json
 \`\`\`
 
 ---
@@ -3887,39 +3818,33 @@ Success shape:
 \`\`\`json
 {
   "success": true,
-  "package": "diagnostics",
-  "version": "1.2.3",
+  "package": "helix",
+  "version": "0.1.0-alpha.25",
   "harness": "claude-code",
-  "scope": "global",
-  "skillInstalled": false,
-  "nextStep": "mutagent-diagnostics init",
+  "scope": "project",
+  "projectPath": "/path/to/the/users/project",
+  "skillInstalled": true,
   "_links": { "install": "...", "login": "..." }
 }
 \`\`\`
 
-\`helix\` instead returns \`"scope": "project"\` with \`"projectPath"\`, and
-\`"skillInstalled": true\`.
-
 - **\`skillInstalled\` is the field to branch on — NOT \`success\`.** \`success: true\`
   reports that the install step did its job, not that the user is ready.
-  \`nextStep\` is present only when work remains.
-- \`skillInstalled: false\` (npm packages — \`diagnostics\`, \`evaluator\`): the npm
-  package is installed; the harness skill is **not**. Say so explicitly and give
-  the user \`nextStep\`. Reporting only "installed" here is a known past defect —
-  users were told a skill had landed when none had.
-- \`skillInstalled: true\` (\`helix\`): the CLI resolved a signed download URL from
-  the login broker, downloaded + sha256-verified the plugin, and ran its init
-  into the project. Nothing further is needed. An \`INTEGRITY_ERROR\` means the
-  download failed checksum verification — retry.
-- **\`scope\` tells you WHERE it went. Read it; do not assume.**
-  - \`"global"\` (\`diagnostics\`, \`evaluator\`) — npm installed the package into its
-    GLOBAL root (\`npm install -g\`). The package is **not** in the user's project;
-    never tell the user it is. No path is reported — run \`npm root -g\` if the
-    user needs the directory.
-  - \`"project"\` (\`helix\`) — installed into \`projectPath\`. Surface it so the user
-    can confirm the location.
+  \`nextStep\` is present only when work remains; on a completed helix install it
+  is absent.
+- \`skillInstalled: true\`: the CLI resolved a signed download URL from the login
+  broker, downloaded + sha256-verified the plugin, and ran its init into the
+  project. Nothing further is needed. An \`INTEGRITY_ERROR\` means the download
+  failed checksum verification — retry.
+- **\`scope\` tells you WHERE it went. Read it; do not assume.** It is \`"project"\`,
+  and \`projectPath\` is the directory. Surface it so the user can confirm the
+  location.
 - On an auth error (including a broker \`AUTH_REQUIRED\`): route to the login
   workflow, then retry.
+- On \`INVALID_ARGUMENTS\` naming a retired target (\`diagnostics\`, \`evaluator\`):
+  the package is gone from npm and the skill ships inside helix. Tell the user
+  that, then offer \`mutagent install helix\`. Do NOT suggest \`npm install
+  @mutagent/diagnostics\` as a fallback — it will 404.
 - On \`INVALID_ARGUMENTS\` naming \`--global\`: the flag is retired. Re-run without
   it, or \`cd\` to the intended project first — the error names the path that
   would have been used.
@@ -3928,16 +3853,17 @@ Success shape:
 
 ## Common pitfalls
 
-- **Treating \`success: true\` as "the user is ready".** For \`diagnostics\` and
-  \`evaluator\` it is not — check \`skillInstalled\` and surface \`nextStep\`. Stopping
-  at \`success\` leaves the user with a package and no skill, believing it works.
-- **Telling the user a globally-installed package is in their project.**
-  \`diagnostics\` and \`evaluator\` install globally (\`npm install -g\`). Report the
-  location from \`scope\`, never from the directory you ran in.
+- **Telling the user to \`npm install @mutagent/diagnostics\` or
+  \`@mutagent/evaluator\`.** Both are unpublished; the install 404s. The skills
+  are inside helix.
+- **Treating a retired-target error as a typo.** \`mutagent install diagnostics\`
+  is a command that used to work. The user is not confused about spelling —
+  they want diagnostics. Route them to helix, which has it.
+- **Treating \`success: true\` as "the user is ready".** Check \`skillInstalled\`.
 - Running before login → auth error (install is login-gated).
 - Assuming \`helix\` installs from public npm — it is fetched from a private registry via a login-brokered signed URL (the CLI holds no static secret).
 - Installing without confirming with the user first (Core Rule 5).
-- Passing \`--global\` — retired; scope is fixed per package and is not selectable.
+- Passing \`--global\` — retired; scope is not selectable.
 
