chore(deps): npm audit fix before release bump; monthly npm-outdated issue

Adds npm audit fix (root + every client) as the first sub-step of the
release skill's bump step, before npm version, so a release is never
gated on remembering to check separately. Never --force; anything
audit fix can't resolve is left to the dependabot-alert pipeline
(#2229) or a follow-up issue.

Disables Dependabot npm version updates in dependabot.yml (a
version-update PR carries no issue and no board card) and replaces
them with a monthly scheduled sweep that runs npm outdated across the
root install and every client, filing or updating one idempotent
tracking issue instead of an auto-generated PR.

Closes #2231
Part of #2229

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_017N9ha27Qg6LHpBQP7G7zPY
Signed-off-by: cliffhall <cliff@futurescale.com>

.claude/skills/release/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: release
-description: Cut an Inspector v2 release — bump the version on v2/main first, merge the milestone into main, tag origin/main with a bare x.y.z, and publish via the GitHub Release. Also covers the v1 line and what the publish jobs gate on.
+description: Cut an Inspector v2 release — npm audit fix and bump the version on v2/main first, merge the milestone into main, tag origin/main with a bare x.y.z, and publish via the GitHub Release. Also covers the v1 line and what the publish jobs gate on.
 disable-model-invocation: true
 ---
 
@@ -27,10 +27,10 @@ job or the coverage gate red:
 There is **one version number** (only the root `package.json` has one — the
 clients carry none), so the flow is three steps.
 
-## 1. Bump on `v2/main`, before the milestone merge
+## 1. `npm audit fix`, then bump, on `v2/main` — before the milestone merge
 
-The bump is part of the milestone's work, so it belongs on the develop branch
+Both are part of the milestone's work, so both belong on the develop branch and
-and flows into `main` with everything else.
+flow into `main` together, in the same PR, audit fix first.
 
 ```sh
 # Branch from the REMOTE ref, and read the version only once you are on it.
@@ -39,11 +39,34 @@ and flows into `main` with everything else.
 # you are bumping from (Copilot).
 git fetch origin v2/main
 git checkout -b v2/chore/<ISSUE>-bump-<X-Y-Z> origin/v2/main
+
+# Audit + fix every install that has its own lockfile — root and each client.
+npm audit fix
+for c in web cli tui launcher; do (cd "clients/$c" && npm audit fix); done
+npm run local:gate   # confirm the fixes didn't break anything before bumping
+
 node -p "require('./package.json').version"          # what is on v2/main now
 npm version minor --no-git-tag-version   # or major / patch; bump only, no tag
 node -p "require('./package.json').version"          # confirm, then PR → v2/main
 ```
 
+**Never `npm audit fix --force`.** It will apply a fix outside a dependency's
+declared semver range — a major bump a client's code was never adjusted for —
+to close an advisory, silently trading a known vulnerability for an unvetted
+breaking change. If `npm audit` still reports something `fix` can't resolve
+(typically a transitive dependency needing an `overrides` pin per
+[Dependency placement](../../../AGENTS.md#dependency-placement)), commit
+whatever `fix` did resolve, leave the rest to the dependabot-alert pipeline
+(#2229) or a follow-up issue, and say so in the release notes rather than
+forcing it here.
+
+This step is a **backstop, not a substitute** for #2229's alert-driven issues —
+those are what surface a transitive vulnerability that needs an `overrides`
+entry `audit fix` cannot apply on its own, tracked and fixed as their own PRs
+well before a release is cut. This step exists for whatever's left standing
+right before a release ships, so a release is never gated on remembering to
+check `npm audit` separately.
+
 The branch name carries the version you are bumping **to**, so it is named after
 that second reading. If you want it before branching:
 `git show origin/v2/main:package.json | node -p "JSON.parse(require('fs').readFileSync(0)).version"`.

