[agent] Found by the scheduled pnpm bug-hunt routine (ledger #303).

Summary

In a Rush monorepo, pnpm installs every package into common/temp/node_modules/.pnpm/…. Each project's node_modules holds only symlinks to its direct dependencies, and there's no .modules.yaml beside them. The npm crawler's workspace walk skips any directory named temp (SKIP_DIRS in crates/socket-patch-core/src/crawlers/npm_crawler.rs:24). So common/temp/node_modules is never crawled, and a transitive dependency that is installed there counts as "not installed". scan from the repo root lists it as notInstalled: true (lockfile-only, found through the Rush lock fallback).

This has two effects:

1. Hosted vex attests without installed evidence. After scan --mode hosted pins common/config/rush/pnpm-lock.yaml, vex finds no installed copy. So it falls back to the not-installed lockfile basis and writes not_affected / inline_mitigations_already_exist, even though common/temp/node_modules/.pnpm/[email protected]/… still holds the upstream bytes. On a plain pnpm project in the same state (lock pinned, tree not yet reinstalled), vex correctly omits the patch (not_applied, "No applied patches … to attest").
2. Agent mode can't patch Rush transitive deps. apply with a manifest entry for the installed transitive package reports skipped / package_not_installed (partialFailure), and the store copy stays unpatched. This failure is loud, not silent.

Direct dependencies aren't affected: apps/app/node_modules/is-number is crawled. With is-number as a direct dep in the same stale state, vex correctly reports not_applied.

Impact

• The VEX document claims not_affected for a vulnerable package whose installed bytes are unpatched. That's the case CLI_CONTRACT's hosted VEX row rules out: "Installed evidence wins: hash_mismatch / not_applied are omitted. With nothing installed, a discovered reference whose lock pins the artifact … attests from that pin." Here something is installed, but the crawler never looked. It's the same window the redirect_pnpm_trust_lockfile warning tells users to check with vex ("Run socket-patch vex after installation to verify the patched files"), so on Rush that check passes before the install has happened, and it would also pass over a tampered or reverted store copy.
• Agent mode doesn't work for any transitive dependency in a Rush repo.
• Note: rush update / rush install (including --purge) do pick up the hosted pin and install patched bytes, so the hosted rewrite itself works. The problem is the evidence check.

Repro (Linux, pnpm via Rush 5.180.0)

npm i -g @microsoft/rush@5
mkdir rr && cd rr && git init -q && rush init
# rush.json: "pnpmVersion": "9.15.9" (also reproduced with "8.15.9");
#            "projects": [{"packageName":"app","projectFolder":"apps/app"}]
mkdir -p apps/app
echo '{"name":"app","version":"1.0.0","dependencies":{"to-regex-range":"5.0.1"}}' > apps/app/package.json   # [email protected] transitively
rush update
head -c 14 common/temp/node_modules/.pnpm/[email protected]/node_modules/is-number/index.js   # upstream bytes

socket-patch scan --json                     # [email protected] -> "notInstalled": true, lockfileOnlyPackages: 1
socket-patch scan --mode hosted --json --yes # success, redirected 1, rewrittenFiles [common/config/rush/pnpm-lock.yaml]
socket-patch vex --output vex.json --product pkg:npm/[email protected]
# -> "Wrote OpenVEX document with 1 statement": not_affected / inline_mitigations_already_exist
head -c 14 common/temp/node_modules/.pnpm/[email protected]/node_modules/is-number/index.js   # still upstream

Agent-mode twin: stage a .socket/manifest.json (plus blobs) for pkg:npm/[email protected] whose beforeHash matches the installed index.js. Then socket-patch apply --json → partialFailure, event skipped / package_not_installed ("No installed package matches this PURL"), and the file is unchanged.

The patch data came from a local mock of the patch API (batch / package grant / view / tarball routes, SOCKET_PATCH_SERVER_URL + SOCKET_NPM_REGISTRY pointed at it), the same shape as tests/e2e_redirect_pnpm_build.rs.

Expected vs actual

Matrix

Tested on main 61cfb9b (CLI 4.0.0 workspace version). Not bisected: the not-installed lockfile basis arrived with the v5 manifest-less VEX (#251), and "temp" has been in SKIP_DIRS for a long time.

Suspect code

• crates/socket-patch-core/src/crawlers/npm_crawler.rs:24: SKIP_DIRS contains "temp", and workspace_children (~line 1500) applies it, so common/temp/node_modules is never reached. A Rush-aware root (when rush.json is present, also crawl common/temp/node_modules, including its .pnpm store) would fix both symptoms. The hosted engine already special-cases Rush locks (hosted/engine.rs rush_repo).
• crates/socket-patch-cli/src/commands/vex_consumed.rs: an empty copy list is read as "not installed" and the lockfile basis excuses it. That's only safe when the crawl could have seen the store.