 ---
 
@@ -4121,7 +4047,7 @@ function getSkillFiles() {
 }
 function installCliSkill(targetRoot) {
   const files = getSkillFiles();
-  const skillDir = join8(targetRoot, SKILL_DIR);
+  const skillDir = join7(targetRoot, SKILL_DIR);
   const writtenFiles = [];
   let totalBytes = 0;
   const sortedKeys = Object.keys(files).sort((a, b) => {
@@ -4132,10 +4058,10 @@ function installCliSkill(targetRoot) {
     return a.localeCompare(b);
   });
   for (const relPath of sortedKeys) {
-    const destPath = join8(skillDir, relPath);
+    const destPath = join7(skillDir, relPath);
     const parentDir = dirname(destPath);
     if (!existsSync6(parentDir)) {
-      mkdirSync4(parentDir, { recursive: true });
+      mkdirSync3(parentDir, { recursive: true });
     }
     const raw = files[relPath] ?? "";
     const finalContent = raw.endsWith(`
@@ -4226,7 +4152,7 @@ What it does:
       let rcConfig;
       if (rcExists) {
         try {
-          rcConfig = JSON.parse(readFileSync5(join9(cwd, ".mutagentrc.json"), "utf-8"));
+          rcConfig = JSON.parse(readFileSync5(join8(cwd, ".mutagentrc.json"), "utf-8"));
         } catch {
           rcConfig = {};
         }
@@ -4298,8 +4224,6 @@ What it does:
         console.log("");
         console.log(chalk13.bold(`  What's next:`));
         console.log(`    ${chalk13.cyan("mutagent install helix".padEnd(30))}${chalk13.dim("# the ADL lifecycle conductor")}`);
-        console.log(`    ${chalk13.cyan("mutagent install diagnostics".padEnd(30))}${chalk13.dim("# trace diagnosis (optional)")}`);
-        console.log(`    ${chalk13.cyan("mutagent install evaluator".padEnd(30))}${chalk13.dim("# eval mining + judging (optional)")}`);
         console.log("");
         console.log(chalk13.dim("  Your coding agent now knows these workflows — restart it to pick up"));
         console.log(chalk13.dim('  the skill, then just say "set up Mutagent on this project".'));
@@ -4522,10 +4446,10 @@ import { randomUUID } from "crypto";
 
 // src/commands/hooks/state.ts
 import { readFileSync as readFileSync6, writeFileSync as writeFileSync5, renameSync as renameSync2, unlinkSync, existsSync as existsSync7 } from "fs";
-import { join as join10 } from "path";
+import { join as join9 } from "path";
 import { tmpdir } from "os";
 function stateFilePath(sessionId) {
-  return join10(tmpdir(), `mutagent-hook-${sessionId}.json`);
+  return join9(tmpdir(), `mutagent-hook-${sessionId}.json`);
 }
 function readState(sessionId) {
   const path = stateFilePath(sessionId);
@@ -5156,8 +5080,8 @@ async function handlePostToolUseFailure() {
 }
 