.github/dependabot.yml

@@ -1,23 +1,26 @@
 version: 2
 
-# Version updates target `v2/main`, the develop branch where all v2 work lands,
+# npm version updates are OFF (#2229): a Dependabot version-update PR carries no
-# not the default branch — `main` is release-only, holding the latest released
+# issue and no board card, which is the same "every PR references an issue"
-# v2 and receiving milestone merges from `v2/main`. (The deprecated v1 line
+# carve-out the security-update flow had. Routine npm bumps are handled instead
-# lives on `v1/main` and takes security fixes only.)
+# by a monthly `npm outdated` sweep (`.github/workflows/dependency-refresh.yml`)
+# that files ONE tracking issue per run, boarded and milestoned like any other
+# work — so a maintainer picks the bump and opens a normal PR against `v2/main`.
+#
+# Security updates are unaffected by this file either way: they are enabled in
+# repo settings, not here. #2229 additionally proposes consuming them as
+# Dependabot ALERTS rather than PRs (tracked, not yet built) — until that lands,
+# security-update PRs still open against `main` and still need retargeting by
+# hand, same as before.
+#
+# github-actions version updates stay on Dependabot's own PR flow below — out of
+# scope for #2229, which was about npm packages specifically.
 #
 # Two things to know about this file:
 #   1. Dependabot reads it from the DEFAULT branch (`main`). Changes here are
 #      inert until the next milestone merge carries them there.
-#   2. `target-branch` scopes VERSION updates. Dependabot SECURITY updates are
+#   2. `target-branch` scopes VERSION updates only (npm updates are removed
-#      enabled in repo settings, not here, and are raised against the default
+#      here, so this now only applies to the github-actions entry below).
-#      branch — they kept working while this file was missing entirely
-#      (see #1833, #1840). Per GitHub's Dependabot options reference, an entry
-#      whose `target-branch` names a non-default branch is NOT applied to
-#      security updates, so the schedule/labels/groups below shape version
-#      updates only. Re-confirm security PRs still appear after this lands.
-#
-# v2 is not an npm workspace: the root and each client under `clients/*` carry
-# their own package.json + lockfile, so each needs its own entry.
 
 updates:
   - package-ecosystem: "github-actions"
@@ -31,63 +34,3 @@ updates:
       github-actions:
         patterns:
           - "*"
-
-  - package-ecosystem: "npm"
-    directory: "/"
-    target-branch: "v2/main"
-    schedule:
-      interval: "monthly"
-    labels:
-      - "v2"
-    groups:
-      root-dependencies:
-        patterns:
-          - "*"
-
-  - package-ecosystem: "npm"
-    directory: "/clients/web"
-    target-branch: "v2/main"
-    schedule:
-      interval: "monthly"
-    labels:
-      - "v2"
-    groups:
-      web-dependencies:
-        patterns:
-          - "*"
-
-  - package-ecosystem: "npm"
-    directory: "/clients/cli"
-    target-branch: "v2/main"
-    schedule:
-      interval: "monthly"
-    labels:
-      - "v2"
-    groups:
-      cli-dependencies:
-        patterns:
-          - "*"
-
-  - package-ecosystem: "npm"
-    directory: "/clients/tui"
-    target-branch: "v2/main"
-    schedule:
-      interval: "monthly"
-    labels:
-      - "v2"
-    groups:
-      tui-dependencies:
-        patterns:
-          - "*"
-
-  - package-ecosystem: "npm"
-    directory: "/clients/launcher"
-    target-branch: "v2/main"
-    schedule:
-      interval: "monthly"
-    labels:
-      - "v2"
-    groups:
-      launcher-dependencies:
-        patterns:
-          - "*"