 // src/commands/hooks/install.ts
-import { readFileSync as readFileSync7, writeFileSync as writeFileSync6, existsSync as existsSync8, mkdirSync as mkdirSync5 } from "fs";
-import { join as join11 } from "path";
+import { readFileSync as readFileSync7, writeFileSync as writeFileSync6, existsSync as existsSync8, mkdirSync as mkdirSync4 } from "fs";
+import { join as join10 } from "path";
 
 class SettingsParseError extends Error {
   settingsPath;
@@ -5219,8 +5143,8 @@ function migrateV1Hooks(settings) {
   return migrated;
 }
 function installHooks(cwd) {
-  const claudeDir = join11(cwd, ".claude");
-  const settingsPath = join11(claudeDir, "settings.local.json");
+  const claudeDir = join10(cwd, ".claude");
+  const settingsPath = join10(claudeDir, "settings.local.json");
   const existed = existsSync8(settingsPath);
   let settings = {};
   if (existed) {
@@ -5260,7 +5184,7 @@ function installHooks(cwd) {
   let userWarning;
   if (added.length > 0 || migrated.length > 0) {
     if (!existsSync8(claudeDir)) {
-      mkdirSync5(claudeDir, { recursive: true });
+      mkdirSync4(claudeDir, { recursive: true });
     }
     writeFileSync6(settingsPath, JSON.stringify(settings, null, 2) + `
 `, "utf-8");
@@ -5319,10 +5243,23 @@ Examples:
 AI Agent Directive: use --dry-run first; it reports span counts and any
 unparseable lines without sending anything.
     `).action(async (files, opts) => {
+    const isJson = getJsonFlag(hooks);
+    const report = [];
+    const say = (msg) => {
+      if (!isJson)
+        process.stderr.write(msg);
+    };
     const maxSpans = Number.parseInt(opts.maxSpans ?? "200", 10);
     if (!Number.isFinite(maxSpans) || maxSpans < 1) {
-      process.stderr.write(`[mutagent hooks] --max-spans must be a positive integer
+      if (isJson) {
+        new OutputFormatter("json").output({
+          error: "InvalidOption",
+          message: "--max-spans must be a positive integer"
+        });
+      } else {
+        process.stderr.write(`[mutagent hooks] --max-spans must be a positive integer
 `);
+      }
       process.exitCode = 2;
       return;
     }
@@ -5332,7 +5269,9 @@ unparseable lines without sending anything.
       try {
         raw = readFileSync8(file, "utf8");
       } catch (err) {
-        process.stderr.write(`[mutagent hooks] skipped ${file}: ${err instanceof Error ? err.message : String(err)}
+        const why = err instanceof Error ? err.message : String(err);
+        report.push({ file: basename(file), skipped: why });
+        say(`[mutagent hooks] skipped ${file}: ${why}
 `);
         continue;
       }
@@ -5343,28 +5282,50 @@ unparseable lines without sending anything.
         skipped
       });
       if (trace === null) {
-        process.stderr.write(`[mutagent hooks] ${basename(file)}: no session record, skipped
+        report.push({ file: basename(file), skipped: "no session record" });
+        say(`[mutagent hooks] ${basename(file)}: no session record, skipped
 `);
         continue;
       }
-      process.stderr.write(`[mutagent hooks] ${basename(file)}: ${String(trace.spans.length)} spans` + `${skipped > 0 ? `, ${String(skipped)} unparseable lines` : ""}` + `${ignored > 0 ? `, ${String(ignored)} records ignored` : ""}
+      report.push({
+        file: basename(file),
+        traceId: trace.traceId,
+        ...trace.sessionId !== undefined ? { sessionId: trace.sessionId } : {},
+        spans: trace.spans.length,
+        unparseableLines: skipped,
+        recordsIgnored: ignored
+      });
+      say(`[mutagent hooks] ${basename(file)}: ${String(trace.spans.length)} spans` + `${skipped > 0 ? `, ${String(skipped)} unparseable lines` : ""}` + `${ignored > 0 ? `, ${String(ignored)} records ignored` : ""}
 `);
       batch.push(trace);
     }
+    const emit = (imported, dryRun) => {
+      if (!isJson)
+        return;
+      new OutputFormatter("json").output({
+        imported,
+        dryRun,
+        sessions: report,
+        count: report.length
+      });
+    };
     if (batch.length === 0) {
-      process.stderr.write(`[mutagent hooks] nothing to import
+      say(`[mutagent hooks] nothing to import
 `);
+      emit(0, opts.dryRun === true);
       process.exitCode = 1;
       return;
     }
     if (opts.dryRun === true) {
-      process.stderr.write(`[mutagent hooks] --dry-run: ${String(batch.length)} trace(s) not sent
+      say(`[mutagent hooks] --dry-run: ${String(batch.length)} trace(s) not sent
 `);
+      emit(0, true);
       return;
     }
     await sendBatchTrace(batch);
-    process.stderr.write(`[mutagent hooks] imported ${String(batch.length)} session(s)
+    say(`[mutagent hooks] imported ${String(batch.length)} session(s)
 `);
+    emit(batch.length, false);
   });
   hooks.command("install").description("Install Mutagent hooks into .claude/settings.local.json (safe merge — never overwrites existing hooks)").option("--cwd <dir>", "Target directory (defaults to cwd)", process.cwd()).addHelpText("after", `
 Reads existing .claude/settings.local.json (if present) and deep-merges
@@ -5472,7 +5433,7 @@ import { Command as Command10 } from "commander";
 import chalk17 from "chalk";
 import { type as osType, release as osRelease } from "os";
 import { readFileSync as readFileSync10 } from "fs";
-import { join as join13, dirname as dirname2 } from "path";
+import { join as join12, dirname as dirname2 } from "path";
 import { fileURLToPath } from "url";
 init_errors();
 init_config();
@@ -5480,12 +5441,12 @@ init_config();
 // src/lib/transcript.ts
 init_errors();
 import { homedir as osHomedir } from "os";
-import { join as join12 } from "path";
+import { join as join11 } from "path";
 import {
   existsSync as fsExistsSync,
   statSync as fsStatSync,
   readFileSync as readFileSync9,
-  readdirSync as readdirSync2,
+  readdirSync,
   openSync,
   readSync,
   closeSync
@@ -5513,12 +5474,12 @@ function defaultScan(dir) {
   const walk = (current) => {
     let entries;
     try {
-      entries = readdirSync2(current, { withFileTypes: true });
+      entries = readdirSync(current, { withFileTypes: true });
     } catch {
       return;
     }
     for (const entry of entries) {
-      const full = join12(current, entry.name);
+      const full = join11(current, entry.name);
       if (entry.isDirectory())
         walk(full);
       else if (entry.isFile() && entry.name.endsWith(".jsonl"))
@@ -5529,11 +5490,11 @@ function defaultScan(dir) {
   return out;
 }
 function buildSources(env, home) {
-  const ompBase = env.PI_CODING_AGENT_DIR ?? join12(home, ".omp", "agent");
+  const ompBase = env.PI_CODING_AGENT_DIR ?? join11(home, ".omp", "agent");
   return [
-    { harness: "claude-code", dir: join12(home, ".claude", "projects") },
-    { harness: "codex", dir: join12(home, ".codex", "sessions") },
-    { harness: "omp", dir: join12(ompBase, "sessions") }
+    { harness: "claude-code", dir: join11(home, ".claude", "projects") },
+    { harness: "codex", dir: join11(home, ".codex", "sessions") },
+    { harness: "omp", dir: join11(ompBase, "sessions") }
   ];
 }
 function resolveTranscript(attach, deps = {}) {
@@ -5722,7 +5683,7 @@ var BY_DESIGN_ENTRIES = [
     id: "mutagent-tools-not-on-npm",
     title: "@mutagent/tools is not published to npm — on purpose",
     looksLike: pairPatterns(TOOLS_PKG, NOT_FOUND),
-    reality: "@mutagent/tools is intentionally not published to the public npm registry, so a 404 there is the expected result rather than a broken release. Its functionality is compiled into the mutagent-cli binary that ships with the diagnostics and evaluator packages — installing either one already gives you the tooling, and there is nothing separate to install."