.github/workflows/dependency-refresh.yml

@@ -0,0 +1,48 @@
+# Monthly npm-outdated sweep (#2229), replacing Dependabot version-update PRs.
+#
+# Dependabot version updates are disabled in `.github/dependabot.yml` because a
+# version-update PR carries no issue and no board card. This workflow runs
+# `scripts/dependency-refresh.mjs` against `v2/main` once a month and files or
+# updates ONE tracking issue listing every outdated package across the root
+# install and each client — no PR is opened automatically. A maintainer reviews
+# the issue, picks what to bump, and opens a normal PR against `v2/main`.
+#
+# `GITHUB_TOKEN` is sufficient: it only needs to read milestones (public) and
+# create/edit an issue (`issues: write`). Board placement is intentionally NOT
+# attempted here — that needs an org-project PAT this token cannot have — so a
+# filed-but-unboarded issue is picked up by the next `/issue-triage` sweep,
+# same as any other maintainer-filed issue.
+name: Dependency Refresh
+
+on:
+  schedule:
+    - cron: "23 6 1 * *" # 06:23 UTC on the 1st of every month
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  issues: write
+
+jobs:
+  npm-outdated:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout v2/main
+        uses: actions/checkout@v7
+        with:
+          ref: v2/main
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v7
+        with:
+          node-version: '22.x'
+          cache: 'npm'
+
+      - name: Install dependencies (root + all clients)
+        run: npm install
+
+      - name: Run the npm-outdated sweep
+        run: node scripts/dependency-refresh.mjs
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_REPOSITORY: ${{ github.repository }}