+    reality: "@mutagent/tools is intentionally not published to the public npm registry, so a 404 there is the expected result rather than a broken release. Its functionality is compiled into the mutagent-cli binary that ships inside helix — installing helix already gives you the tooling, and there is nothing separate to install. Install it with: mutagent install helix"
   },
   {
     id: "mutagent-helix-not-on-npm",
@@ -5737,7 +5698,7 @@ var BY_DESIGN_ENTRIES = [
       ...pairPatterns(String.raw`mutagent\s+trace`, NOT_A_COMMAND),
       /\btrace\b[^\n]{0,40}?(?:not\s+a\s+(?:valid\s+)?(?:sub)?command|unknown\s+command)/i
     ],
-    reality: "trace is not a subcommand of mutagent. It lives in mutagent-cli — a different binary — which is installed alongside @mutagent/diagnostics, @mutagent/evaluator, or helix. Run: mutagent-cli trace <args>"
+    reality: "trace is not a subcommand of mutagent. It lives in mutagent-cli — a different binary — which ships inside helix. Install it with: mutagent install helix, then run: mutagent-cli trace <args>"
   },
   {
     id: "two-separate-binaries",
@@ -5747,7 +5708,7 @@ var BY_DESIGN_ENTRIES = [
       /mutagent-cli\s+(?:binary|executable|command)[^\n]{0,60}?(?:missing|not\s+found|doesn'?t\s+exist|does\s+not\s+exist|not\s+installed)/i,
       new RegExp(String.raw`no\s+mutagent-cli[^\n]{0,40}?in\s+@mutagent\/cli`, "i")
     ],
-    reality: "mutagent and mutagent-cli are separate binaries that come from separate packages. @mutagent/cli provides the mutagent binary only — account, configuration, and installation commands. The mutagent-cli binary ships with the diagnostics and evaluator packages and carries the trace tooling. Having both installed is normal and expected."
+    reality: "mutagent and mutagent-cli are separate binaries that come from separate packages. @mutagent/cli provides the mutagent binary only — account, configuration, and installation commands. The mutagent-cli binary ships inside helix and carries the trace tooling. Having both installed is normal and expected."
   }
 ];
 function matchByDesign(draft) {
@@ -5857,7 +5818,7 @@ function getCliVersion() {
     return process.env.CLI_VERSION;
   try {
     const __dirname2 = dirname2(fileURLToPath(import.meta.url));
-    const pkgPath = join13(__dirname2, "..", "..", "package.json");
+    const pkgPath = join12(__dirname2, "..", "..", "package.json");
     const pkg = JSON.parse(readFileSync10(pkgPath, "utf-8"));
     return pkg.version ?? "0.1.1";
   } catch {
@@ -6065,7 +6026,7 @@ import { Command as Command11 } from "commander";
 import chalk18 from "chalk";
 init_errors();
 function createInstallCommand(deps) {
-  const install = new Command11("install").description("Install a Mutagent package (helix, diagnostics, evaluator)").argument("<package>", `Package to install: ${VALID_PACKAGES.join(", ")}`).option("--harness <harness>", `Target harness: ${VALID_HARNESSES.join(", ")}`, "claude-code").option("--global", "(retired) Install scope is fixed per package").option("--version <version>", "Package version to install (default: latest)").addHelpText("after", `
+  const install = new Command11("install").description("Install a Mutagent package (helix)").argument("<package>", `Package to install: ${VALID_PACKAGES.join(", ")}`).option("--harness <harness>", `Target harness: ${VALID_HARNESSES.join(", ")}`, "claude-code").option("--global", "(retired) Install scope is fixed per package").option("--version <version>", "Package version to install (default: latest)").addHelpText("after", `
 ${chalk18.bold("Arguments & flags:")}
   ${chalk18.bold("<package>")}            ${VALID_PACKAGES.join(" | ")}
   ${chalk18.bold("--harness <h>")}        ${VALID_HARNESSES.join(" | ")} ${chalk18.dim("(default: claude-code)")}
@@ -6074,24 +6035,20 @@ ${chalk18.bold("Arguments & flags:")}
 