scripts/dependency-refresh.mjs

@@ -0,0 +1,208 @@
+#!/usr/bin/env node
+// Monthly npm-outdated sweep (#2229), replacing Dependabot version-update PRs.
+//
+// Dependabot's version updates were disabled in `.github/dependabot.yml`
+// because a version-update PR carries no issue and no board card — the same
+// carve-out from "every PR references an issue" that the security-update flow
+// had (that half is handled separately by the alert-driven pipeline, also
+// #2229). This script replaces the routine-bump half: once a month it runs
+// `npm outdated` across the root install and every client under `clients/*`
+// (each has its own package.json + lockfile — v2 is not a workspace), and
+// files or updates ONE tracking issue listing everything behind. A maintainer
+// picks what to bump and opens a normal PR against `v2/main`; there is no
+// auto-generated PR here at all.
+//
+// Idempotent by design: the issue body starts with a fixed HTML marker
+// (ISSUE_MARKER below), which is how a second run in the same month finds and
+// updates the existing open issue instead of filing a duplicate.
+//
+// `parseOutdated` and `buildIssueBody` are pure and covered by
+// `dependency-refresh.test.mjs`; `main()` is the CLI entry point, exercised
+// against the real repo only via `workflow_dispatch` in CI, not by the test
+// suite (it shells out to `npm outdated` and `gh`, per the workflow-script
+// convention `verify-skills.mjs` and its siblings already use).
+
+import { spawnSync } from "node:child_process";
+
+export const ISSUE_MARKER = "<!-- dependency-refresh:monthly-sweep -->";
+
+/** Installs to check, relative to the repo root, and their npm-outdated label. */
+export const INSTALLS = [
+  { dir: ".", label: "root" },
+  { dir: "clients/web", label: "clients/web" },
+  { dir: "clients/cli", label: "clients/cli" },
+  { dir: "clients/tui", label: "clients/tui" },
+  { dir: "clients/launcher", label: "clients/launcher" },
+];
+
+/**
+ * Normalize one install's `npm outdated --json` output.
+ *
+ * @param {string} json raw stdout from `npm outdated --json` (may be `""` or `"{}"`)
+ * @returns {Array<{name: string, current: string, wanted: string, latest: string}>}
+ */
+export function parseOutdated(json) {
+  const trimmed = json.trim();
+  if (trimmed === "") return [];
+  const parsed = JSON.parse(trimmed);
+  return Object.entries(parsed)
+    .map(([name, info]) => ({
+      name,
+      current: info.current ?? "(missing)",
+      wanted: info.wanted ?? info.current ?? "?",
+      latest: info.latest ?? "?",
+    }))
+    .sort((a, b) => a.name.localeCompare(b.name));
+}
+
+/**
+ * @param {Array<{label: string, packages: ReturnType<typeof parseOutdated>}>} installs
+ * @returns {string | null} the issue body, or `null` when nothing is outdated anywhere
+ */
+export function buildIssueBody(installs) {
+  const withPackages = installs.filter((i) => i.packages.length > 0);
+  if (withPackages.length === 0) return null;
+
+  const sections = withPackages.map(({ label, packages }) => {
+    const rows = packages
+      .map(
+        (p) => `| \`${p.name}\` | ${p.current} | ${p.wanted} | ${p.latest} |`,
+      )
+      .join("\n");
+    return `### \`${label}\`\n\n| Package | Current | Wanted | Latest |\n| --- | --- | --- | --- |\n${rows}`;
+  });
+
+  return [
+    ISSUE_MARKER,
+    "Routine dependency refresh — `npm outdated` run against `v2/main` on a monthly schedule, replacing Dependabot version-update PRs (#2229).",
+    "",
+    "This is a tracking issue, not a diff: pick what's worth bumping (`wanted` is the safe default; `latest` may cross a major and needs its own judgment call, especially for anything root-declared per [Dependency placement](https://github.com/modelcontextprotocol/inspector/blob/v2/main/AGENTS.md#dependency-placement)) and open a normal PR against `v2/main`.",
+    "",
+    ...sections,
+    "",
+    "A second run of this sweep before this issue closes updates this body in place rather than filing a duplicate.",
+  ].join("\n");
+}
+
+function runOutdated(dir) {
+  const result = spawnSync("npm", ["outdated", "--json"], {
+    cwd: dir,
+    encoding: "utf8",
+  });
+  // `npm outdated` exits 1 when it finds anything outdated — that is not a
+  // failure of the command, only stderr / a thrown parse is.
+  if (result.error) throw result.error;
+  return result.stdout ?? "";
+}
+
+function findExistingIssue(repo) {
+  const result = spawnSync(
+    "gh",
+    [
+      "issue",
+      "list",
+      "--repo",
+      repo,
+      "--state",
+      "open",
+      "--search",
+      ISSUE_MARKER,
+      "--json",
+      "number,body",
+      "--limit",
+      "10",
+    ],
+    { encoding: "utf8" },
+  );
+  if (result.status !== 0) {
+    throw new Error(`gh issue list failed: ${result.stderr}`);
+  }
+  const issues = JSON.parse(result.stdout || "[]");
+  return issues.find((i) => i.body?.startsWith(ISSUE_MARKER)) ?? null;
+}
+
+function currentMilestone(repo) {
+  const result = spawnSync(
+    "gh",
+    [
+      "api",
+      `repos/${repo}/milestones`,
+      "--jq",
+      'map(select(.state=="open")) | sort_by(.due_on) | .[0].title // empty',
+    ],
+    { encoding: "utf8" },
+  );
+  if (result.status !== 0) {
+    throw new Error(`milestone lookup failed: ${result.stderr}`);
+  }
+  return result.stdout.trim() || null;
+}
+
+export function main(repo = process.env.GITHUB_REPOSITORY) {
+  if (!repo) throw new Error("repo not specified (GITHUB_REPOSITORY unset)");
+
+  const installs = INSTALLS.map(({ dir, label }) => ({
+    label,
+    packages: parseOutdated(runOutdated(dir)),
+  }));
+
+  const body = buildIssueBody(installs);
+  if (body === null) {
+    console.log("dependency-refresh: nothing outdated in any install — no-op");
+    return;
+  }
+
+  const existing = findExistingIssue(repo);
+  if (existing) {
+    const edit = spawnSync(
+      "gh",
+      [
+        "issue",
+        "edit",
+        String(existing.number),
+        "--repo",
+        repo,
+        "--body",
+        body,
+      ],
+      { encoding: "utf8" },
+    );
+    if (edit.status !== 0)
+      throw new Error(`gh issue edit failed: ${edit.stderr}`);
+    console.log(`dependency-refresh: updated existing #${existing.number}`);
+    return;
+  }
+
+  const milestone = currentMilestone(repo);
+  const args = [
+    "issue",
+    "create",
+    "--repo",
+    repo,
+    "--title",
+    "chore(deps): monthly dependency refresh",
+    "--label",
+    "v2",
+    "--label",
+    "chore",
+    "--label",
+    "dependabot",
+    "--body",
+    body,
+  ];
+  if (milestone) args.push("--milestone", milestone);
+
+  const create = spawnSync("gh", args, { encoding: "utf8" });
+  if (create.status !== 0)
+    throw new Error(`gh issue create failed: ${create.stderr}`);
+  if (!milestone) {
+    console.log(
+      "dependency-refresh: no open milestone — issue filed unmilestoned, will be swept into Todo at next triage",
+    );
+  }
+  console.log(`dependency-refresh: filed ${create.stdout.trim()}`);
+}
+
+if (import.meta.url === `file://${process.argv[1]}`) {
+  main();
+}