 ${chalk18.bold("Install scope")} ${chalk18.dim("(fixed per package — not selectable)")}:
   ${chalk18.bold("helix")}                    → installed into the current directory
-  ${chalk18.bold("diagnostics")} | ${chalk18.bold("evaluator")}  → ${chalk18.yellow("installed GLOBALLY")} by npm; run the
-                             package's own init from your project afterwards.
   ${chalk18.dim("--global")} is retired: scope is no longer a choice.
 
 ${chalk18.bold("Examples:")}
   ${chalk18.dim("$")} mutagent install helix
   ${chalk18.dim("$")} mutagent install helix --harness codex
-  ${chalk18.dim("$")} mutagent install diagnostics
-  ${chalk18.dim("$")} mutagent install evaluator --version 1.2.3
-  ${chalk18.dim("$")} mutagent install diagnostics --harness codex --json
+  ${chalk18.dim("$")} mutagent install helix --version 1.2.3
+  ${chalk18.dim("$")} mutagent install helix --json
 
 ${chalk18.bold("Packages:")}
   ${chalk18.bold("helix")}        ${chalk18.green("(available)")} — the ADLC (Agent Development Life Cycle Orchestrator). Downloaded from a private
                  registry via a login-brokered signed URL, sha256-verified, then
                  initialized into your project. No static secret ships in the CLI.
                  ${chalk18.dim("Installs every harness itself (Claude + Codex) — --harness does not apply.")}
-  ${chalk18.bold("diagnostics")}  Public npm package @mutagent/diagnostics ${chalk18.green("(available)")}
-  ${chalk18.bold("evaluator")}    Public npm package @mutagent/evaluator ${chalk18.green("(available)")}
+                 ${chalk18.dim("Carries the diagnostics and evaluator skills, plus the mutagent-cli binary.")}
 
 ${chalk18.yellow("Note:")} install is login-gated. Run ${chalk18.cyan("mutagent login")} first (else exits with a login directive).
     `).action(async (pkg, options) => {
@@ -6117,8 +6074,8 @@ ${chalk18.yellow("Note:")} install is login-gated. Run ${chalk18.cyan("mutagent
       } else if (result.skillInstalled) {
         output.success(`Installed ${result.package}@${result.version} for ${result.harness} in ${result.projectPath ?? "this project"}`);
       } else {
-        output.success(`Installed npm package ${result.package}@${result.version} globally` + (result.command ? ` (${result.command})` : ""));
-        console.log(`${chalk18.yellow("⚠")} No skill was installed yet — the package ships its own setup step.`);
+        output.success(`Installed ${result.package}@${result.version}, but the skill is not in place yet`);
+        console.log(`${chalk18.yellow("⚠")} No skill was installed yet — a setup step still has to run.`);
         if (result.nextStep) {
           console.log(`${chalk18.blue("→")} Run next: ${chalk18.cyan(result.nextStep)}`);
         }
@@ -6133,7 +6090,7 @@ ${chalk18.yellow("Note:")} install is login-gated. Run ${chalk18.cyan("mutagent
 // src/commands/trace.ts
 import { Command as Command12 } from "commander";
 init_errors();
-var TRACE_RELOCATION_HINT = "trace lives in the `mutagent-cli` binary, installed with @mutagent/diagnostics, @mutagent/evaluator or helix";
+var TRACE_RELOCATION_HINT = "trace lives in the `mutagent-cli` binary, which ships inside helix (install it with: mutagent install helix)";
 function createTraceCommand() {
   const trace = new Command12("trace").description("Not in this binary — trace lives in mutagent-cli").allowUnknownOption(true).allowExcessArguments(true).argument("[args...]", "Arguments intended for `mutagent-cli trace`").addHelpText("after", `
 This binary (mutagent) does not provide trace.
@@ -6147,7 +6104,7 @@ Install one of those, then run:
     const isJson = getJsonFlag(trace);
     const forwarded = args.length > 0 ? ` ${args.join(" ")}` : " <args>";
     handleError(new MutagentError("INVALID_ARGUMENTS", `\`mutagent trace\` is not a command — ${TRACE_RELOCATION_HINT}.`, `Run it with the other binary instead: mutagent-cli trace${forwarded}
-If mutagent-cli is not installed: mutagent install diagnostics`), isJson);
+If mutagent-cli is not installed: mutagent install helix`), isJson);
   });
   return trace;
 }
@@ -6167,12 +6124,12 @@ init_errors();
 // src/lib/sandbox-token.ts
 init_secure_file();
 init_errors();
-import { existsSync as existsSync9, readFileSync as readFileSync11, mkdirSync as mkdirSync6, rmSync as rmSync2 } from "fs";
-import { homedir as homedir4 } from "os";
-import { join as join14, dirname as dirname3 } from "path";
+import { existsSync as existsSync9, readFileSync as readFileSync11, mkdirSync as mkdirSync5, rmSync as rmSync2 } from "fs";
+import { homedir as homedir3 } from "os";
+import { join as join13, dirname as dirname3 } from "path";
 function sandboxTokenFile() {
   const override = process.env.MUTAGENT_SANDBOX_TOKEN_FILE;
-  return override !== undefined && override !== "" ? override : join14(homedir4(), ".config", "mutagent", "sandbox-token.json");
+  return override !== undefined && override !== "" ? override : join13(homedir3(), ".config", "mutagent", "sandbox-token.json");
 }
 var EXPIRY_SKEW_MS = 60000;
 function isCacheShape(value) {
@@ -6196,7 +6153,7 @@ function createFileTokenStore(path) {
     write(entry) {
       const dir = dirname3(path);
       if (!existsSync9(dir))
-        mkdirSync6(dir, { recursive: true });
+        mkdirSync5(dir, { recursive: true });
       writeSecureFile(path, JSON.stringify(entry, null, 2));
     },
     clear() {
@@ -7591,7 +7548,7 @@ if (process.env.CLI_VERSION) {
 } else {
   try {
     const __dirname2 = dirname4(fileURLToPath2(import.meta.url));
-    const pkgPath = join15(__dirname2, "..", "..", "package.json");
+    const pkgPath = join14(__dirname2, "..", "..", "package.json");
     const pkg = JSON.parse(readFileSync12(pkgPath, "utf-8"));
     cliVersion = pkg.version ?? cliVersion;
   } catch {}
@@ -7609,7 +7566,7 @@ program.addHelpText("beforeAll", () => renderBanner());
 program.addHelpText("after", `
 ${chalk25.bold.cyan("WORKFLOWS:")}
   ${chalk25.bold("Setup")}                mutagent login  →  mutagent init
-  ${chalk25.bold("Lifecycle Tools")}      mutagent install <helix|diagnostics|evaluator>  ${chalk25.dim("(login-gated)")}
+  ${chalk25.bold("Lifecycle Tools")}      mutagent install helix  ${chalk25.dim("(login-gated)")}
   ${chalk25.bold("Feedback")}             mutagent feedback send "<what happened>" --category <cli|helix|stage:<x>>  ${chalk25.dim("[--session <id>] [--attach-transcript]")}
 
 ${chalk25.dim("For CLI usage guidance for AI agents, see the Skill at")}
@@ -7640,8 +7597,8 @@ ${chalk25.yellow("Command Navigation:")}
   mutagent helix rm <id> --force        ${chalk25.dim("Destroy a sandbox (the only thing that does)")}
 
   mutagent install helix                ${chalk25.dim("Install the ADL lifecycle conductor locally (login-gated)")}
-  mutagent install evaluator --version 1.2.3  ${chalk25.dim("Pin a version")}
-  mutagent install --help               ${chalk25.dim("helix | diagnostics | evaluator")}
+  mutagent install helix --version 1.2.3  ${chalk25.dim("Pin a version")}
+  mutagent install --help               ${chalk25.dim("helix")}
 
   mutagent hooks --help                 ${chalk25.dim("Hook setup for Claude Code session telemetry upload")}
 
@@ -7718,5 +7675,5 @@ program.addCommand(createFeedbackCommand());
 program.addCommand(createTraceCommand());
 program.parse();
 
-//# debugId=4276BD959C14332264756E2164756E21
+//# debugId=8A72E382D57F3D0964756E2164756E21
 //# sourceMappingURL=cli.js.map