scripts/dependency-refresh.test.mjs

@@ -0,0 +1,61 @@
+// Unit tests for the pure parsing/formatting halves of dependency-refresh.mjs
+// (#2229). The impure half (`main()`, which shells out to `npm` and `gh`) is
+// exercised only via `workflow_dispatch` in CI, per the same split
+// `verify-skills.mjs` uses. Run via `npm run test:scripts`.
+
+import { test } from "node:test";
+import assert from "node:assert/strict";
+import {
+  buildIssueBody,
+  parseOutdated,
+  ISSUE_MARKER,
+} from "./dependency-refresh.mjs";
+
+test("parseOutdated returns [] for empty npm-outdated output", () => {
+  assert.deepEqual(parseOutdated(""), []);
+  assert.deepEqual(parseOutdated("{}"), []);
+});
+
+test("parseOutdated normalizes and sorts entries by name", () => {
+  const json = JSON.stringify({
+    zod: { current: "3.0.0", wanted: "3.1.0", latest: "4.0.0" },
+    ajv: { current: "8.0.0", wanted: "8.0.0", latest: "8.1.0" },
+  });
+  assert.deepEqual(parseOutdated(json), [
+    { name: "ajv", current: "8.0.0", wanted: "8.0.0", latest: "8.1.0" },
+    { name: "zod", current: "3.0.0", wanted: "3.1.0", latest: "4.0.0" },
+  ]);
+});
+
+test("parseOutdated falls back when a field is missing", () => {
+  const json = JSON.stringify({ pkg: { current: "1.0.0" } });
+  assert.deepEqual(parseOutdated(json), [
+    { name: "pkg", current: "1.0.0", wanted: "1.0.0", latest: "?" },
+  ]);
+});
+
+test("buildIssueBody returns null when every install is up to date", () => {
+  assert.equal(
+    buildIssueBody([
+      { label: "root", packages: [] },
+      { label: "clients/web", packages: [] },
+    ]),
+    null,
+  );
+});
+
+test("buildIssueBody starts with the idempotency marker and skips empty installs", () => {
+  const body = buildIssueBody([
+    { label: "root", packages: [] },
+    {
+      label: "clients/web",
+      packages: [
+        { name: "zod", current: "3.0.0", wanted: "3.1.0", latest: "4.0.0" },
+      ],
+    },
+  ]);
+  assert.ok(body.startsWith(ISSUE_MARKER));
+  assert.ok(body.includes("### `clients/web`"));
+  assert.ok(!body.includes("### `root`"));
+  assert.ok(body.includes("| `zod` | 3.0.0 | 3.1.0 | 4.0.0 |"));
+});